NCGR_LOCUS29329

UniProt ID: A0A811PKG6
Organism: Miscanthus lutarioriparius
Review Status: DRAFT
📝 Provide Detailed Feedback

Gene Description

Bifunctional aspartate kinase / homoserine dehydrogenase (AK-HSD) that catalyzes the first and third steps in the aspartate-derived amino acid biosynthetic pathway, leading to the production of lysine (via DAP pathway), threonine, and methionine from L-aspartate. The N-terminal domain has aspartate kinase activity (EC 2.7.2.4) and the C-terminal domain has homoserine dehydrogenase activity (EC 1.1.1.3). Contains two ACT regulatory domains for allosteric feedback inhibition by threonine. Localized to the chloroplast where the aspartate pathway operates in plants. Unreviewed TrEMBL entry from whole genome shotgun data.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004072 aspartate kinase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Aspartate kinase activity is the core N-terminal enzymatic function of this bifunctional AK-HSD enzyme. The protein contains a well-defined AA_kinase domain (Pfam PF00696), aspartate kinase signature (PROSITE PS00324), and specific CDD domain cd04257 (AAK_AK-HSDH). Multiple InterPro signatures (IPR001341, IPR018042) confirm the aspartate kinase classification. EC 2.7.2.4 is the correct enzyme commission number for this activity.
Reason: Strong domain evidence from multiple databases (InterPro, PROSITE, CDD, Pfam) consistently supports aspartate kinase activity. This is a core catalytic function of the bifunctional enzyme, catalyzing L-aspartate + ATP -> 4-phospho-L-aspartate + ADP.
Supporting Evidence:
UniProt:A0A811PKG6
Belongs to the aspartokinase family (N-terminal section)
PMID:8507831
the isolated carrot cDNA appears to encode a bifunctional aspartokinase-homoserine dehydrogenase enzyme
GO:0004412 homoserine dehydrogenase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Homoserine dehydrogenase activity is the core C-terminal enzymatic function. The protein contains a Homoserine_dh domain (Pfam PF00742), HSD catalytic site (PROSITE PS01042), NAD-binding domain (PF03447), and the bifunctional-specific InterPro signature IPR011147. PANTHER subfamily PTHR43070:SF5 specifically classifies this as homoserine dehydrogenase. EC 1.1.1.3 is correct.
Reason: Strong domain evidence from multiple databases. This is the second core catalytic function of the bifunctional enzyme, catalyzing L-aspartate 4-semialdehyde + NAD(P)H -> L-homoserine + NAD(P)+. The reaction is the third step in the aspartate pathway.
Supporting Evidence:
UniProt:A0A811PKG6
Belongs to the homoserine dehydrogenase family (C-terminal section)
PMID:8507831
the isolated carrot cDNA appears to encode a bifunctional aspartokinase-homoserine dehydrogenase enzyme
GO:0016491 oxidoreductase activity
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Oxidoreductase activity is a parent term of homoserine dehydrogenase activity (GO:0004412). While technically correct, it is redundant with the more specific GO:0004412 annotation already present.
Reason: This is a true but overly general annotation. The more specific GO:0004412 (homoserine dehydrogenase activity) already captures this function precisely. Annotating both the parent and child term is redundant.
GO:0050661 NADP binding
IEA
GO_REF:0000002 		ACCEPT
Summary: The homoserine dehydrogenase domain uses NAD(P)+ as cofactor. The protein contains a NAD-binding Rossmann-fold domain (Pfam PF03447, InterPro IPR005106). The enzyme can use both NAD+ and NADP+ as cofactors based on the UniProt catalytic activity annotations.
Reason: NADP binding is supported by the NAD(P)-binding Rossmann-fold domain and is functionally relevant to the homoserine dehydrogenase activity. The enzyme uses NADP+ as an alternative cofactor to NAD+.
Supporting Evidence:
UniProt:A0A811PKG6
L-homoserine + NADP(+) = L-aspartate 4-semialdehyde + NADPH + H(+)
GO:0006520 amino acid metabolic process
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Amino acid metabolic process is a high-level parent of the more specific biosynthetic process annotations already present (GO:0009067, GO:0009088, GO:0009090). While technically correct, it adds no additional information.
Reason: Redundant with the more specific biological process annotations. The protein is specifically involved in aspartate family amino acid biosynthesis (GO:0009067), threonine biosynthesis (GO:0009088), and homoserine biosynthesis (GO:0009090), all of which are children of this term.
GO:0006531 aspartate metabolic process
IEA
GO_REF:0000117 		ACCEPT
Summary: The aspartate kinase domain directly uses L-aspartate as substrate, phosphorylating it to 4-phospho-L-aspartate. This is the committed first step in aspartate-derived amino acid biosynthesis.
Reason: Correct and informative. The enzyme directly metabolizes aspartate via the aspartate kinase reaction. While the downstream pathway annotations (GO:0009067 etc.) are more specific about the biosynthetic outcome, this term correctly captures the substrate utilization aspect.
Supporting Evidence:
UniProt:A0A811PKG6
L-aspartate + ATP = 4-phospho-L-aspartate + ADP
GO:0008652 amino acid biosynthetic process
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Amino acid biosynthetic process is a parent term of the more specific aspartate family amino acid biosynthetic process (GO:0009067) already annotated.
Reason: Redundant with GO:0009067 (aspartate family amino acid biosynthetic process), which is a more specific child term that better captures the function.
GO:0009067 aspartate family amino acid biosynthetic process
IEA
GO_REF:0000118 		ACCEPT
Summary: This term encompasses the biosynthesis of aspartate-derived amino acids (lysine, methionine, threonine, asparagine). As a bifunctional AK-HSD, this enzyme catalyzes the first step common to all branches and the third step in the threonine/methionine branch.
Reason: This is the most appropriate level of specificity for the overall pathway role. The enzyme acts at the branch point of multiple amino acid biosynthetic pathways derived from aspartate. TreeGrafter classification via PANTHER:PTN009166675 supports this annotation.
Supporting Evidence:
PMID:8507831
Aspartokinase (EC 2.7.2.4) and homoserine dehydrogenase (EC 1.1.1.3) catalyze steps in the pathway for the synthesis of lysine, threonine, and methionine from aspartate
GO:0009088 threonine biosynthetic process
IEA
GO_REF:0000041 		ACCEPT
Summary: The enzyme catalyzes steps 1 and 3 of the 5-step threonine biosynthetic pathway from L-aspartate. Step 1 (AK) phosphorylates aspartate, and step 3 (HSD) reduces aspartate semialdehyde to homoserine, which is then converted to threonine. The ACT domains provide threonine-mediated feedback inhibition, indicating a direct regulatory link to threonine levels.
Reason: Directly supported by UniPathway annotations (UPA00050) and the enzyme's dual catalytic activities. Threonine feedback inhibition of the ACT domains further confirms the enzyme's role in threonine biosynthesis.
Supporting Evidence:
UniProt:A0A811PKG6
L-threonine biosynthesis; L-threonine from L-aspartate: step 1/5 and step 3/5
GO:0009090 L-homoserine biosynthetic process
IEA
GO_REF:0000118 		ACCEPT
Summary: The homoserine dehydrogenase domain directly produces L-homoserine from L-aspartate 4-semialdehyde. This is the most direct product of the HSD enzymatic activity.
Reason: Directly catalyzed by the HSD domain. L-homoserine is the direct product of the enzyme's C-terminal catalytic activity and serves as a precursor for both threonine and methionine biosynthesis. TreeGrafter classification supports this annotation.
Supporting Evidence:
UniProt:A0A811PKG6
L-methionine biosynthesis via de novo pathway; L-homoserine from L-aspartate: step 3/3
GO:0009507 chloroplast
IEA
GO_REF:0000044 		ACCEPT
Summary: Chloroplast localization is expected for plant AK-HSD enzymes. The aspartate-derived amino acid biosynthetic pathway operates in the chloroplast/plastid in plants. The protein has a predicted N-terminal transit peptide consistent with chloroplast targeting.
Reason: Consistent with known biology of plant aspartate pathway enzymes. All steps of the pathway except the final methylation of homocysteine to methionine occur in the chloroplast. The UniProt subcellular location annotation supports this.
Supporting Evidence:
UniProt:A0A811PKG6
SUBCELLULAR LOCATION: Plastid, chloroplast

