Bacterial L-threonine biosynthesis from L-aspartate

Three species-native examples of the five-reaction aspartate-to-threonine pathway distinguish Pseudomonas standalone enzymes, E. coli bifunctional AK/HDH isozymes, and the Corynebacterium alpha2beta2 aspartokinase. Every complete route requires the intervening aspartate-semialdehyde dehydrogenase. Shared upstream steps also supply other amino-acid branches. The boundary begins at intracellular aspartate and ends at threonine; cofactors and reductant are supplied. A separate P. aeruginosa ThrH comparison uses phosphoserine instead of ATP for homoserine phosphorylation.

MODULE:bacterial_aspartate_to_threonine_biosynthesisCOMPLETECONCRETEMetabolic Pathwaymodules/bacterial_aspartate_to_threonine_biosynthesis.yaml

L-threonine biosynthetic processGO:0009088

PMID:11352712

The central enzymes of the aspartate family of amino acid biosynthesis.

The shared aspartate-family trunk feeds several amino-acid branches; this module ends at threonine and does not make every upstream enzyme threonine-specific.

The aspartate pathway is responsible for the biosynthesis of lysine, threonine, isoleucine, and methionine in most plants and microorganisms.

PMID:19946135

Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.

The broader aspartokinase network is a composite across lineages. Three complete species-native examples are modeled here without asserting universal bacterial pathway presence.

The figure is a composite illustration of known branches, not all of which coexist in any given organism.

PMID:4391829

Regulation of the biosynthesis of amino acids of the aspartate family in Coliform bacteria and Pseudomonads.

Homoserine-dehydrogenase pyridine-nucleotide usage varies among organisms. NADPH is the represented biosynthetic donor; a second native NADH route is not inferred from a generic enzyme name.

In most of the bacteria examined, either nicotinamide adenine dinucleotide (NAD) or nicotinamide adenine dinucleotide phosphate can serve as a cofactor for this enzyme, though the relative activity with the two pyridine nucleotides varies widely.

Three complete sampled native routes do not imply universal bacterial presence. Three PSEPK candidate paralogs remain assessed outside required-route satisfaction; their membership and review status are recorded in the audit members table. NADPH capacity is distinguished from exclusive donor preference and from native kinetic evidence. Symbolic reaction descriptions show principal reactants and products, not a proton-balanced quantitative model. Literature assessments and retrieval limits are documented in the accompanying notes.

25Nodes

16Parts

3Variant Sets

8Variants

19Annotons

12Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_aspartate_to_threonine_biosynthesis deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

18 gene-function check(s) reflected in core functions · 0 conflict(s) · 1 evidence or coverage gap(s) (37 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

Annoton	Participant	Function	Assessment
pseae_thrh_phosphotransfer	thrH (PSEAE) UniProtKB:Q9I2Y2 Gene	phosphoserine:homoserine phosphotransferase activity GO:0043899	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psepk_pp_4473_ak	PP_4473 (PSEPK) UniProtKB:Q88EI9 Gene	aspartate kinase activity GO:0004072	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psepk_asd_q88le4_asd	asd__Q88LE4 (PSEPK) UniProtKB:Q88LE4 Gene	aspartate-semialdehyde dehydrogenase (NADP+) activity GO:0004073	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psepk_hom_hom	hom (PSEPK) UniProtKB:Q88MU8 Gene	homoserine dehydrogenase activity GO:0004412	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psepk_thrb_thrb	thrB (PSEPK) UniProtKB:Q88RK8 Gene	homoserine kinase activity GO:0004413	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psepk_thrc_thrc	thrC (PSEPK) UniProtKB:Q88MU7 Gene	threonine synthase activity GO:0004795	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_thra_ak	thrA (ECOLI) UniProtKB:P00561 Gene	aspartate kinase activity GO:0004072	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_metl_ak	metL (ECOLI) UniProtKB:P00562 Gene	aspartate kinase activity GO:0004072	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_lysc_ak	lysC (ECOLI) UniProtKB:P08660 Gene	aspartate kinase activity GO:0004072	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_asd_asd	asd (ECOLI) UniProtKB:P0A9Q9 Gene	aspartate-semialdehyde dehydrogenase (NADP+) activity GO:0004073	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_thra_hom	thrA (ECOLI) UniProtKB:P00561 Gene	homoserine dehydrogenase activity GO:0004412	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_metl_hom	metL (ECOLI) UniProtKB:P00562 Gene	homoserine dehydrogenase activity GO:0004412	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_thrb_thrb	thrB (ECOLI) UniProtKB:P00547 Gene	homoserine kinase activity GO:0004413	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_thrc_thrc	thrC (ECOLI) UniProtKB:P00934 Gene	threonine synthase activity GO:0004795	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
corgl_lysc_ak	PROTEIN_COMPLEX Gene	aspartate kinase activity GO:0004072	Participant Unchecked No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
corgl_asd_asd	asd (CORGL) UniProtKB:P0C1D8 Gene	aspartate-semialdehyde dehydrogenase (NADP+) activity GO:0004073	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
corgl_hom_hom	hom (CORGL) UniProtKB:P08499 Gene	homoserine dehydrogenase activity GO:0004412	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
corgl_thrb_thrb	thrB (CORGL) UniProtKB:P07128 Gene	homoserine kinase activity GO:0004413	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
corgl_thrc_thrc	thrC (CORGL) UniProtKB:P23669 Gene	threonine synthase activity GO:0004795	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
pseae_thrh_phosphotransfer	Classification of PSEAE thrH PANTHER:PTHR43344:SF2 Family	phosphoserine:homoserine phosphotransferase activity GO:0043899	Family Function Unreviewed Family review leaves GO:0043899 UNRESOLVED. Demonstrated only for P. aeruginosa ThrH (Q9I2Y2), which transfers the phosphoryl group of phosphoserine to homoserine and thereby complements thrB mutants. ThrH has no subfamily of its own: PANTHER places it in SF2 together with the canonical phosphoserine phosphatases (human PSPH, yeast SER2, E. coli SerB, S. pombe SPBC3H7.07c), for which the activity has not been reported and is not inferred; its discoverers called it novel. No PAINT node asserts it. The term therefore cannot be scoped to SF2 or to any other subfamily and is left as a member-level property of ThrH, as with amino acid kinase activity in PTHR21064.
psepk_pp_4473_ak	Classification of PSEPK PP_4473 PANTHER:PTHR21499:SF3 Family	aspartate kinase activity GO:0004072	Family Supported Family review supports GO:0004072 FAMILY_WIDE. The module's core activity for this family (monofunctional_aspartate_kinase_activity). PAINT IBD at PTN000487132 from yeast HOM3, E. coli LysC and MetL, B. subtilis YclM and M. tuberculosis Ask; reviewed recipients span every subfamily in the inventory. Yeast HOM3 mutants lack detectable aspartokinase activity and the purified enzyme has been characterised kinetically. The HOM3 gene review accepts the IBA; S. pombe hom3 is a stub. The one member annotated as inactive (H. influenzae HI_1632) is excepted.
psepk_asd_q88le4_asd	Classification of PSEPK asd__Q88LE4 PANTHER:PTHR46278:SF4 Family	aspartate-semialdehyde dehydrogenase (NADP+) activity GO:0004073	Family Supported Family review supports GO:0004073 FAMILY_WIDE. The module's activity (it uses SF4 for the enterobacterial enzyme) and a PAINT IBD at PTN000019341 with experimental seeds in both subfamilies, so the activity is ancestral to the family. The USG-1 paralogues are the one unverified group: they inherit the term but their activity has not been checked here; they are flagged in the node assessment rather than excepted, because no evidence of loss was found.
psepk_hom_hom	Classification of PSEPK hom PANTHER:PTHR43331:SF1 Family	homoserine dehydrogenase activity GO:0004412	Family Supported Family review supports GO:0004412 FAMILY_WIDE. The family's defining activity, asserted at PTN000752178 with seeds from two bacterial phyla and received by 41 bacterial, archaeal and algal reference-proteome members. The GO definition is written with NADP+, so a strictly NAD-dependent member is the one exception.
psepk_thrb_thrb	Classification of PSEPK thrB PANTHER:PTHR21064:SF6 Family	homoserine kinase activity GO:0004413	Family Supported Family review supports GO:0004413 for PANTHER:PTHR21064:SF6. Asserted at the bacterial node PTN001464661 from P. aeruginosa ThrB and correct for the SF6 type II homoserine kinases, including the module's P. putida KT2440 ThrB. Not applicable to SF1 (hydroxylysine kinase) or SF5 (N-acetylhexosamine kinase). AmiN is a documented exception within SF6.
psepk_thrc_thrc	Classification of PSEPK thrC PANTHER:PTHR42690:SF1 Family	threonine synthase activity GO:0004795	Family Supported Family review supports GO:0004795 FAMILY_WIDE. Safe for the bacterial ThrC and fungal THR4 members, which make up most of the family and all of the members the aspartate-family threonine module uses (THR4, S. pombe thrc, E. coli thrC). Because PANTHER has one subfamily (SF1) for the whole family, scope cannot be set by subfamily. The vertebrate THNSL2 proteins are the exception: they belong to the same SF1 but do not make threonine, and PAINT already records the loss at PTN000816888.
ecoli_thra_ak	Classification of ECOLI thrA PANTHER:PTHR43070:SF3 Family	aspartate kinase activity GO:0004072	Family Supported Family review supports GO:0004072 for PANTHER:PTHR43070:SF3. Architecture-determined. The bifunctional bacterial (SF3 ThrA) and plant (SF6-SF9, and AKHSDH2 in SF5) members carry the N-terminal aspartokinase domain (Pfam AA_kinase, InterPro Asp_kinase) and catalyse the reaction; the fungal monofunctional HDHs that share SF5 lack the domain and are listed as exceptions. PAINT asserts the activity within this family only at the gamma-proteobacterial ThrA node PTN001852279, which is correct; no fungal member receives it.
ecoli_metl_ak	Classification of ECOLI metL PANTHER:PTHR43070:SF3 Family	aspartate kinase activity GO:0004072	Family Supported Family review supports GO:0004072 for PANTHER:PTHR43070:SF3. Architecture-determined. The bifunctional bacterial (SF3 ThrA) and plant (SF6-SF9, and AKHSDH2 in SF5) members carry the N-terminal aspartokinase domain (Pfam AA_kinase, InterPro Asp_kinase) and catalyse the reaction; the fungal monofunctional HDHs that share SF5 lack the domain and are listed as exceptions. PAINT asserts the activity within this family only at the gamma-proteobacterial ThrA node PTN001852279, which is correct; no fungal member receives it.
ecoli_lysc_ak	Classification of ECOLI lysC PANTHER:PTHR21499:SF59 Family	aspartate kinase activity GO:0004072	Family Supported Family review supports GO:0004072 FAMILY_WIDE. The module's core activity for this family (monofunctional_aspartate_kinase_activity). PAINT IBD at PTN000487132 from yeast HOM3, E. coli LysC and MetL, B. subtilis YclM and M. tuberculosis Ask; reviewed recipients span every subfamily in the inventory. Yeast HOM3 mutants lack detectable aspartokinase activity and the purified enzyme has been characterised kinetically. The HOM3 gene review accepts the IBA; S. pombe hom3 is a stub. The one member annotated as inactive (H. influenzae HI_1632) is excepted.
ecoli_asd_asd	Classification of ECOLI asd PANTHER:PTHR46278:SF4 Family	aspartate-semialdehyde dehydrogenase (NADP+) activity GO:0004073	Family Supported Family review supports GO:0004073 FAMILY_WIDE. The module's activity (it uses SF4 for the enterobacterial enzyme) and a PAINT IBD at PTN000019341 with experimental seeds in both subfamilies, so the activity is ancestral to the family. The USG-1 paralogues are the one unverified group: they inherit the term but their activity has not been checked here; they are flagged in the node assessment rather than excepted, because no evidence of loss was found.
ecoli_thra_hom	Classification of ECOLI thrA PANTHER:PTHR43070:SF3 Family	homoserine dehydrogenase activity GO:0004412	Family Supported Family review supports GO:0004412 FAMILY_WIDE. Defining activity of every architecture in the family. Asserted independently at the eukaryotic node PTN000487079 (seeds Arabidopsis AKHSDH1 and AKHSDH2 and yeast HOM6) and the gamma-proteobacterial ThrA node PTN001852279 (seed E. coli ThrA). Gene reviews accept it for ThrA, HOM6, S. pombe hom6 and both Arabidopsis enzymes.
ecoli_metl_hom	Classification of ECOLI metL PANTHER:PTHR43070:SF3 Family	homoserine dehydrogenase activity GO:0004412	Family Supported Family review supports GO:0004412 FAMILY_WIDE. Defining activity of every architecture in the family. Asserted independently at the eukaryotic node PTN000487079 (seeds Arabidopsis AKHSDH1 and AKHSDH2 and yeast HOM6) and the gamma-proteobacterial ThrA node PTN001852279 (seed E. coli ThrA). Gene reviews accept it for ThrA, HOM6, S. pombe hom6 and both Arabidopsis enzymes.
ecoli_thrb_thrb	Classification of ECOLI thrB PANTHER:PTHR20861:SF1 Family	homoserine kinase activity GO:0004413	Family Supported Family review supports GO:0004413 for PANTHER:PTHR20861:SF1. The module's activity for this family (homoserine_kinase_activity, SF1). Yeast THR1 was cloned by complementation, its disruption causes threonine auxotrophy, the purified enzyme was followed by homoserine kinase activity, and it is homologous to the bacterial ThrB enzymes in the same subfamily. Not safe for SF3 or SF6. The obo also lists subfamilies SF8 and SF9 named HOMOSERINE KINASE that have no reviewed members in the inventory; they were not examined. Within SF1 the Aeropyrum shikimate kinase is excepted.
ecoli_thrc_thrc	Classification of ECOLI thrC PANTHER:PTHR42690:SF1 Family	threonine synthase activity GO:0004795	Family Supported Family review supports GO:0004795 FAMILY_WIDE. Safe for the bacterial ThrC and fungal THR4 members, which make up most of the family and all of the members the aspartate-family threonine module uses (THR4, S. pombe thrc, E. coli thrC). Because PANTHER has one subfamily (SF1) for the whole family, scope cannot be set by subfamily. The vertebrate THNSL2 proteins are the exception: they belong to the same SF1 but do not make threonine, and PAINT already records the loss at PTN000816888.
corgl_asd_asd	Classification of CORGL asd PANTHER:PTHR46278:SF2 Family	aspartate-semialdehyde dehydrogenase (NADP+) activity GO:0004073	Family Supported Family review supports GO:0004073 FAMILY_WIDE. The module's activity (it uses SF4 for the enterobacterial enzyme) and a PAINT IBD at PTN000019341 with experimental seeds in both subfamilies, so the activity is ancestral to the family. The USG-1 paralogues are the one unverified group: they inherit the term but their activity has not been checked here; they are flagged in the node assessment rather than excepted, because no evidence of loss was found.
corgl_hom_hom	Classification of CORGL hom PANTHER:PTHR43331:SF1 Family	homoserine dehydrogenase activity GO:0004412	Family Supported Family review supports GO:0004412 FAMILY_WIDE. The family's defining activity, asserted at PTN000752178 with seeds from two bacterial phyla and received by 41 bacterial, archaeal and algal reference-proteome members. The GO definition is written with NADP+, so a strictly NAD-dependent member is the one exception.
corgl_thrb_thrb	Classification of CORGL thrB PANTHER:PTHR20861:SF1 Family	homoserine kinase activity GO:0004413	Family Supported Family review supports GO:0004413 for PANTHER:PTHR20861:SF1. The module's activity for this family (homoserine_kinase_activity, SF1). Yeast THR1 was cloned by complementation, its disruption causes threonine auxotrophy, the purified enzyme was followed by homoserine kinase activity, and it is homologous to the bacterial ThrB enzymes in the same subfamily. Not safe for SF3 or SF6. The obo also lists subfamilies SF8 and SF9 named HOMOSERINE KINASE that have no reviewed members in the inventory; they were not examined. Within SF1 the Aeropyrum shikimate kinase is excepted.
corgl_thrc_thrc	Classification of CORGL thrC PANTHER:PTHR42690:SF1 Family	threonine synthase activity GO:0004795	Family Supported Family review supports GO:0004795 FAMILY_WIDE. Safe for the bacterial ThrC and fungal THR4 members, which make up most of the family and all of the members the aspartate-family threonine module uses (THR4, S. pombe thrc, E. coli thrC). Because PANTHER has one subfamily (SF1) for the whole family, scope cannot be set by subfamily. The vertebrate THNSL2 proteins are the exception: they belong to the same SF1 but do not make threonine, and PAINT already records the loss at PTN000816888.