Core Functions

Catalyzes the phosphorylation of L-aspartate to 4-phospho-L-aspartate (aspartate kinase activity, EC 2.7.2.4), the first committed step in aspartate-derived amino acid biosynthesis

Molecular Function:
aspartate kinase activity
Directly Involved In:
aspartate family amino acid biosynthetic process
Cellular Locations:
chloroplast

Catalyzes the reduction of L-aspartate 4-semialdehyde to L-homoserine (homoserine dehydrogenase activity, EC 1.1.1.3), the third step in the threonine/methionine branch of the aspartate pathway

Molecular Function:
homoserine dehydrogenase activity
Directly Involved In:
L-homoserine biosynthetic process
Cellular Locations:
chloroplast

References

UniProt:A0A811PKG6
UniProt entry for NCGR_LOCUS29329
PMID:33911077
Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome
PMID:8507831
Identification and expression of a cDNA from Daucus carota encoding a bifunctional aspartokinase-homoserine dehydrogenase
file:9POAL/NCGR_LOCUS29329/NCGR_LOCUS29329-notes.md
Notes file for NCGR_LOCUS29329
file:9POAL/NCGR_LOCUS29329/NCGR_LOCUS29329-deep-research-falcon.md
Deep research for NCGR_LOCUS29329 (Falcon)
GO_REF:0000120
Phylogenomic-based GO annotation by ARBA and InterPro
GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms
GO_REF:0000117
Automatic Gene Ontology annotation by ARBA
GO_REF:0000118
TreeGrafter annotation based on PANTHER
GO_REF:0000041
UniPathway-based Gene Ontology annotation
GO_REF:0000044
UniProtKB-SubCell based Gene Ontology annotation

Deep Research

Falcon

(NCGR_LOCUS29329-deep-research-falcon.md)
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 41 citations 2026-04-22T23:06:33.808331

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: Functional annotation of Miscanthus lutarioriparius NCGR_LOCUS29329 (UniProt A0A811PKG6) — ACT domain-containing, aspartokinase-family protein

0) Target verification and evidence scope

The target protein identity is constrained to the UniProt entry A0A811PKG6 from Miscanthus lutarioriparius, annotated as an ACT domain-containing protein with signatures consistent with the aspartokinase (AK) / amino-acid kinase superfamily and multiple ACT regulatory domains. Within the retrieved literature corpus, there were no direct mentions of the locus name NCGR_LOCUS29329 or the UniProt accession A0A811PKG6, so the functional annotation below relies on (i) conserved domain/family inference and (ii) experimentally validated plant AK/ACT-domain literature (mainly Arabidopsis) plus recent (2023–2024) work on ACT-domain metabolite sensing. The report therefore distinguishes direct experimental evidence (other species) vs inference for Miscanthus. (jander2009aspartatederivedaminoacid pages 3-4, miao2021chromosomescaleassemblyand pages 10-11)

1) Key concepts and definitions (current understanding)

1.1 Aspartate kinase (AK) and the aspartate-derived amino-acid pathway

In plants, aspartate kinase (AK; EC 2.7.2.4) catalyzes the first committed step of the aspartate-derived pathway that produces essential amino acids including lysine (Lys), threonine (Thr), methionine (Met), and isoleucine (Ile). (jander2009aspartatederivedaminoacid pages 3-4, jander2009aspartatederivedaminoacid pages 1-3, jander2010recentprogressin pages 1-2)

The pathway begins with AK-mediated activation of L-aspartate using ATP, producing aspartyl phosphate (Asp-4-P) (or equivalently “Asp-4-P” as an activated intermediate), which is subsequently converted to aspartate semialdehyde and then split into branches leading to Lys vs homoserine-derived products (Met/Thr/Ile). (clark2015analysisoflossoffunction pages 1-2, jander2009aspartatederivedaminoacid pages 3-4)

1.2 Monofunctional AK vs bifunctional AK–HSDH

Plant genomes typically encode multiple AK-related enzymes, including:
- Monofunctional AKs, which carry a catalytic kinase domain plus C-terminal regulatory segments, and
- Bifunctional AK–homoserine dehydrogenases (AK–HSDHs), fusion proteins that perform both kinase and dehydrogenase steps in the branch that supplies homoserine-derived amino acids. (jander2009aspartatederivedaminoacid pages 3-4, clark2015analysisoflossoffunction pages 1-2)

In Arabidopsis, genetic/biochemical work supports that distinct isoforms make major contributions to overall AK/HSDH activity and influence the balance of end products (Lys vs Met/Thr/Ile). (clark2015analysisoflossoffunction pages 1-2)

1.3 ACT domains as metabolite-sensing regulatory modules

ACT domains are small regulatory modules (named from aspartate kinase–chorismate mutase–TyrA) that bind small ligands (often amino acids) and mediate allosteric regulation and/or oligomerization of metabolic enzymes. (masdroux2006anovelorganization pages 1-2, scholtysek2024theactivationof pages 17-18)

A strong, plant-specific structural example is Arabidopsis AK1, whose regulatory region comprises two ACT subdomains (ACT1/ACT2). In the AK1 crystal structure, ACT1 binds the allosteric effectors lysine and S-adenosylmethionine (SAM). (masdroux2006anovelorganization pages 2-4, masdroux2006anovelorganization pages 1-2)

2) Gene/protein functional annotation for NCGR_LOCUS29329 (A0A811PKG6)

2.1 Most likely molecular function (primary function)

Given the UniProt-provided domain architecture (aspartokinase-family membership plus ACT regulatory domains) and the well-established biochemical role of plant AKs, NCGR_LOCUS29329 is most plausibly an aspartate kinase-like enzyme that catalyzes ATP-dependent phosphorylation of L-aspartate at the pathway entry point. (jander2009aspartatederivedaminoacid pages 3-4, clark2015analysisoflossoffunction pages 1-2, masdroux2006anovelorganization pages 9-10)

Reaction (family-supported): Aspartate + ATP → Aspartyl-phosphate (Asp-4-P) + ADP. (clark2015analysisoflossoffunction pages 1-2)

Substrate specificity (inferred): primary substrates L-aspartate and ATP, as supported by active-site modeling of plant AK1 where Asp and ATP are positioned for catalysis. (masdroux2006anovelorganization pages 9-10)

2.2 Biological process / pathway roles

NCGR_LOCUS29329 is best placed in the aspartate-derived amino-acid biosynthesis network, controlling entry and flux toward Lys, Thr, Met, and Ile. (jander2009aspartatederivedaminoacid pages 3-4, jander2010recentprogressin pages 1-2)

Arabidopsis mutant analyses highlight that the relative activities of AK isoforms and AK–HSDH isoforms can shift pathway output, consistent with AK functioning as a major control node. (clark2015analysisoflossoffunction pages 1-2)

2.3 Expected regulation by end-product feedback inhibition

A defining functional feature of AK-family enzymes in plants is feedback inhibition by pathway end products mediated by ACT domains:

  • Lysine feedback inhibition (monofunctional AKs): Plant monofunctional AKs are typically lysine-inhibited and use C-terminal ACT domains as regulatory modules. (jander2009aspartatederivedaminoacid pages 3-4, clark2015analysisoflossoffunction pages 1-2, jander2010recentprogressin pages 1-2)
  • Synergistic inhibition by Lys + SAM (AK1 example): In Arabidopsis AK1, lysine and SAM bind in the ACT1 region and explain synergistic inhibition, with structural evidence that inhibitor binding propagates conformational effects toward the catalytic site (including reduced apparent ATP affinity). (masdroux2006anovelorganization pages 1-2, masdroux2006anovelorganization pages 10-11)
  • Threonine feedback inhibition (AK–HSDH family): In plant bifunctional AK–HSDH proteins, threonine binds regulatory sites (ACT-like modules) and can inhibit the kinase activity and promote inhibition of the HSDH activity; Arabidopsis work identified two non-equivalent Thr-binding sites as a mechanistic basis. (jander2009aspartatederivedaminoacid pages 3-4, clark2015analysisoflossoffunction pages 1-2)