Gene-review completeness (17/17 grounded genes reviewed)

17 complete review(s) · 2 with deep research · 0 missing review · 15 reviewed but lacking deep research

Gene	Review	Complete	Deep research
asd P0A9Q9	✓	✓	✗
asd P0C1D8	✓	✓	✗
asd Q88LE4	✓	✓	✗
hom P08499	✓	✓	✗
hom Q88MU8	✓	✓	✗
lysC P08660	✓	✓	✗
lysC P26512	✓	✓	✗
metL P00562	✓	✓	✗
PP_4473 Q88EI9	✓	✓	✗
thrA P00561	✓	✓	✗
thrB P00547	✓	✓	✗
thrB P07128	✓	✓	✗
thrB Q88RK8	✓	✓	✓
thrC P00934	✓	✓	✗
thrC P23669	✓	✓	✗
thrC Q88MU7	✓	✓	✓
thrH Q9I2Y2	✓	✓	✗

Tree

Species-native bacterial aspartate-to-threonine routesMetabolic Pathwaybacterial_aspartate_to_threonine_biosynthesis

Parts
1. Separately scoped alternative-step comparison optional
2. PAO1 phosphoserine-dependent homoserine phosphorylationReactionpseae_thrh_comparator
  
  Annotons
  - PSEAE thrH: phosphoserine:homoserine phosphotransferase activity Gene Product: thrH (PSEAE)
Variants
1. Complete native route by organism and enzyme architecture (Exactly One)
  1. Pseudomonas putida KT2440 aspartate-to-threonine routeMetabolic Pathwaypsepk_route
    
    Parts
    
    1. shared aspartate-family activation
    
    shared aspartate-family activationReactionpsepk_ak
    
    Annotons
    
    PSEPK PP_4473: aspartate kinase activity Gene Product: PP_4473 (PSEPK)
    
    2. shared semialdehyde formation
    
    shared semialdehyde formationReactionpsepk_asd
    
    Annotons
    
    PSEPK asd__Q88LE4: aspartate-semialdehyde dehydrogenase (NADP+) activity Gene Product: asd__Q88LE4 (PSEPK)
    
    3. homoserine branch formation
    
    homoserine branch formationReactionpsepk_hom
    
    Annotons
    
    PSEPK hom: homoserine dehydrogenase activity Gene Product: hom (PSEPK)
    
    4. homoserine phosphorylation
    
    homoserine phosphorylationReactionpsepk_thrb
    
    Annotons
    
    PSEPK thrB: homoserine kinase activity Gene Product: thrB (PSEPK)
    
    5. terminal threonine formation
    
    terminal threonine formationReactionpsepk_thrc
    
    Annotons
    
    PSEPK thrC: threonine synthase activity Gene Product: thrC (PSEPK)
  2. Escherichia coli K-12 aspartate-to-threonine routeMetabolic Pathwayecoli_route
    
    Parts
    
    1. shared aspartate-family activation
    
    shared aspartate-family activationReactionecoli_ak
    
    Variants
    
    Native isozyme alternatives by native gene product (One Or More)
    
    thrAReactionecoli_thra_ak_variant
    
    Annotons
    
    ECOLI thrA: aspartate kinase activity Gene Product: thrA (ECOLI)
    
    metLReactionecoli_metl_ak_variant
    
    Annotons
    
    ECOLI metL: aspartate kinase activity Gene Product: metL (ECOLI)
    
    lysCReactionecoli_lysc_ak_variant
    
    Annotons
    
    ECOLI lysC: aspartate kinase activity Gene Product: lysC (ECOLI)
    
    2. shared semialdehyde formation
    
    shared semialdehyde formationReactionecoli_asd
    
    Annotons
    
    ECOLI asd: aspartate-semialdehyde dehydrogenase (NADP+) activity Gene Product: asd (ECOLI)
    
    3. homoserine branch formation
    
    homoserine branch formationReactionecoli_hom
    
    Variants
    
    Native isozyme alternatives by native gene product (One Or More)
    
    thrAReactionecoli_thra_hom_variant
    
    Annotons
    
    ECOLI thrA: homoserine dehydrogenase activity Gene Product: thrA (ECOLI)
    
    metLReactionecoli_metl_hom_variant
    
    Annotons
    
    ECOLI metL: homoserine dehydrogenase activity Gene Product: metL (ECOLI)
    
    4. homoserine phosphorylation
    
    homoserine phosphorylationReactionecoli_thrb
    
    Annotons
    
    ECOLI thrB: homoserine kinase activity Gene Product: thrB (ECOLI)
    
    5. terminal threonine formation
    
    terminal threonine formationReactionecoli_thrc
    
    Annotons
    
    ECOLI thrC: threonine synthase activity Gene Product: thrC (ECOLI)
  3. Corynebacterium glutamicum ATCC 13032 aspartate-to-threonine routeMetabolic Pathwaycorgl_route
    
    Parts
    
    1. shared aspartate-family activation
    
    shared aspartate-family activationReactioncorgl_ak
    
    Annotons
    
    CORGL lysC: aspartate kinase activity Protein Complex: ATCC 13032 LysC alpha2beta2 aspartokinase
    
    2. shared semialdehyde formation
    
    shared semialdehyde formationReactioncorgl_asd
    
    Annotons
    
    CORGL asd: aspartate-semialdehyde dehydrogenase (NADP+) activity Gene Product: asd (CORGL)
    
    3. homoserine branch formation
    
    homoserine branch formationReactioncorgl_hom
    
    Annotons
    
    CORGL hom: homoserine dehydrogenase activity Gene Product: hom (CORGL)
    
    4. homoserine phosphorylation
    
    homoserine phosphorylationReactioncorgl_thrb
    
    Annotons
    
    CORGL thrB: homoserine kinase activity Gene Product: thrB (CORGL)
    
    5. terminal threonine formation
    
    terminal threonine formationReactioncorgl_thrc
    
    Annotons
    
    CORGL thrC: threonine synthase activity Gene Product: thrC (CORGL)

Details

Context

BacteriaNCBITaxon:2

Bacteria is the taxonomic envelope, not a universal-presence assertion. Exact native taxa are specified for each route.