For NCGR_LOCUS29329 specifically, the exact effector profile (Lys, Thr, SAM, others) is not experimentally established in the retrieved literature, so regulation remains a family-based inference strongly supported by plant homologs. (jander2009aspartatederivedaminoacid pages 3-4, masdroux2006anovelorganization pages 1-2, clark2015analysisoflossoffunction pages 1-2)

3) Structural evidence supporting ACT-mediated regulation (authoritative primary literature)

Mas-Droux et al. solved the crystal structure of Arabidopsis AK1 in complex with Lys and SAM, showing:
- AK1 is dimeric and composed of an N-terminal catalytic domain and a C-terminal regulatory region with ACT1 and ACT2. (masdroux2006anovelorganization pages 2-4, masdroux2006anovelorganization media 2307c2ed)
- ACT1 forms the primary effector-binding site; Lys and SAM are located at the regulatory interface and connected to catalytic elements, providing a structural rationale for allostery. (masdroux2006anovelorganization pages 2-4, masdroux2006anovelorganization pages 10-11, masdroux2006anovelorganization media f2c610d3)
- Key quantitative structural statistics include 2.85 Å resolution and reported refinement metrics (R/Rfree). (masdroux2006anovelorganization pages 2-4)

These experimentally validated principles directly support annotating the ACT domains of A0A811PKG6 as allosteric regulatory modules, not merely “domains of unknown function.” (masdroux2006anovelorganization pages 1-2, masdroux2006anovelorganization pages 2-4)

4) Subcellular localization: what is known vs inferred

No direct subcellular localization data were found for the Miscanthus protein NCGR_LOCUS29329 in the retrieved sources.

However, evidence from the broader aspartate-derived network supports plastid/chloroplast compartmentation for key steps: for example, homoserine kinase (HSK) (a downstream enzyme in Met/Thr synthesis) has been localized to chloroplasts in pea and contains a chloroplast targeting sequence in Arabidopsis; experimental targeting of bacterial HSK to chloroplast vs cytosol in potato produced distinct regulatory outcomes. (rinder2008regulationofaspartatederived pages 1-2)

Therefore, a plastid/chloroplast localization is plausible for NCGR_LOCUS29329 (consistent with many amino-acid biosynthetic enzymes), but this remains unproven without localization experiments or a clear transit-peptide annotation for A0A811PKG6 in the provided evidence set. (rinder2008regulationofaspartatederived pages 1-2)

5) Recent developments (prioritizing 2023–2024)

5.1 2023: Structure-guided and computational engineering of feedback-resistant enzymes

Naz et al. (2023) reviewed how end-product feedback inhibition in amino-acid biosynthesis is increasingly addressed using structure-based analysis and computational + experimental mutagenesis to create feedback-resistant variants. The review explicitly includes aspartokinase (AK) among relevant targets and emphasizes strategies such as mutating ligand-binding pockets and allosteric interfaces, supported by tools like computational saturation mutagenesis and normal mode analysis approaches. (naz2023insightintoderegulation pages 22-23, naz2023insightintoderegulation pages 23-24)

Although largely microbial/industrial in emphasis, these concepts are directly relevant to plant AK/ACT systems because they clarify how ACT-domain ligand binding can be altered rationally and how allosteric networks can be remodeled. (naz2023insightintoderegulation pages 15-19, naz2023insightintoderegulation pages 9-11)

Citation details: Naz et al., 2023-08 (Microbial Cell Factories). URL: https://doi.org/10.1186/s12934-023-02178-z (naz2023insightintoderegulation pages 22-23)

5.2 2024: ACT domains as amino-acid sensors in photosynthetic eukaryotes

Scholtysek et al. (2024) provide direct experimental evidence that an ACT domain can function as an amino-acid sensing module in a photosynthetic eukaryote enzyme (in Chlamydomonas reinhardtii). They showed:
- L-glutamine (Gln) specifically stimulates full-length α-amylase AMA2 but not an ACT-deleted variant, indicating ACT dependence. (scholtysek2024theactivationof pages 10-11, scholtysek2024theactivationof pages 15-17)
- Quantitative ligand-response: EC50 ≈ 2.1 ± 0.7 mM for Gln-dependent activation. (scholtysek2024theactivationof pages 17-18)
- Targeted point mutations within the ACT domain can greatly alter responsiveness (e.g., variants with reduced or strongly enhanced activation), consistent with a discrete ligand-binding/regulatory site. (scholtysek2024theactivationof pages 14-15, scholtysek2024theactivationof pages 17-18)

This is not an aspartate kinase study, but it reinforces a modern interpretation of ACT domains as generalizable metabolite sensors that can coordinate major metabolic programs (here, nitrogen status via glutamine with carbon/starch metabolism). These findings strengthen confidence that the ACT domains in A0A811PKG6 could serve similar ligand-sensing roles. (scholtysek2024theactivationof pages 1-2, scholtysek2024theactivationof pages 19-20)

Citation details: Scholtysek et al., 2024-06 (Plant Direct). URL: https://doi.org/10.1002/pld3.609 (scholtysek2024theactivationof pages 1-2)