Species-native bacterial aspartate-to-threonine routesMetabolic Pathwaybacterial_aspartate_to_threonine_biosynthesis

L-threonine biosynthetic processGO:0009088

Context

BacteriaNCBITaxon:2

Bacteria is the taxonomic envelope, not a universal-presence assertion. Exact native taxa are specified for each route.

PMID:11352712

The central enzymes of the aspartate family of amino acid biosynthesis.

The shared aspartate-family trunk feeds several amino-acid branches; this module ends at threonine and does not make every upstream enzyme threonine-specific.

The aspartate pathway is responsible for the biosynthesis of lysine, threonine, isoleucine, and methionine in most plants and microorganisms.

PMID:19946135

Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.

The broader aspartokinase network is a composite across lineages. Three complete species-native examples are modeled here without asserting universal bacterial pathway presence.

The figure is a composite illustration of known branches, not all of which coexist in any given organism.

PMID:4391829

Regulation of the biosynthesis of amino acids of the aspartate family in Coliform bacteria and Pseudomonads.

Homoserine-dehydrogenase pyridine-nucleotide usage varies among organisms. NADPH is the represented biosynthetic donor; a second native NADH route is not inferred from a generic enzyme name.

Part: Separately scoped alternative-step comparison (optional)

PAO1 phosphoserine-dependent homoserine phosphorylationReactionpseae_thrh_comparator

Context

Pseudomonas aeruginosa PAO1NCBITaxon:208964

The double-mutant evidence and HPLC chemistry support this native alternative. Other PAO1 pathway steps are outside the sampled panel; this optional comparison cannot satisfy the required route variant.

Annotons

PSEAE thrH: phosphoserine:homoserine phosphotransferase activity

pseae_thrh_phosphotransfer

Participant: Gene Product: thrH (PSEAE)

Gene Product:

thrH (PSEAE)UniProtKB:Q9I2Y2

Family:

Classification of PSEAE thrHPANTHER:PTHR43344:SF2

Representative Members: thrH (PSEAE)UniProtKB:Q9I2Y2

Taxon:

Pseudomonas aeruginosa PAO1NCBITaxon:208964

Function

phosphoserine:homoserine phosphotransferase activityGO:0043899

Substrates: L-homoserine L-phosphoserine

Products: O-phospho-L-homoserine L-serine

Separately scoped PAO1 alternative step; does not complete a full aspartate-to-threonine route or replace ThrB in another organism.

PMID:14699121

The thrH gene product of Pseudomonas aeruginosa is a dual activity enzyme with a novel phosphoserine:homoserine phosphotransferase activity.

HPLC assays establish phosphoserine-dependent phosphorylation of homoserine, distinct from ATP-dependent homoserine kinase. The parallel phosphoserine hydrolysis assay supports a second demonstrated catalytic activity.

ThrH is able to further transfer the phosphoryl group to homoserine using phosphoserine as the phosphoryl group donor

PMID:10220164

ThrH, a homoserine kinase isozyme with in vivo phosphoserine phosphatase activity in Pseudomonas aeruginosa.

Native P. aeruginosa thrB/thrH double inactivation causes threonine auxotrophy, supporting alternative homoserine-phosphorylation capacity.

threonine auxotrophy is observed only when both thrB and thrH are simultaneously inactivated.

PMID:14699121 uses HPLC-based assays to demonstrate transfer of the phosphoserine phosphoryl group to homoserine. Serine is the coproduct and ATP is not the donor. This direct chemistry explains complementation of thrB mutants without calling ThrH an ATP-dependent homoserine kinase; its separate hydrolytic phosphoserine-phosphatase activity is also retained.

Variant set: Complete native route by organism and enzyme architecture (Exactly One)

Pseudomonas putida KT2440 aspartate-to-threonine routeMetabolic Pathwaypsepk_route

Five required sequential reactions. Presence denotes supported native catalytic capacity, not measured flux under every condition. No inter-enzyme metabolon or substrate channeling is asserted.

Context

Pseudomonas putida KT2440NCBITaxon:160488

Intracellular aspartate, ATP, NADPH and required catalytic cofactors available

Canonical five-locus assignments combine curated family/rule evidence with strain-specific literature and qualified engineering results. Q88LE2, Q88Q34 and Q88Q36 are assessed separately; their native flux contributions are unresolved and cannot rescue a missing canonical step in this model. Historical P. putida papers do not establish exact KT2440 protein assays.

Connections

psepk_ak -> psepk_asd Precedes

The preceding product 4-phospho-L-aspartate is substrate for this reaction. This is chemical continuity, not physical channeling.

file:PSEPK/PP_4473/PP_4473-uniprot.txt

UniProtKB record for Q88EI9 (PP_4473)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

NCBIfam; TIGR00656; asp_kin_monofn; 1.

file:PSEPK/PP_4473/PP_4473-uniprot.txt

UniProtKB record for Q88EI9 (PP_4473)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Reaction=L-aspartate + ATP = 4-phospho-L-aspartate + ADP

PMID:40236303

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440.

Native constructs were overexpressed in KT2440; terminal primer mapping identifies the corresponding locus. Joint engineering and soluble expression do not establish individual kinetics, necessity or feedback inhibition.

Despite the successful overproduction of two key enzymes, aspartate kinase (LysC) and homoserine dehydrogenase (Hom) from different plasmid combinations

file:PSEPK/PP_4473/PP_4473-bioinformatics/primer-identity/RESULTS.md

Terminal-primer identity analysis of native KT2440 constructs in PMID:40236303

Published terminal primers distinguish the named native constructs; this does not verify the full cloned CDS or measure enzymatic activity.

The Table S2 lysC_xba_R reverse primer matches the terminal PARQGE of PP_4473/Q88EI9, followed by a stop codon.

file:PSEPK/asd__Q88LE4/asd__Q88LE4-uniprot.txt

UniProtKB record for Q88LE4 (asd__Q88LE4)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Catalyzes the NADPH-dependent formation of L-aspartate-

file:PSEPK/asd__Q88LE4/asd__Q88LE4-uniprot.txt

UniProtKB record for Q88LE4 (asd__Q88LE4)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

HAMAP; MF_02121; ASADH; 1.

psepk_asd -> psepk_hom Precedes

The preceding product L-aspartate 4-semialdehyde is substrate for this reaction. This is chemical continuity, not physical channeling.

file:PSEPK/asd__Q88LE4/asd__Q88LE4-uniprot.txt

UniProtKB record for Q88LE4 (asd__Q88LE4)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Catalyzes the NADPH-dependent formation of L-aspartate-

file:PSEPK/asd__Q88LE4/asd__Q88LE4-uniprot.txt

UniProtKB record for Q88LE4 (asd__Q88LE4)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

HAMAP; MF_02121; ASADH; 1.

file:PSEPK/hom/hom-uniprot.txt

UniProtKB record for Q88MU8 (hom)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Belongs to the homoserine dehydrogenase family.

file:PSEPK/hom/hom-uniprot.txt

UniProtKB record for Q88MU8 (hom)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

PROSITE; PS01042; HOMOSER_DHGENASE; 1.

file:PSEPK/hom/hom-uniprot.txt

UniProtKB record for Q88MU8 (hom)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

/ligand="NADPH"

PMID:40236303

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440.

Despite the successful overproduction of two key enzymes, aspartate kinase (LysC) and homoserine dehydrogenase (Hom) from different plasmid combinations

file:PSEPK/PP_4473/PP_4473-bioinformatics/primer-identity/RESULTS.md

Terminal-primer identity analysis of native KT2440 constructs in PMID:40236303

Published terminal primers distinguish the named native constructs; this does not verify the full cloned CDS or measure enzymatic activity.

The hom_nhe_R reverse primer matches terminal RVEQLN of Hom/PP_1470/Q88MU8, followed by a stop.

psepk_hom -> psepk_thrb Precedes

The preceding product L-homoserine is substrate for this reaction. This is chemical continuity, not physical channeling.

file:PSEPK/hom/hom-uniprot.txt

UniProtKB record for Q88MU8 (hom)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Belongs to the homoserine dehydrogenase family.

file:PSEPK/hom/hom-uniprot.txt

UniProtKB record for Q88MU8 (hom)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

PROSITE; PS01042; HOMOSER_DHGENASE; 1.

file:PSEPK/hom/hom-uniprot.txt

UniProtKB record for Q88MU8 (hom)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

/ligand="NADPH"

PMID:40236303

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440.

Despite the successful overproduction of two key enzymes, aspartate kinase (LysC) and homoserine dehydrogenase (Hom) from different plasmid combinations

file:PSEPK/PP_4473/PP_4473-bioinformatics/primer-identity/RESULTS.md

Terminal-primer identity analysis of native KT2440 constructs in PMID:40236303

Published terminal primers distinguish the named native constructs; this does not verify the full cloned CDS or measure enzymatic activity.

The hom_nhe_R reverse primer matches terminal RVEQLN of Hom/PP_1470/Q88MU8, followed by a stop.

file:PSEPK/thrB/thrB-uniprot.txt

UniProtKB record for Q88RK8 (thrB)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Reaction=L-homoserine + ATP = O-phospho-L-homoserine + ADP + H(+)

file:PSEPK/thrB/thrB-uniprot.txt

UniProtKB record for Q88RK8 (thrB)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

HAMAP; MF_00301; Homoser_kinase_2; 1.

PMID:40236303

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440.

the remaining genes of the metabolic pathway – thrB and thrC – were overexpressed as well.

file:PSEPK/PP_4473/PP_4473-bioinformatics/primer-identity/RESULTS.md

Terminal-primer identity analysis of native KT2440 constructs in PMID:40236303

Published terminal primers distinguish the named native constructs; this does not verify the full cloned CDS or measure enzymatic activity.

The thrB_ecoRI_F primer matches MSVFTPVT at the N terminus of ThrB/PP_0121/Q88RK8, and thrB_not_R matches its terminal LHLPFAL.

psepk_thrb -> psepk_thrc Precedes

The preceding product O-phospho-L-homoserine is substrate for this reaction. This is chemical continuity, not physical channeling.

file:PSEPK/thrB/thrB-uniprot.txt

UniProtKB record for Q88RK8 (thrB)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Reaction=L-homoserine + ATP = O-phospho-L-homoserine + ADP + H(+)

file:PSEPK/thrB/thrB-uniprot.txt

UniProtKB record for Q88RK8 (thrB)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

HAMAP; MF_00301; Homoser_kinase_2; 1.

PMID:40236303

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440.

the remaining genes of the metabolic pathway – thrB and thrC – were overexpressed as well.

file:PSEPK/PP_4473/PP_4473-bioinformatics/primer-identity/RESULTS.md

Terminal-primer identity analysis of native KT2440 constructs in PMID:40236303

Published terminal primers distinguish the named native constructs; this does not verify the full cloned CDS or measure enzymatic activity.

The thrB_ecoRI_F primer matches MSVFTPVT at the N terminus of ThrB/PP_0121/Q88RK8, and thrB_not_R matches its terminal LHLPFAL.

file:PSEPK/thrC/thrC-uniprot.txt

UniProtKB record for Q88MU7 (thrC)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

NCBIfam; TIGR00260; thrC; 1.

file:PSEPK/thrC/thrC-uniprot.txt

UniProtKB record for Q88MU7 (thrC)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

N6-(pyridoxal phosphate)lysine

PMID:40236303

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440.

the remaining genes of the metabolic pathway – thrB and thrC – were overexpressed as well.

file:PSEPK/PP_4473/PP_4473-bioinformatics/primer-identity/RESULTS.md

Terminal-primer identity analysis of native KT2440 constructs in PMID:40236303

Published terminal primers distinguish the named native constructs; this does not verify the full cloned CDS or measure enzymatic activity.

The thrC_ecor_F primer matches MRYISTR at the N terminus of ThrC/PP_1471/Q88MU7; thrC_xba_R matches terminal HGNRGKPL.

Part 1: shared aspartate-family activation

shared aspartate-family activationReactionpsepk_ak

Annotons

PSEPK PP_4473: aspartate kinase activity

psepk_pp_4473_ak

Participant: Gene Product: PP_4473 (PSEPK)

Gene Product:

PP_4473 (PSEPK)UniProtKB:Q88EI9

Family:

Classification of PSEPK PP_4473PANTHER:PTHR21499:SF3

Representative Members: PP_4473 (PSEPK)UniProtKB:Q88EI9

Taxon:

Pseudomonas putida KT2440NCBITaxon:160488

Function

aspartate kinase activityGO:0004072

Substrates: L-aspartate ATP

Products: 4-phospho-L-aspartate ADP

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:PSEPK/PP_4473/PP_4473-uniprot.txt

UniProtKB record for Q88EI9 (PP_4473)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

NCBIfam; TIGR00656; asp_kin_monofn; 1.

file:PSEPK/PP_4473/PP_4473-uniprot.txt

UniProtKB record for Q88EI9 (PP_4473)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Reaction=L-aspartate + ATP = 4-phospho-L-aspartate + ADP

PMID:40236303

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440.

Despite the successful overproduction of two key enzymes, aspartate kinase (LysC) and homoserine dehydrogenase (Hom) from different plasmid combinations

file:PSEPK/PP_4473/PP_4473-bioinformatics/primer-identity/RESULTS.md

Terminal-primer identity analysis of native KT2440 constructs in PMID:40236303

Published terminal primers distinguish the named native constructs; this does not verify the full cloned CDS or measure enzymatic activity.

The Table S2 lysC_xba_R reverse primer matches the terminal PARQGE of PP_4473/Q88EI9, followed by a stop codon.

Both existing activity rows describe the same well-supported function. PMID:5441401 is linked by UniProt to biochemical work, but its unavailable text and unresolved 1970 strain do not establish direct KT2440-specific kinetics. The original IDA attribution is preserved, not rejected; modern native cloning is not a purified activity assay.

Part 2: shared semialdehyde formation

shared semialdehyde formationReactionpsepk_asd

Annotons

PSEPK asd__Q88LE4: aspartate-semialdehyde dehydrogenase (NADP+) activity

psepk_asd_q88le4_asd

Participant: Gene Product: asd__Q88LE4 (PSEPK)

Gene Product:

asd__Q88LE4 (PSEPK)UniProtKB:Q88LE4

Family:

Classification of PSEPK asd__Q88LE4PANTHER:PTHR46278:SF4

Representative Members: asd__Q88LE4 (PSEPK)UniProtKB:Q88LE4

Taxon:

Pseudomonas putida KT2440NCBITaxon:160488

Function

aspartate-semialdehyde dehydrogenase (NADP+) activityGO:0004073

Substrates: 4-phospho-L-aspartate NADPH

Products: L-aspartate 4-semialdehyde NADP+ phosphate

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:PSEPK/asd__Q88LE4/asd__Q88LE4-uniprot.txt

UniProtKB record for Q88LE4 (asd__Q88LE4)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Catalyzes the NADPH-dependent formation of L-aspartate-

file:PSEPK/asd__Q88LE4/asd__Q88LE4-uniprot.txt

UniProtKB record for Q88LE4 (asd__Q88LE4)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

HAMAP; MF_02121; ASADH; 1.

HAMAP MF_02121, TIGR01745, the Asd active-site signature and Cys135/His275 assignments converge. A UniProt caution about missing residues limits complete feature propagation but does not by itself negate this coherent family assignment. Native purified kinetics have not been established.

Part 3: homoserine branch formation

homoserine branch formationReactionpsepk_hom

NADPH-supported reductive direction is represented. This does not assert exclusive donor preference, nor discard independently supported NADH capacity in a gene review.

Annotons

PSEPK hom: homoserine dehydrogenase activity

psepk_hom_hom

Participant: Gene Product: hom (PSEPK)

Gene Product:

hom (PSEPK)UniProtKB:Q88MU8

Family:

Classification of PSEPK homPANTHER:PTHR43331:SF1

Representative Members: hom (PSEPK)UniProtKB:Q88MU8

Taxon:

Pseudomonas putida KT2440NCBITaxon:160488

Function

homoserine dehydrogenase activityGO:0004412

Substrates: L-aspartate 4-semialdehyde NADPH

Products: L-homoserine NADP+

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:PSEPK/hom/hom-uniprot.txt

UniProtKB record for Q88MU8 (hom)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Belongs to the homoserine dehydrogenase family.

file:PSEPK/hom/hom-uniprot.txt

UniProtKB record for Q88MU8 (hom)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

PROSITE; PS01042; HOMOSER_DHGENASE; 1.

file:PSEPK/hom/hom-uniprot.txt

UniProtKB record for Q88MU8 (hom)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

/ligand="NADPH"

PMID:40236303

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440.

Despite the successful overproduction of two key enzymes, aspartate kinase (LysC) and homoserine dehydrogenase (Hom) from different plasmid combinations

file:PSEPK/PP_4473/PP_4473-bioinformatics/primer-identity/RESULTS.md

Terminal-primer identity analysis of native KT2440 constructs in PMID:40236303

Published terminal primers distinguish the named native constructs; this does not verify the full cloned CDS or measure enzymatic activity.

The hom_nhe_R reverse primer matches terminal RVEQLN of Hom/PP_1470/Q88MU8, followed by a stop.

The live QuickGO definition, quoted and linked in hom-notes.md and retained in the module audit go-terms.yaml, specifies NADP+ rather than NAD(P)+. Independent RuleBase family assignment, PROSITE signature and PIRSR NADP/NADPH contacts support that capacity. The native overexpression study identifies PP_1470 but does not measure cofactor preference or purified kinetics.

Part 4: homoserine phosphorylation

homoserine phosphorylationReactionpsepk_thrb

Annotons

PSEPK thrB: homoserine kinase activity

psepk_thrb_thrb

Participant: Gene Product: thrB (PSEPK)

Gene Product:

thrB (PSEPK)UniProtKB:Q88RK8

Family:

Classification of PSEPK thrBPANTHER:PTHR21064:SF6

Representative Members: thrB (PSEPK)UniProtKB:Q88RK8

Taxon:

Pseudomonas putida KT2440NCBITaxon:160488

Function

homoserine kinase activityGO:0004413

Substrates: L-homoserine ATP

Products: O-phospho-L-homoserine ADP

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:PSEPK/thrB/thrB-uniprot.txt

UniProtKB record for Q88RK8 (thrB)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

Reaction=L-homoserine + ATP = O-phospho-L-homoserine + ADP + H(+)

file:PSEPK/thrB/thrB-uniprot.txt

UniProtKB record for Q88RK8 (thrB)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

HAMAP; MF_00301; Homoser_kinase_2; 1.

PMID:40236303

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440.

the remaining genes of the metabolic pathway – thrB and thrC – were overexpressed as well.

file:PSEPK/PP_4473/PP_4473-bioinformatics/primer-identity/RESULTS.md

Terminal-primer identity analysis of native KT2440 constructs in PMID:40236303

Published terminal primers distinguish the named native constructs; this does not verify the full cloned CDS or measure enzymatic activity.

The thrB_ecoRI_F primer matches MSVFTPVT at the N terminus of ThrB/PP_0121/Q88RK8, and thrB_not_R matches its terminal LHLPFAL.

HAMAP MF_00301, TIGR00938 and the Pseudomonas-type ThrB family establish the inference; the generic APH fold does not imply antibiotic phosphorylation. PMID:40236303 corroborates native construct identity and pathway engineering, not individual kinetic measurements.

Part 5: terminal threonine formation

terminal threonine formationReactionpsepk_thrc

Annotons

PSEPK thrC: threonine synthase activity

psepk_thrc_thrc

Participant: Gene Product: thrC (PSEPK)

Gene Product:

thrC (PSEPK)UniProtKB:Q88MU7

Family:

Classification of PSEPK thrCPANTHER:PTHR42690:SF1

Representative Members: thrC (PSEPK)UniProtKB:Q88MU7

Taxon:

Pseudomonas putida KT2440NCBITaxon:160488

Function

threonine synthase activityGO:0004795

Substrates: O-phospho-L-homoserine water

Products: L-threonine phosphate

Cofactors: pyridoxal 5'-phosphate

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:PSEPK/thrC/thrC-uniprot.txt

UniProtKB record for Q88MU7 (thrC)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

NCBIfam; TIGR00260; thrC; 1.

file:PSEPK/thrC/thrC-uniprot.txt

UniProtKB record for Q88MU7 (thrC)

Family, domain or curated catalytic-feature support; evidence remains an inference unless specifically stated as measured.