6) Current applications and real-world implementations

6.1 Industrial biotechnology: amino-acid overproduction by deregulating feedback inhibition

A major real-world application of understanding AK/ACT regulation is industrial amino-acid production (e.g., lysine, threonine), where feedback inhibition is relieved by engineering enzyme variants and regulatory circuits. Naz et al. (2023) synthesizes these approaches and highlights the importance of structural methods for identifying mutational targets that reduce inhibitor binding while maintaining activity. (naz2023insightintoderegulation pages 25-25, naz2023insightintoderegulation pages 22-23)

6.2 Plant/crop metabolic engineering: improving essential amino-acid content

Plant reviews emphasize that the aspartate-derived pathway has long been a target for improving nutritional quality because Lys and Met are often limiting in crops, and pathway understanding supports breeding/transgenic strategies. (jander2010recentprogressin pages 1-2)

For Miscanthus lutarioriparius, a bioenergy crop, the most relevant available resource in the retrieved corpus is a chromosome-scale genome assembly and annotation paper, which provides the genomic foundation for future gene-family analyses and engineering but does not connect directly to NCGR_LOCUS29329 in the accessible text. (miao2021chromosomescaleassemblyand pages 2-4)

7) Relevant statistics and quantitative data from studies

  • Structural resolution and model statistics (plant AK1): AK1 structure solved at 2.85 Å with reported refinement metrics; AK1 is a dimer in the crystal, with ACT1/ACT2 regulatory architecture. (masdroux2006anovelorganization pages 2-4, masdroux2006anovelorganization pages 1-2)
  • Isoform-dependent lysine sensitivity (Arabidopsis AKs): Reported Lys sensitivity differs drastically among AK isoforms (e.g., AK1 much less sensitive than AK2/AK3). (masdroux2006anovelorganization pages 9-10)
  • Glutamine sensing by ACT domain (2024): Gln activation EC50 2.1 ± 0.7 mM for ACT-mediated regulation in Chlamydomonas AMA2. (scholtysek2024theactivationof pages 17-18)
  • Miscanthus genome annotation scale: 68,328 predicted gene models; BUSCO completeness 98.2%; functional annotation rates via InterProScan/eggNOG/KEGG/GO reported, supporting robust genome-wide annotation context (but not mapping NCGR_LOCUS29329). (miao2021chromosomescaleassemblyand pages 2-4)

8) Expert interpretation (evidence-weighted)

Taken together, the strongest evidence-supported annotation for NCGR_LOCUS29329 (A0A811PKG6) is:
1. Primary biochemical role: an aspartate kinase-family enzyme catalyzing the ATP-dependent activation/phosphorylation of aspartate at the entry to the aspartate-derived amino-acid pathway. (jander2009aspartatederivedaminoacid pages 3-4, clark2015analysisoflossoffunction pages 1-2)
2. Regulatory logic: likely feedback-controlled by amino-acid effectors via ACT domains, consistent with plant AK and AK–HSDH paradigms (Lys; Lys+SAM synergy; Thr regulation in AK–HSDH). (masdroux2006anovelorganization pages 1-2, masdroux2006anovelorganization pages 10-11, jander2010recentprogressin pages 1-2)
3. Cellular compartment: most defensibly described as unknown for this protein with a hypothesis of plastid/chloroplast involvement based on pathway compartmentation evidence in related steps; confirmation requires direct targeting predictions or experimental localization. (rinder2008regulationofaspartatederived pages 1-2)

9) Summary table for annotation

Aspect Inferred/Supported conclusion Best supporting evidence (with paper titles, year, URL, and cite IDs)
identity/domains NCGR_LOCUS29329 is ambiguous or literature is limited for this specific protein. Based on UniProt A0A811PKG6 in Miscanthus lutarioriparius, the protein is best annotated as an ACT-domain-containing, aspartokinase-family protein with an N-terminal AceGlu_kinase-like / AK-HSDH_N catalytic region and C-terminal ACT regulatory domains; this architecture matches plant aspartate-kinase regulators rather than an unrelated protein family. Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome (2021), https://doi.org/10.1038/s41467-021-22738-4 — useful for species/gene-model context but does not map NCGR_LOCUS29329 directly (miao2021chromosomescaleassemblyand pages 10-11, miao2021chromosomescaleassemblyand pages 2-4). A Novel Organization of ACT Domains in Allosteric Enzymes Revealed by the Crystal Structure of Arabidopsis Aspartate Kinase (2006), https://doi.org/10.1105/tpc.105.040451 — establishes plant AK catalytic + ACT-domain architecture (masdroux2006anovelorganization pages 2-4, masdroux2006anovelorganization pages 1-2).
catalytic reaction Most likely catalyzes the ATP-dependent phosphorylation of L-aspartate as the first committed step of the aspartate-family amino-acid pathway (Asp + ATP → 4-aspartyl-phosphate + ADP); active-site modeling in plant AK1 places Asp and ATP in the catalytic site. Substrate specificity is therefore inferred to center on L-aspartate and ATP, not transport or signaling substrates. Aspartate-derived amino acid biosynthesis in Arabidopsis thaliana (2009), https://doi.org/10.1199/tab.0121 — AK is EC 2.7.2.4 and catalyzes the first pathway step (jander2009aspartatederivedaminoacid pages 3-4, jander2009aspartatederivedaminoacid pages 1-3). A Novel Organization of ACT Domains... (2006), https://doi.org/10.1105/tpc.105.040451 — structural modeling places Asp and ATP in the active site (masdroux2006anovelorganization pages 9-10). Analysis of loss-of-function mutants in aspartate kinase and homoserine dehydrogenase genes... (2015), https://doi.org/10.1104/pp.15.00364 — AK activates Asp to Asp-4-P (clark2015analysisoflossoffunction pages 1-2).
pathway role Functions at the entry point to the aspartate-derived amino-acid network, controlling flux toward lysine, threonine, methionine, and isoleucine. In plants, the AK/AK-HSDH node is a major branchpoint that helps determine relative output of the lysine branch versus the homoserine/Thr/Met/Ile branch. Aspartate-derived amino acid biosynthesis in Arabidopsis thaliana (2009), https://doi.org/10.1199/tab.0121 — pathway overview and branch logic (jander2009aspartatederivedaminoacid pages 3-4, jander2009aspartatederivedaminoacid pages 1-3). Recent progress in deciphering the biosynthesis of aspartate-derived amino acids in plants (2010), https://doi.org/10.1093/mp/ssp104 — emphasizes AK as the committing enzyme for Met/Thr/Ile/Lys synthesis (jander2010recentprogressin pages 1-2). Analysis of loss-of-function mutants... (2015), https://doi.org/10.1104/pp.15.00364 — AK:HSDH activity ratio influences Lys:(Met+Thr+Ile) balance (clark2015analysisoflossoffunction pages 1-2).
allosteric regulation Best family-based inference: the protein is likely feedback regulated by amino-acid end products through ACT domains. Plant monofunctional AKs are typically lysine-sensitive; in Arabidopsis AK1, lysine + SAM act synergistically. In bifunctional AK-HSDH proteins, threonine binds ACT sites and can inhibit AK and HSDH activities. The exact effector set for NCGR_LOCUS29329 is untested. A Novel Organization of ACT Domains... (2006), https://doi.org/10.1105/tpc.105.040451 — Lys and SAM bind AK1 regulatory ACT1 and explain synergistic inhibition (masdroux2006anovelorganization pages 2-4, masdroux2006anovelorganization pages 1-2, masdroux2006anovelorganization pages 10-11, masdroux2006anovelorganization pages 9-10). Mechanism of Control of Arabidopsis thaliana Aspartate Kinase-Homoserine Dehydrogenase by Threonine (2003), https://doi.org/10.1074/jbc.m207379200 — two non-equivalent Thr-binding sites mediate inhibition (jander2009aspartatederivedaminoacid pages 3-4). Recent progress... (2010), https://doi.org/10.1093/mp/ssp104 — summarizes lysine, SAM, threonine, and leucine feedback control in plant isozymes (jander2010recentprogressin pages 1-2).
ACT-domain structural evidence Strong structural support exists for assigning a metabolite-sensing regulatory function to the ACT region. In Arabidopsis AK1, the protein is a dimer with an N-terminal catalytic domain plus two ACT subdomains (ACT1/ACT2); ACT1 forms the lysine/SAM effector-binding site at the dimer interface. This is highly consistent with the UniProt domain composition of A0A811PKG6. A Novel Organization of ACT Domains... (2006), https://doi.org/10.1105/tpc.105.040451 — crystal structure solved at 2.85 Å; one dimer per asymmetric unit; ACT1 binds Lys and SAM; figures show catalytic domain + ACT1/ACT2 organization (masdroux2006anovelorganization pages 2-4, masdroux2006anovelorganization pages 1-2, masdroux2006anovelorganization media 2307c2ed, masdroux2006anovelorganization media f2c610d3, masdroux2006anovelorganization media dc47af90). The activation of Chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its N-terminal ACT domain (2024), https://doi.org/10.1002/pld3.609 — recent evidence that ACT domains in photosynthetic eukaryotes act as amino-acid sensors fused to enzymes (scholtysek2024theactivationof pages 10-11, scholtysek2024theactivationof pages 1-2, scholtysek2024theactivationof pages 17-18, scholtysek2024theactivationof pages 15-17).
localization/compartment Direct localization of NCGR_LOCUS29329 is not available in retrieved sources. For plant aspartate-family biosynthesis, the pathway is widely associated with plastid/chloroplast-localized steps, and related enzymes such as homoserine kinase carry chloroplast targeting sequences in plants. Thus, a plastid/chloroplast localization is plausible but not proven for this Miscanthus protein. Regulation of aspartate-derived amino acid homeostasis in potato plants... (2008), https://doi.org/10.1007/s00726-007-0504-5 — HSK is chloroplast-localized and compartmentation affects pathway regulation (rinder2008regulationofaspartatederived pages 1-2). Aspartate-derived amino acid biosynthesis in Arabidopsis thaliana (2009), https://doi.org/10.1199/tab.0121 — supports compartmentation of downstream pathway enzymes, though not AK directly in the retrieved excerpt (jander2009aspartatederivedaminoacid pages 10-11).
real-world applications Family-level knowledge of AK/ACT regulation is already used in metabolic engineering to create feedback-resistant enzymes for overproduction of amino acids (especially L-lysine, L-threonine, L-arginine) in industrial microbes. In crops, manipulating the aspartate pathway has been pursued to improve essential amino-acid content and seed nutritional quality; Miscanthus-specific application remains unreported for this locus. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method (2023), https://doi.org/10.1186/s12934-023-02178-z — reviews structure-guided mutagenesis and computational design of deregulated AK-family enzymes for industrial amino-acid production (naz2023insightintoderegulation pages 25-25, naz2023insightintoderegulation pages 15-19, naz2023insightintoderegulation pages 22-23, naz2023insightintoderegulation pages 23-24). Recent progress in deciphering the biosynthesis of aspartate-derived amino acids in plants (2010), https://doi.org/10.1093/mp/ssp104 — explains agricultural interest in engineering amino-acid content (jander2010recentprogressin pages 1-2).
key quantitative data Representative quantitative evidence for the family: AK1 crystal structure 2.85 Å, R = 20.2%, Rfree = 24.4%; AK1 is mainly dimeric (~120 kD) with tetramer equilibrium. Isoform Lys sensitivity differs strongly in Arabidopsis: reported K0.5 for Lys ~570 mM for AK1, versus ~10 mM for AK2 and ~7 mM for AK3. Recent ACT-domain work in algae found glutamine EC50 = 2.1 ± 0.7 mM for ACT-mediated activation and ~2.8-fold higher basal activity after ACT-domain deletion in AMA2. A Novel Organization of ACT Domains... (2006), https://doi.org/10.1105/tpc.105.040451 — structural statistics, oligomeric state, and Lys-sensitivity values (masdroux2006anovelorganization pages 2-4, masdroux2006anovelorganization pages 1-2, masdroux2006anovelorganization pages 10-11, masdroux2006anovelorganization pages 9-10). The activation of Chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its N-terminal ACT domain (2024), https://doi.org/10.1002/pld3.609 — ACT-mediated Gln sensing with EC50 2.1 ± 0.7 mM and deletion effects on basal activity (scholtysek2024theactivationof pages 10-11, scholtysek2024theactivationof pages 14-15, scholtysek2024theactivationof pages 17-18).