N6-(pyridoxal phosphate)lysine

PMID:40236303

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440.

the remaining genes of the metabolic pathway – thrB and thrC – were overexpressed as well.

file:PSEPK/PP_4473/PP_4473-bioinformatics/primer-identity/RESULTS.md

Terminal-primer identity analysis of native KT2440 constructs in PMID:40236303

Published terminal primers distinguish the named native constructs; this does not verify the full cloned CDS or measure enzymatic activity.

The thrC_ecor_F primer matches MRYISTR at the N terminus of ThrC/PP_1471/Q88MU7; thrC_xba_R matches terminal HGNRGKPL.

TIGR00260 and the threonine-synthase architecture support the reaction, with a PIRSR-assigned PLP-linked Lys112. Native ThrB/ThrC engineering corroborates pathway participation but does not separately assay ThrC kinetics.

Escherichia coli K-12 aspartate-to-threonine routeMetabolic Pathwayecoli_route

Five required sequential reactions. Presence denotes supported native catalytic capacity, not measured flux under every condition. No inter-enzyme metabolon or substrate channeling is asserted.

Context

Escherichia coli K-12NCBITaxon:83333

Intracellular aspartate, ATP, NADPH and required catalytic cofactors available

PMID:11368768

An integrated study of threonine-pathway enzyme kinetics in Escherichia coli.

The E. coli aspartate-to-threonine sequence has been examined as an integrated set of enzyme reactions under physiologically relevant assay conditions.

We have determined the kinetic parameters of the individual steps of the threonine pathway from aspartate in Escherichia coli under a single set of experimental conditions chosen to be physiologically relevant.

ThrA and MetL each supply AK and HDH activities at nonadjacent steps. Neither fusion supplies Asd; removal of Asd must break the route even if both fusions are present. LysC can supply the shared entry activity but cannot replace HDH. No fixed MetL oligomer stoichiometry is asserted.

Connections

ecoli_ak -> ecoli_asd Precedes

The preceding product 4-phospho-L-aspartate is substrate for this reaction. This is chemical continuity, not physical channeling.

file:ECOLI/thrA/thrA-uniprot.txt

UniProt record for ECOLI thrA

The ThrA kinase domain converts aspartate and ATP to aspartyl phosphate and ADP.

Reaction=L-aspartate + ATP = 4-phospho-L-aspartate + ADP;

file:ECOLI/asd/asd-uniprot.txt

UniProt record for ECOLI asd

Asd reductively dephosphorylates aspartyl phosphate to aspartate semialdehyde using NADPH.

Catalyzes the NADPH-dependent formation of L-aspartate- CC semialdehyde (L-ASA) by the reductive dephosphorylation of L-aspartyl- CC 4-phosphate.

PMID:6102909

Aspartate-beta-semialdehyde dehydrogenase from Escherichia coli. Purification and general properties.

Detection of an acyl-enzyme intermediate supports the Asd reaction mechanism.

Formation of an acyl-enzyme intermediate was also detected.

PMID:14726201

L-cystine inhibits aspartate-beta-semialdehyde dehydrogenase by covalently binding to the essential 135Cys of the enzyme.

Cystine modifies the essential Asd Cys135 in the tested inhibition assay.

thus demonstrating that the essential 135Cys is the amino acid residue modified by the treatment with cystine.

ecoli_asd -> ecoli_hom Precedes

The preceding product L-aspartate 4-semialdehyde is substrate for this reaction. This is chemical continuity, not physical channeling.

file:ECOLI/asd/asd-uniprot.txt

UniProt record for ECOLI asd

Asd reductively dephosphorylates aspartyl phosphate to aspartate semialdehyde using NADPH.

Catalyzes the NADPH-dependent formation of L-aspartate- CC semialdehyde (L-ASA) by the reductive dephosphorylation of L-aspartyl- CC 4-phosphate.

PMID:6102909

Aspartate-beta-semialdehyde dehydrogenase from Escherichia coli. Purification and general properties.

Detection of an acyl-enzyme intermediate supports the Asd reaction mechanism.

Formation of an acyl-enzyme intermediate was also detected.

PMID:14726201

L-cystine inhibits aspartate-beta-semialdehyde dehydrogenase by covalently binding to the essential 135Cys of the enzyme.

Cystine modifies the essential Asd Cys135 in the tested inhibition assay.

thus demonstrating that the essential 135Cys is the amino acid residue modified by the treatment with cystine.

file:ECOLI/thrA/thrA-uniprot.txt

UniProt record for ECOLI thrA

The ThrA dehydrogenase domain reduces aspartate semialdehyde to homoserine with NADPH.

Reaction=L-homoserine + NADP(+) = L-aspartate 4-semialdehyde + NADPH + CC H(+);

ecoli_hom -> ecoli_thrb Precedes

The preceding product L-homoserine is substrate for this reaction. This is chemical continuity, not physical channeling.

file:ECOLI/thrA/thrA-uniprot.txt

UniProt record for ECOLI thrA

The ThrA dehydrogenase domain reduces aspartate semialdehyde to homoserine with NADPH.

Reaction=L-homoserine + NADP(+) = L-aspartate 4-semialdehyde + NADPH + CC H(+);

PMID:8973190

Substrate specificity and identification of functional groups of homoserine kinase from Escherichia coli.

ThrB phosphorylates homoserine; substrate analogs were used to interrogate specificity.

Homoserine kinase, an enzyme in the aspartate pathway of amino acid biosynthesis in Escherichia coli, catalyzes the conversion of L-homoserine to L-homoserine phosphate.

PMID:177283

Homoserine kinase from Escherichia coli K12.

Threonine competitively inhibits homoserine phosphorylation without cooperativity.

L-Threonine is a competitive inhibitor of the substrate L-homoserine; this inhibition is straighforward and shows no sign of co-operativity.

ecoli_thrb -> ecoli_thrc Precedes

The preceding product O-phospho-L-homoserine is substrate for this reaction. This is chemical continuity, not physical channeling.

PMID:8973190

Substrate specificity and identification of functional groups of homoserine kinase from Escherichia coli.

ThrB phosphorylates homoserine; substrate analogs were used to interrogate specificity.

Homoserine kinase, an enzyme in the aspartate pathway of amino acid biosynthesis in Escherichia coli, catalyzes the conversion of L-homoserine to L-homoserine phosphate.

PMID:177283

Homoserine kinase from Escherichia coli K12.

Threonine competitively inhibits homoserine phosphorylation without cooperativity.

L-Threonine is a competitive inhibitor of the substrate L-homoserine; this inhibition is straighforward and shows no sign of co-operativity.

file:ECOLI/thrC/thrC-uniprot.txt

UniProt record for ECOLI thrC

PLP-dependent ThrC converts phosphohomoserine to threonine by phosphate elimination and water addition.

Catalyzes the gamma-elimination of phosphate from L- CC phosphohomoserine and the beta-addition of water to produce L- CC threonine.

PMID:6316258

Nucleotide sequence of thrC and of the transcription termination region of the threonine operon in Escherichia coli K12.

The native thrC initiation site was identified using the threonine synthase N-terminal sequence.

The translation initiation codon was identified by sequencing the N-terminal part of threonine synthase, the thrC gene product.

Part 1: shared aspartate-family activation

shared aspartate-family activationReactionecoli_ak

Variant set: Native isozyme alternatives by native gene product (One Or More)

thrAReactionecoli_thra_ak_variant

Annotons

ECOLI thrA: aspartate kinase activity

ecoli_thra_ak

Participant: Gene Product: thrA (ECOLI)

Gene Product:

thrA (ECOLI)UniProtKB:P00561

Family:

Classification of ECOLI thrAPANTHER:PTHR43070:SF3

Representative Members: thrA (ECOLI)UniProtKB:P00561

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

aspartate kinase activityGO:0004072

Substrates: L-aspartate ATP

Products: 4-phospho-L-aspartate ADP

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:ECOLI/thrA/thrA-uniprot.txt

UniProt record for ECOLI thrA

The ThrA kinase domain converts aspartate and ATP to aspartyl phosphate and ADP.

Reaction=L-aspartate + ATP = 4-phospho-L-aspartate + ADP;

The PAINT PTN001852279 assertion covers the kinase activity of the bifunctional ThrA lineage. P00561 is this target among the experimentally grounded descendants, which is expected and not circular. Its N-terminal kinase domain activates aspartate; the C-terminal homoserine reaction is a separate activity. PMID:11368768 determines the kinetic parameters of the E. coli threonine-pathway reactions under a common physiological assay regime, including the first aspartate-activation step and feedback inhibition. This supports the ThrA kinase activity alongside the independently curated ATP/aspartate reaction; the study is not treated as a localization assay. RHEA:23776 and the IPR001341/IPR018042 kinase signatures describe ATP-dependent aspartate activation in the N-terminal portion of this fusion. The reaction is independently established for ThrA; a second dehydrogenase domain does not erase the kinase activity. The Q9SA18 transfer concerns the conserved aspartate-kinase reaction of Arabidopsis AKHSDH1. PMID:16216875 tests that donor isoform directly, and PMID:11368768 independently characterizes the E. coli pathway. The transfer does not import plant chloroplast location or isoform-specific allosteric responses into ThrA.

metLReactionecoli_metl_ak_variant

Annotons

ECOLI metL: aspartate kinase activity

ecoli_metl_ak

Participant: Gene Product: metL (ECOLI)

Gene Product:

metL (ECOLI)UniProtKB:P00562

Family:

Classification of ECOLI metLPANTHER:PTHR43070:SF3

Representative Members: metL (ECOLI)UniProtKB:P00562

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

aspartate kinase activityGO:0004072

Substrates: L-aspartate ATP

Products: 4-phospho-L-aspartate ADP

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:ECOLI/metL/metL-uniprot.txt

UniProt record for ECOLI metL

The MetL kinase domain phosphorylates aspartate as the first step toward homoserine.

Reaction=L-aspartate + ATP = 4-phospho-L-aspartate + ADP;

PAINT PTN000487132 supports the inherited aspartate-kinase activity of MetL. The source set includes target P00562 itself and other characterized aspartokinases; that is legitimate descendant evidence. MetL contains the kinase function in a bifunctional polypeptide, with methionine-regulated synthesis rather than a requirement for ThrA-like feedback. PMID:4889171 is the legacy purification source for methionine-repressible AKII/HSDHII. The cached entry has bibliographic information but no experimental abstract or full results, so no numerical kinetic or oligomer claim is reconstructed from its title. Retain the experimentally curated kinase claim with independent curated MetL reaction evidence. The kinase-domain signatures and RHEA:23776 support ATP-dependent aspartate phosphorylation in MetL. Curated target reaction evidence corroborates this mapping independently of the ARBA association; the methionine-repressible synthesis context does not change the substrate chemistry. The Q9SA18 donor is Arabidopsis AKHSDH1, whose aspartate-kinase reaction is directly characterized in PMID:16216875. MetL shares the bifunctional architecture and has independent curated AKII activity; the inference transfers the chemistry, not plastid targeting or the donor allosteric profile.

lysCReactionecoli_lysc_ak_variant

Annotons

ECOLI lysC: aspartate kinase activity

ecoli_lysc_ak

Participant: Gene Product: lysC (ECOLI)

Gene Product:

lysC (ECOLI)UniProtKB:P08660

Family:

Classification of ECOLI lysCPANTHER:PTHR21499:SF59

Representative Members: lysC (ECOLI)UniProtKB:P08660

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

aspartate kinase activityGO:0004072

Substrates: L-aspartate ATP

Products: 4-phospho-L-aspartate ADP

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

PMID:14623187

Site-directed mutagenesis of Escherichia coli acetylglutamate kinase and aspartokinase III probes the catalytic and substrate-binding mechanisms of these amino acid kinase family enzymes and allows three-dimensional modelling of aspartokinase.

AKIII phosphorylates aspartate rather than acetylglutamate.

AKIII phosphorylates aspartate instead of acetylglutamate

PMID:14623187

AKIII residues K8 and D202 contribute to the catalytic-site mechanism.

identified in AKIII two residues, K8 and D202, that appear to play roles similar to those of K8 and D162 of NAGK

PMID:6249791

Regulation of aspartokinase III synthesis in Escherichia coli: isolation of mutants containing lysC-lac fusions.

The study isolated lysC-lac fusions to examine lysC expression; the quoted experiment is not a purified catalytic assay.

Mutants containing fusions of the lac gene to the lysC gene were isolated.

PAINT PTN000487132 places aspartate kinase activity in the inherited aspartokinase lineage. The target is the monofunctional, lysine-regulated LysC enzyme, independently supported by its catalytic-site mutagenesis in PMID:14623187; the kinase claim does not depend on the number of descendant donors. PMID:14623187 specifically mutates E. coli AKIII as well as N-acetylglutamate kinase. In AKIII, K8/D202 support catalysis and E119/R198 substrate recognition. These target experiments establish aspartate phosphorylation; the NAGK results are comparative mechanistic context, not a substitute target assay. PMID:6249791 studies lysC–lac fusion mutants and lysine/arginine regulation of aspartokinase III expression. Its accessible abstract does not provide purified-enzyme kinetics, so it is not relabeled as that experiment. The enzyme-function claim is nevertheless independently established by target mutagenesis in PMID:14623187 and substrate-bound structures in PMID:16905770; the curated legacy row is retained on that combined evidence. The amino-acid-kinase InterPro signatures and RHEA:23776 identify ATP-dependent aspartate phosphorylation. This electronic inference agrees with direct LysC mutagenesis in PMID:14623187 and aspartate/ADP-bound structural evidence in PMID:16905770; it is not accepted solely from the ARBA field or the enzyme name.

Part 2: shared semialdehyde formation

shared semialdehyde formationReactionecoli_asd

Annotons

ECOLI asd: aspartate-semialdehyde dehydrogenase (NADP+) activity

ecoli_asd_asd

Participant: Gene Product: asd (ECOLI)

Gene Product:

asd (ECOLI)UniProtKB:P0A9Q9

Family:

Classification of ECOLI asdPANTHER:PTHR46278:SF4

Representative Members: asd (ECOLI)UniProtKB:P0A9Q9

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

aspartate-semialdehyde dehydrogenase (NADP+) activityGO:0004073

Substrates: 4-phospho-L-aspartate NADPH

Products: L-aspartate 4-semialdehyde NADP+ phosphate

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:ECOLI/asd/asd-uniprot.txt

UniProt record for ECOLI asd

Asd reductively dephosphorylates aspartyl phosphate to aspartate semialdehyde using NADPH.

Catalyzes the NADPH-dependent formation of L-aspartate- CC semialdehyde (L-ASA) by the reductive dephosphorylation of L-aspartyl- CC 4-phosphate.

PMID:6102909

Aspartate-beta-semialdehyde dehydrogenase from Escherichia coli. Purification and general properties.

Detection of an acyl-enzyme intermediate supports the Asd reaction mechanism.

Formation of an acyl-enzyme intermediate was also detected.

PMID:14726201

L-cystine inhibits aspartate-beta-semialdehyde dehydrogenase by covalently binding to the essential 135Cys of the enzyme.

Cystine modifies the essential Asd Cys135 in the tested inhibition assay.

thus demonstrating that the essential 135Cys is the amino acid residue modified by the treatment with cystine.

PMID:11368768 integrates the E. coli threonine-pathway enzyme kinetics and includes the aspartyl-phosphate reduction step. Asd catalyzes NADPH-dependent reductive dephosphorylation, supplying aspartate semialdehyde; the NADP-specific activity is corroborated by purified-target chemistry in PMID:6102909. PMID:6102909 purifies E. coli Asd, detects an acyl-enzyme intermediate and establishes pro-S hydride transfer from NADPH. Those mechanistic observations directly support the NADP-dependent semialdehyde-dehydrogenase reaction, beyond a sequence-family assignment. PAINT PTN000019341 places the NADP-dependent aspartate-semialdehyde dehydrogenase reaction in the inherited Asd lineage. P0A9Q9 is the target and an experimentally characterized descendant, not a circular donor. Its catalytic cysteine and direct NADPH chemistry in PMID:6102909 corroborate this placement. The IDA row from PMID:11368768 concerns the same measured pathway reaction as the separate EXP row: reduction of aspartyl phosphate to aspartate semialdehyde. The study models substrate/product effects under one assay regime; it does not assert equal NAD and NADP efficiencies. PMID:14726201 directly studies purified E. coli Asd inhibition by cystine and maps the covalent modification to catalytic Cys135. This target activity assay supports the phosphoacyl reduction mechanism; failure of NADP/NADPH to protect against cystine does not mean the enzyme lacks those cofactors. The Asd domain signatures, RHEA:24284 and curated UniRule assignment identify the NADPH-dependent reductive dephosphorylation of aspartyl phosphate. Independent purified-enzyme hydride-transfer evidence in PMID:6102909 supports the reaction, so the decision does not rest on an unvetted ARBA prediction.

Part 3: homoserine branch formation

homoserine branch formationReactionecoli_hom

NADPH-supported reductive direction is represented. This does not assert exclusive donor preference, nor discard independently supported NADH capacity in a gene review.

Variant set: Native isozyme alternatives by native gene product (One Or More)

thrAReactionecoli_thra_hom_variant

Annotons

ECOLI thrA: homoserine dehydrogenase activity

ecoli_thra_hom

Participant: Gene Product: thrA (ECOLI)

Gene Product:

thrA (ECOLI)UniProtKB:P00561

Family:

Classification of ECOLI thrAPANTHER:PTHR43070:SF3

Representative Members: thrA (ECOLI)UniProtKB:P00561

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

homoserine dehydrogenase activityGO:0004412

Substrates: L-aspartate 4-semialdehyde NADPH

Products: L-homoserine NADP+

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:ECOLI/thrA/thrA-uniprot.txt

UniProt record for ECOLI thrA

The ThrA dehydrogenase domain reduces aspartate semialdehyde to homoserine with NADPH.

Reaction=L-homoserine + NADP(+) = L-aspartate 4-semialdehyde + NADPH + CC H(+);

The C-terminal domain catalyzes reduction of aspartate semialdehyde to homoserine. The NADP(H) reaction is retained independently of the separate NAD(H) inference.

metLReactionecoli_metl_hom_variant

Annotons

ECOLI metL: homoserine dehydrogenase activity

ecoli_metl_hom

Participant: Gene Product: metL (ECOLI)

Gene Product:

metL (ECOLI)UniProtKB:P00562

Family:

Classification of ECOLI metLPANTHER:PTHR43070:SF3

Representative Members: metL (ECOLI)UniProtKB:P00562

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

homoserine dehydrogenase activityGO:0004412

Substrates: L-aspartate 4-semialdehyde NADPH

Products: L-homoserine NADP+

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:ECOLI/metL/metL-uniprot.txt

UniProt record for ECOLI metL

MetL homoserine dehydrogenase II reduces aspartate semialdehyde using NADPH.

Reaction=L-homoserine + NADP(+) = L-aspartate 4-semialdehyde + NADPH + CC H(+);

The C-terminal domain catalyzes reduction of aspartate semialdehyde to homoserine. The NADP(H) reaction is retained independently of the separate NAD(H) inference.

Part 4: homoserine phosphorylation

homoserine phosphorylationReactionecoli_thrb

Annotons

ECOLI thrB: homoserine kinase activity

ecoli_thrb_thrb

Participant: Gene Product: thrB (ECOLI)

Gene Product:

thrB (ECOLI)UniProtKB:P00547

Family:

Classification of ECOLI thrBPANTHER:PTHR20861:SF1

Representative Members: thrB (ECOLI)UniProtKB:P00547

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

homoserine kinase activityGO:0004413

Substrates: L-homoserine ATP

Products: O-phospho-L-homoserine ADP

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

PMID:8973190

Substrate specificity and identification of functional groups of homoserine kinase from Escherichia coli.

ThrB phosphorylates homoserine; substrate analogs were used to interrogate specificity.

Homoserine kinase, an enzyme in the aspartate pathway of amino acid biosynthesis in Escherichia coli, catalyzes the conversion of L-homoserine to L-homoserine phosphate.

PMID:177283

Homoserine kinase from Escherichia coli K12.

Threonine competitively inhibits homoserine phosphorylation without cooperativity.

L-Threonine is a competitive inhibitor of the substrate L-homoserine; this inhibition is straighforward and shows no sign of co-operativity.

PMID:177283 purifies native E. coli homoserine kinase and measures homoserine/threonine competition and magnesium effects. Threonine inhibition is competitive rather than cooperative allostery. Together with the target reaction characterization in PMID:8973190, this establishes ATP-dependent phosphohomoserine formation. The homoserine-kinase family signature, RHEA:13985 and curated UniRule identify ATP as phosphate donor and homoserine as acceptor. Native purified ThrB measurements in PMID:177283 and target mechanistic work in PMID:8973190 independently corroborate this mapping; it is distinct from the phosphoserine-donor ThrH route.

Part 5: terminal threonine formation

terminal threonine formationReactionecoli_thrc

Annotons

ECOLI thrC: threonine synthase activity

ecoli_thrc_thrc

Participant: Gene Product: thrC (ECOLI)

Gene Product:

thrC (ECOLI)UniProtKB:P00934

Family:

Classification of ECOLI thrCPANTHER:PTHR42690:SF1

Representative Members: thrC (ECOLI)UniProtKB:P00934

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

threonine synthase activityGO:0004795

Substrates: O-phospho-L-homoserine water

Products: L-threonine phosphate

Cofactors: pyridoxal 5'-phosphate

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:ECOLI/thrC/thrC-uniprot.txt

UniProt record for ECOLI thrC

PLP-dependent ThrC converts phosphohomoserine to threonine by phosphate elimination and water addition.

Catalyzes the gamma-elimination of phosphate from L- CC phosphohomoserine and the beta-addition of water to produce L- CC threonine.