Table: This table summarizes the best-supported functional annotation for Miscanthus lutarioriparius NCGR_LOCUS29329 / UniProt A0A811PKG6, explicitly separating direct evidence from family-based inference. It is useful because locus-specific literature is lacking, so the annotation must rely on validated plant aspartate-kinase and ACT-domain evidence.

10) Visual evidence (ACT-domain architecture and effector binding)

Cropped figure panels from the AK1 structural study illustrate the catalytic + ACT-domain organization and the effector-binding site at the ACT1 dimer interface. (masdroux2006anovelorganization media 2307c2ed, masdroux2006anovelorganization media f2c610d3, masdroux2006anovelorganization media dc47af90)

References

  1. (jander2009aspartatederivedaminoacid pages 3-4): Georg Jander and Vijay Joshi. Aspartate-derived amino acid biosynthesis in arabidopsis thaliana. The arabidopsis book, 7:e0121, Jun 2009. URL: https://doi.org/10.1199/tab.0121, doi:10.1199/tab.0121. This article has 114 citations and is from a peer-reviewed journal.

  2. (miao2021chromosomescaleassemblyand pages 10-11): Jiashun Miao, Qi Feng, Yan Li, Qiang Zhao, Congcong Zhou, Hengyun Lu, Danlin Fan, Juan Yan, Yiqi Lu, Qilin Tian, Wenjun Li, Qijun Weng, Lei S. Zhang, Yan Zhao, Tao Huang, Laigeng Li, Xuehui Huang, T. Sang, and B. Han. Chromosome-scale assembly and analysis of biomass crop miscanthus lutarioriparius genome. Nature Communications, Apr 2021. URL: https://doi.org/10.1038/s41467-021-22738-4, doi:10.1038/s41467-021-22738-4. This article has 51 citations and is from a highest quality peer-reviewed journal.

  3. (jander2009aspartatederivedaminoacid pages 1-3): Georg Jander and Vijay Joshi. Aspartate-derived amino acid biosynthesis in arabidopsis thaliana. The arabidopsis book, 7:e0121, Jun 2009. URL: https://doi.org/10.1199/tab.0121, doi:10.1199/tab.0121. This article has 114 citations and is from a peer-reviewed journal.

  4. (jander2010recentprogressin pages 1-2): Georg Jander and Vijay Joshi. Recent progress in deciphering the biosynthesis of aspartate-derived amino acids in plants. Molecular plant, 3 1:54-65, Jan 2010. URL: https://doi.org/10.1093/mp/ssp104, doi:10.1093/mp/ssp104. This article has 156 citations and is from a highest quality peer-reviewed journal.

  5. (clark2015analysisoflossoffunction pages 1-2): T. J. Clark and Yan Lu. Analysis of loss-of-function mutants in aspartate kinase and homoserine dehydrogenase genes points to complexity in the regulation of aspartate-derived amino acid contents1[open]. Plant Physiology, 168:1512-1526, Jun 2015. URL: https://doi.org/10.1104/pp.15.00364, doi:10.1104/pp.15.00364. This article has 33 citations and is from a highest quality peer-reviewed journal.

  6. (masdroux2006anovelorganization pages 1-2): Corine Mas-Droux, Gilles Curien, Mylène Robert-Genthon, Mathieu Laurencin, Jean-Luc Ferrer, and Renaud Dumas. A novel organization of act domains in allosteric enzymes revealed by the crystal structure of arabidopsis aspartate kinase. The Plant Cell, 18:1681-1692, May 2006. URL: https://doi.org/10.1105/tpc.105.040451, doi:10.1105/tpc.105.040451. This article has 74 citations.