PMID:6316258

Nucleotide sequence of thrC and of the transcription termination region of the threonine operon in Escherichia coli K12.

The native thrC initiation site was identified using the threonine synthase N-terminal sequence.

The translation initiation codon was identified by sequencing the N-terminal part of threonine synthase, the thrC gene product.

PMID:6316258 links the thrC gene sequence to the N-terminal sequence of purified threonine synthase. The detailed chemistry is independently recorded in the curated target FUNCTION/COFACTOR fields: PLP-dependent gamma-elimination of phosphate from phosphohomoserine followed by beta-addition of water yields threonine. The sequence paper is not misrepresented as a complete kinetic mechanism study. RHEA:10840 maps the PLP-dependent conversion of phosphohomoserine to threonine and phosphate. Curated target mechanism and cofactor statements, together with the sequence-to-protein linkage in PMID:6316258, substantiate the electronic assignment independently of ARBA. The reaction is elimination/addition, not simple phosphomonoester hydrolysis.

Corynebacterium glutamicum ATCC 13032 aspartate-to-threonine routeMetabolic Pathwaycorgl_route

Five required sequential reactions. Presence denotes supported native catalytic capacity, not measured flux under every condition. No inter-enzyme metabolon or substrate channeling is asserted.

Context

Corynebacterium glutamicum ATCC 13032NCBITaxon:196627

Intracellular aspartate, ATP, NADPH and required catalytic cofactors available

The native LysC alpha/beta assembly is explicit. Asd has curated family support; biochemical Hom/ThrC studies from other coryneform strains are treated as qualified comparative evidence rather than relabeled ATCC 13032 assays.

Connections

corgl_ak -> corgl_asd Precedes

The preceding product 4-phospho-L-aspartate is substrate for this reaction. This is chemical continuity, not physical channeling.

PMID:20573952

Mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from Corynebacterium glutamicum.

The structural study describes aspartokinase phosphorylation of aspartate as the shared pathway entry reaction.

The enzyme catalyzing the first step of this pathway is aspartate kinase (AK2; EC 2.7.2.4), which phosphorylates the β-carboxyl group of aspartate using ATP.

PMID:1956296

Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum.

The lysC/asd locus was cloned and sequenced from ATCC 13032, establishing strain-specific genetic provenance.

The lysC/asd gene cluster of Corynebacterium glutamicum ATCC 13032 was cloned and sequenced.

PMID:20573952

Mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from Corynebacterium glutamicum.

Catalysis resides in alpha N-terminal domains; beta and alpha C-terminal regions regulate.

The N-terminal portion of the α subunit functions as a catalytic domain, whereas the β subunit and C-terminal portion of the α subunit serve as regulatory domains.

PMID:1980002

Aspartokinase genes lysC alpha and lysC beta overlap and are adjacent to the aspartate beta-semialdehyde dehydrogenase gene asd in Corynebacterium glutamicum.

Native asd DNA complements an asd-deficient host and elevates Asd activity in C. glutamicum.

Plasmids carrying the C. glutamicum asd gene complemented Escherichia coli asd mutants. Increase in ASD activity by a factor of 30-60 was measured for C. glutamicum cells harbouring high copy-number plasmids with the C. glutamicum asd gene.

file:CORGL/asd/asd-uniprot.txt

UniProtKB asd reviewed record (P0C1D8)

The curated Asd family rule supports NADPH-dependent reductive dephosphorylation.

CC -!- FUNCTION: Catalyzes the NADPH-dependent formation of L-aspartate- CC semialdehyde (L-ASA) by the reductive dephosphorylation of L-aspartyl- CC 4-phosphate. {ECO:0000255|HAMAP-Rule:MF_02121}.

corgl_asd -> corgl_hom Precedes

The preceding product L-aspartate 4-semialdehyde is substrate for this reaction. This is chemical continuity, not physical channeling.

PMID:1980002

Aspartokinase genes lysC alpha and lysC beta overlap and are adjacent to the aspartate beta-semialdehyde dehydrogenase gene asd in Corynebacterium glutamicum.

Native asd DNA complements an asd-deficient host and elevates Asd activity in C. glutamicum.

file:CORGL/asd/asd-uniprot.txt

UniProtKB asd reviewed record (P0C1D8)

The curated Asd family rule supports NADPH-dependent reductive dephosphorylation.

CC -!- FUNCTION: Catalyzes the NADPH-dependent formation of L-aspartate- CC semialdehyde (L-ASA) by the reductive dephosphorylation of L-aspartyl- CC 4-phosphate. {ECO:0000255|HAMAP-Rule:MF_02121}.

file:CORGL/hom/hom-uniprot.txt

UniProtKB hom reviewed record (P08499)

Hom belongs to the homoserine dehydrogenase family.

CC -!- SIMILARITY: Belongs to the homoserine dehydrogenase family. CC {ECO:0000305}.

file:CORGL/hom/hom-uniprot.txt

UniProtKB hom reviewed record (P08499)

The curated target record assigns conversion of aspartate semialdehyde to homoserine; this excerpt does not by itself establish donor preference.

CC -!- FUNCTION: Catalyzes the conversion of L-aspartate-beta-semialdehyde (L- CC Asa) to L-homoserine (L-Hse), the third step in the biosynthesis of CC threonine and methionine from aspartate. CC {ECO:0000250|UniProtKB:P31116}.

url:https://www.jstage.jst.go.jp/article/biochemistry1922/68/3/68_3_311/_pdf

Regulation of Aspartate Family Amino Acid Biosynthesis in Brevibacterium flavum III. Properites of Homoserine Dehydrogenase

A partially purified B. flavum No.2247 enzyme was assayed with NADPH and showed ordered substrate/product interaction.

These results suggest an ordered mechanism for the reaction, in which NADPH is the first binding substrate and NADP+ is the last releasing product.

PMID:1743520

A C-terminal deletion in Corynebacterium glutamicum homoserine dehydrogenase abolishes allosteric inhibition by L-threonine.

Wild-type C. glutamicum Hom is inhibited by threonine; mutant deregulation is a distinct phenotype.

L-Threonine inhibits the wild-type (wt) enzyme with a Ki of 0.16 mM.

corgl_hom -> corgl_thrb Precedes

The preceding product L-homoserine is substrate for this reaction. This is chemical continuity, not physical channeling.

file:CORGL/hom/hom-uniprot.txt

UniProtKB hom reviewed record (P08499)

Hom belongs to the homoserine dehydrogenase family.

CC -!- SIMILARITY: Belongs to the homoserine dehydrogenase family. CC {ECO:0000305}.

file:CORGL/hom/hom-uniprot.txt

UniProtKB hom reviewed record (P08499)

The curated target record assigns conversion of aspartate semialdehyde to homoserine; this excerpt does not by itself establish donor preference.

url:https://www.jstage.jst.go.jp/article/biochemistry1922/68/3/68_3_311/_pdf

Regulation of Aspartate Family Amino Acid Biosynthesis in Brevibacterium flavum III. Properites of Homoserine Dehydrogenase

A partially purified B. flavum No.2247 enzyme was assayed with NADPH and showed ordered substrate/product interaction.

These results suggest an ordered mechanism for the reaction, in which NADPH is the first binding substrate and NADP+ is the last releasing product.

PMID:1743520

A C-terminal deletion in Corynebacterium glutamicum homoserine dehydrogenase abolishes allosteric inhibition by L-threonine.

Wild-type C. glutamicum Hom is inhibited by threonine; mutant deregulation is a distinct phenotype.

L-Threonine inhibits the wild-type (wt) enzyme with a Ki of 0.16 mM.

PMID:30023797

Reduction of Feedback Inhibition in Homoserine Kinase (ThrB) of Corynebacterium glutamicum Enhances l-Threonine Biosynthesis.

Recombinant wild-type ThrB uses homoserine and ATP.

The concentration of ADP (Y axis) was determined after incubating each enzyme with l-homoserine and ATP at 27 °C for 30 min.

PMID:30023797

Reduction of Feedback Inhibition in Homoserine Kinase (ThrB) of Corynebacterium glutamicum Enhances l-Threonine Biosynthesis.

The cloned template is native ATCC13032 genomic DNA.

were amplified by PCR using ThrBFor and ThrBRev primers (Table 2) and the C. glutamicum ATCC 13032 genomic DNA as a template.

corgl_thrb -> corgl_thrc Precedes

The preceding product O-phospho-L-homoserine is substrate for this reaction. This is chemical continuity, not physical channeling.

PMID:30023797

Reduction of Feedback Inhibition in Homoserine Kinase (ThrB) of Corynebacterium glutamicum Enhances l-Threonine Biosynthesis.

Recombinant wild-type ThrB uses homoserine and ATP.

The concentration of ADP (Y axis) was determined after incubating each enzyme with l-homoserine and ATP at 27 °C for 30 min.

PMID:30023797

Reduction of Feedback Inhibition in Homoserine Kinase (ThrB) of Corynebacterium glutamicum Enhances l-Threonine Biosynthesis.

The cloned template is native ATCC13032 genomic DNA.

were amplified by PCR using ThrBFor and ThrBRev primers (Table 2) and the C. glutamicum ATCC 13032 genomic DNA as a template.

PMID:8074505

Analysis and expression of the thrC gene of Brevibacterium lactofermentum and characterization of the encoded threonine synthase.

Purified B.lactofermentum enzyme directly converts phosphohomoserine to threonine with PLP.

The purified enzyme required pyridoxal phosphate as its only cofactor to convert homoserine phosphate into threonine.

PMID:2127631

The molecular structure of the Corynebacterium glutamicum threonine synthase gene.

C. glutamicum thrC was mapped using complementation.

The minimal region encoding the Corynebacterium glutamicum threonine synthase structural gene and its promoter was mapped by deletion analysis and complementation of the C. glutamicum thrC allele to a 1.6 kb region of the recombinant plasmid pFS80.

file:CORGL/thrC/thrC-uniprot.txt

UniProtKB thrC reviewed record (P23669)

Specific ThrC family membership supports the target reaction.

DR NCBIfam; TIGR00260; thrC; 1.

Part 1: shared aspartate-family activation

shared aspartate-family activationReactioncorgl_ak

Annotons

CORGL lysC: aspartate kinase activity

corgl_lysc_ak

Participant: Protein Complex: ATCC 13032 LysC alpha2beta2 aspartokinase

Protein Complex:

ATCC 13032 LysC alpha2beta2 aspartokinase

Active units:

Catalytic and regulatory alpha chain2

Participant: Gene Product: lysC (CORGL, P26512-1)

Gene Product:

lysC (CORGL, P26512-1)UniProtKB:P26512-1

Family:

Classification of CORGL lysCPANTHER:PTHR21499:SF3

Representative Members: lysC (CORGL)UniProtKB:P26512

Taxon:

Corynebacterium glutamicum ATCC 13032NCBITaxon:196627

Role: Catalytic and regulatory alpha chain (its N-terminal domain carries the aspartate kinase catalytic site of the complex-level activity)

PMID:20573952

Mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from Corynebacterium glutamicum.

C. glutamicum LysC forms an alpha2beta2 assembly; alpha and beta are alternative-initiation products of one locus, with catalytic and regulatory roles.

CgAK has a characteristic alpha(2)beta(2)-type heterotetrameric structure made up of two alpha subunits and two beta subunits.

PMID:1956296

Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum.

The native ATCC 13032 lysC locus supplies overlapping alpha and beta products; they are not separate independent loci.

The lysC locus coding for aspartokinase consists of two in-frame overlapping genes, lysC alpha encoding a protein of 421 amino acids (Mr 44,300) and lysC beta encoding a protein of 172 amino acids (Mr 18,600). The C. glutamicum aspartokinase was purified and found to contain two proteins of Mr 47,000 and Mr 18,000.

Regulatory beta chain2

Participant: Gene Product: lysC (CORGL, P26512-2)

Gene Product:

lysC (CORGL, P26512-2)UniProtKB:P26512-2

Taxon:

Corynebacterium glutamicum ATCC 13032NCBITaxon:196627

Role: Regulatory beta chain (ACT-domain feedback regulation; no catalytic function is assigned to this unit)

PMID:20573952

Mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from Corynebacterium glutamicum.

C. glutamicum LysC forms an alpha2beta2 assembly; alpha and beta are alternative-initiation products of one locus, with catalytic and regulatory roles.

CgAK has a characteristic alpha(2)beta(2)-type heterotetrameric structure made up of two alpha subunits and two beta subunits.

PMID:1956296

Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum.

The native ATCC 13032 lysC locus supplies overlapping alpha and beta products; they are not separate independent loci.

Function

aspartate kinase activityGO:0004072

Substrates: L-aspartate ATP

Products: 4-phospho-L-aspartate ADP

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

PMID:20573952

Mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from Corynebacterium glutamicum.

The structural study describes aspartokinase phosphorylation of aspartate as the shared pathway entry reaction.

The enzyme catalyzing the first step of this pathway is aspartate kinase (AK2; EC 2.7.2.4), which phosphorylates the β-carboxyl group of aspartate using ATP.

PMID:1956296

Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum.

The lysC/asd locus was cloned and sequenced from ATCC 13032, establishing strain-specific genetic provenance.

The lysC/asd gene cluster of Corynebacterium glutamicum ATCC 13032 was cloned and sequenced.

PMID:20573952

Mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from Corynebacterium glutamicum.

Catalysis resides in alpha N-terminal domains; beta and alpha C-terminal regions regulate.

The N-terminal portion of the α subunit functions as a catalytic domain, whereas the β subunit and C-terminal portion of the α subunit serve as regulatory domains.

PMID:20573952

Mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from Corynebacterium glutamicum.

C. glutamicum LysC forms an alpha2beta2 assembly; alpha and beta are alternative-initiation products of one locus, with catalytic and regulatory roles.

CgAK has a characteristic alpha(2)beta(2)-type heterotetrameric structure made up of two alpha subunits and two beta subunits.

PMID:1956296

Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum.

The native ATCC 13032 lysC locus supplies overlapping alpha and beta products; they are not separate independent loci.

Native ATCC 13032 cloning and protein purification establish this enzyme, and recombinant structural and biochemical work resolves its catalytic alpha and regulatory beta products. The gene-level activity describes the alpha2beta2 enzyme; it does not assign independent aspartokinase catalysis to the beta chain.

Part 2: shared semialdehyde formation

shared semialdehyde formationReactioncorgl_asd

Annotons

CORGL asd: aspartate-semialdehyde dehydrogenase (NADP+) activity

corgl_asd_asd

Participant: Gene Product: asd (CORGL)

Gene Product:

asd (CORGL)UniProtKB:P0C1D8

Family:

Classification of CORGL asdPANTHER:PTHR46278:SF2

Representative Members: asd (CORGL)UniProtKB:P0C1D8

Taxon:

Corynebacterium glutamicum ATCC 13032NCBITaxon:196627

Function

aspartate-semialdehyde dehydrogenase (NADP+) activityGO:0004073

Substrates: 4-phospho-L-aspartate NADPH

Products: L-aspartate 4-semialdehyde NADP+ phosphate

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

PMID:1980002

Aspartokinase genes lysC alpha and lysC beta overlap and are adjacent to the aspartate beta-semialdehyde dehydrogenase gene asd in Corynebacterium glutamicum.

Native asd DNA complements an asd-deficient host and elevates Asd activity in C. glutamicum.

file:CORGL/asd/asd-uniprot.txt

UniProtKB asd reviewed record (P0C1D8)

The curated Asd family rule supports NADPH-dependent reductive dephosphorylation.

CC -!- FUNCTION: Catalyzes the NADPH-dependent formation of L-aspartate- CC semialdehyde (L-ASA) by the reductive dephosphorylation of L-aspartyl- CC 4-phosphate. {ECO:0000255|HAMAP-Rule:MF_02121}.

Native asd cloning complements an E. coli asd defect and elevates aspartate-semialdehyde dehydrogenase activity in C. glutamicum. The target HAMAP MF_02121 rule and conserved Asd family support NADP specificity independently of the combined electronic annotation. The ISS donor is corroborative rather than the sole basis.

Part 3: homoserine branch formation

homoserine branch formationReactioncorgl_hom

NADPH-supported reductive direction is represented. This does not assert exclusive donor preference, nor discard independently supported NADH capacity in a gene review.

Annotons

CORGL hom: homoserine dehydrogenase activity

corgl_hom_hom

Participant: Gene Product: hom (CORGL)

Gene Product:

hom (CORGL)UniProtKB:P08499

Family:

Classification of CORGL homPANTHER:PTHR43331:SF1

Representative Members: hom (CORGL)UniProtKB:P08499

Taxon:

Corynebacterium glutamicum ATCC 13032NCBITaxon:196627

Function

homoserine dehydrogenase activityGO:0004412

Substrates: L-aspartate 4-semialdehyde NADPH

Products: L-homoserine NADP+

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

file:CORGL/hom/hom-uniprot.txt

UniProtKB hom reviewed record (P08499)

Hom belongs to the homoserine dehydrogenase family.

CC -!- SIMILARITY: Belongs to the homoserine dehydrogenase family. CC {ECO:0000305}.

file:CORGL/hom/hom-uniprot.txt

UniProtKB hom reviewed record (P08499)

The curated target record assigns conversion of aspartate semialdehyde to homoserine; this excerpt does not by itself establish donor preference.

url:https://www.jstage.jst.go.jp/article/biochemistry1922/68/3/68_3_311/_pdf

Regulation of Aspartate Family Amino Acid Biosynthesis in Brevibacterium flavum III. Properites of Homoserine Dehydrogenase

A partially purified B. flavum No.2247 enzyme was assayed with NADPH and showed ordered substrate/product interaction.

These results suggest an ordered mechanism for the reaction, in which NADPH is the first binding substrate and NADP+ is the last releasing product.

PMID:1743520

A C-terminal deletion in Corynebacterium glutamicum homoserine dehydrogenase abolishes allosteric inhibition by L-threonine.

Wild-type C. glutamicum Hom is inhibited by threonine; mutant deregulation is a distinct phenotype.

L-Threonine inhibits the wild-type (wt) enzyme with a Ki of 0.16 mM.

Hom family membership, corynebacterial operon genetics and biochemical homoserine-dehydrogenase evidence agree on this activity. PMID:4394351 is B. flavum No. 2247 and provides comparative NADPH chemistry; PMID:1743520 directly establishes a C. glutamicum wild-type Hom activity and its feedback regulation without identifying ATCC 13032 in the abstract. The two experimental rows are retained on the synthesized function, with those strain and access limits made explicit.

Part 4: homoserine phosphorylation

homoserine phosphorylationReactioncorgl_thrb

Annotons

CORGL thrB: homoserine kinase activity

corgl_thrb_thrb

Participant: Gene Product: thrB (CORGL)

Gene Product:

thrB (CORGL)UniProtKB:P07128

Family:

Classification of CORGL thrBPANTHER:PTHR20861:SF1

Representative Members: thrB (CORGL)UniProtKB:P07128

Taxon:

Corynebacterium glutamicum ATCC 13032NCBITaxon:196627

Function

homoserine kinase activityGO:0004413

Substrates: L-homoserine ATP

Products: O-phospho-L-homoserine ADP

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

PMID:30023797

Reduction of Feedback Inhibition in Homoserine Kinase (ThrB) of Corynebacterium glutamicum Enhances l-Threonine Biosynthesis.

Recombinant wild-type ThrB uses homoserine and ATP.

The concentration of ADP (Y axis) was determined after incubating each enzyme with l-homoserine and ATP at 27 °C for 30 min.

PMID:30023797

Reduction of Feedback Inhibition in Homoserine Kinase (ThrB) of Corynebacterium glutamicum Enhances l-Threonine Biosynthesis.

The cloned template is native ATCC13032 genomic DNA.

were amplified by PCR using ThrBFor and ThrBRev primers (Table 2) and the C. glutamicum ATCC 13032 genomic DNA as a template.

Purified recombinant wild-type protein cloned from ATCC13032 produces ADP from ATP in the presence of homoserine; kinetic analysis and structure distinguish its activity from the engineered A20 variants.

Part 5: terminal threonine formation

terminal threonine formationReactioncorgl_thrc

Annotons

CORGL thrC: threonine synthase activity

corgl_thrc_thrc

Participant: Gene Product: thrC (CORGL)

Gene Product:

thrC (CORGL)UniProtKB:P23669

Family:

Classification of CORGL thrCPANTHER:PTHR42690:SF1

Representative Members: thrC (CORGL)UniProtKB:P23669

Taxon:

Corynebacterium glutamicum ATCC 13032NCBITaxon:196627

Function

threonine synthase activityGO:0004795

Substrates: O-phospho-L-homoserine water

Products: L-threonine phosphate

Cofactors: pyridoxal 5'-phosphate

A reaction in the represented native route. Shared upstream activity is not exclusive commitment to threonine.

PMID:8074505

Analysis and expression of the thrC gene of Brevibacterium lactofermentum and characterization of the encoded threonine synthase.

Purified B.lactofermentum enzyme directly converts phosphohomoserine to threonine with PLP.

The purified enzyme required pyridoxal phosphate as its only cofactor to convert homoserine phosphate into threonine.

PMID:2127631

The molecular structure of the Corynebacterium glutamicum threonine synthase gene.

C. glutamicum thrC was mapped using complementation.

file:CORGL/thrC/thrC-uniprot.txt

UniProtKB thrC reviewed record (P23669)

Specific ThrC family membership supports the target reaction.

DR NCBIfam; TIGR00260; thrC; 1.

The target has the specific ThrC family signature. C. glutamicum thrC complementation and purified B. lactofermentum enzyme chemistry corroborate the reaction; the latter experiment is explicitly comparative strain evidence rather than a purified ATCC13032 assay.