  7. (scholtysek2024theactivationof pages 17-18): Lisa Scholtysek, Ansgar Poetsch, Eckhard Hofmann, and Anja Hemschemeier. The activation of chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its n‐terminal aspartate kinase–chorismate mutase–tyra (act) domain. Plant Direct, Jun 2024. URL: https://doi.org/10.1002/pld3.609, doi:10.1002/pld3.609. This article has 2 citations and is from a peer-reviewed journal.

  8. (masdroux2006anovelorganization pages 2-4): Corine Mas-Droux, Gilles Curien, Mylène Robert-Genthon, Mathieu Laurencin, Jean-Luc Ferrer, and Renaud Dumas. A novel organization of act domains in allosteric enzymes revealed by the crystal structure of arabidopsis aspartate kinase. The Plant Cell, 18:1681-1692, May 2006. URL: https://doi.org/10.1105/tpc.105.040451, doi:10.1105/tpc.105.040451. This article has 74 citations.

  9. (masdroux2006anovelorganization pages 9-10): Corine Mas-Droux, Gilles Curien, Mylène Robert-Genthon, Mathieu Laurencin, Jean-Luc Ferrer, and Renaud Dumas. A novel organization of act domains in allosteric enzymes revealed by the crystal structure of arabidopsis aspartate kinase. The Plant Cell, 18:1681-1692, May 2006. URL: https://doi.org/10.1105/tpc.105.040451, doi:10.1105/tpc.105.040451. This article has 74 citations.

  10. (masdroux2006anovelorganization pages 10-11): Corine Mas-Droux, Gilles Curien, Mylène Robert-Genthon, Mathieu Laurencin, Jean-Luc Ferrer, and Renaud Dumas. A novel organization of act domains in allosteric enzymes revealed by the crystal structure of arabidopsis aspartate kinase. The Plant Cell, 18:1681-1692, May 2006. URL: https://doi.org/10.1105/tpc.105.040451, doi:10.1105/tpc.105.040451. This article has 74 citations.

  11. (masdroux2006anovelorganization media 2307c2ed): Corine Mas-Droux, Gilles Curien, Mylène Robert-Genthon, Mathieu Laurencin, Jean-Luc Ferrer, and Renaud Dumas. A novel organization of act domains in allosteric enzymes revealed by the crystal structure of arabidopsis aspartate kinase. The Plant Cell, 18:1681-1692, May 2006. URL: https://doi.org/10.1105/tpc.105.040451, doi:10.1105/tpc.105.040451. This article has 74 citations.

  12. (masdroux2006anovelorganization media f2c610d3): Corine Mas-Droux, Gilles Curien, Mylène Robert-Genthon, Mathieu Laurencin, Jean-Luc Ferrer, and Renaud Dumas. A novel organization of act domains in allosteric enzymes revealed by the crystal structure of arabidopsis aspartate kinase. The Plant Cell, 18:1681-1692, May 2006. URL: https://doi.org/10.1105/tpc.105.040451, doi:10.1105/tpc.105.040451. This article has 74 citations.

  13. (rinder2008regulationofaspartatederived pages 1-2): J. Rinder, A. P. Casazza, R. Hoefgen, and H. Hesse. Regulation of aspartate-derived amino acid homeostasis in potato plants (solanum tuberosum l.) by expression of e. coli homoserine kinase. Amino Acids, 34:213-222, Feb 2008. URL: https://doi.org/10.1007/s00726-007-0504-5, doi:10.1007/s00726-007-0504-5. This article has 35 citations and is from a peer-reviewed journal.

  14. (naz2023insightintoderegulation pages 22-23): Sadia Naz, Pi Liu, Umar Farooq, and Hongwu Ma. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microbial Cell Factories, Aug 2023. URL: https://doi.org/10.1186/s12934-023-02178-z, doi:10.1186/s12934-023-02178-z. This article has 20 citations and is from a peer-reviewed journal.

  15. (naz2023insightintoderegulation pages 23-24): Sadia Naz, Pi Liu, Umar Farooq, and Hongwu Ma. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microbial Cell Factories, Aug 2023. URL: https://doi.org/10.1186/s12934-023-02178-z, doi:10.1186/s12934-023-02178-z. This article has 20 citations and is from a peer-reviewed journal.

  16. (naz2023insightintoderegulation pages 15-19): Sadia Naz, Pi Liu, Umar Farooq, and Hongwu Ma. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microbial Cell Factories, Aug 2023. URL: https://doi.org/10.1186/s12934-023-02178-z, doi:10.1186/s12934-023-02178-z. This article has 20 citations and is from a peer-reviewed journal.

  17. (naz2023insightintoderegulation pages 9-11): Sadia Naz, Pi Liu, Umar Farooq, and Hongwu Ma. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microbial Cell Factories, Aug 2023. URL: https://doi.org/10.1186/s12934-023-02178-z, doi:10.1186/s12934-023-02178-z. This article has 20 citations and is from a peer-reviewed journal.

  18. (scholtysek2024theactivationof pages 10-11): Lisa Scholtysek, Ansgar Poetsch, Eckhard Hofmann, and Anja Hemschemeier. The activation of chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its n‐terminal aspartate kinase–chorismate mutase–tyra (act) domain. Plant Direct, Jun 2024. URL: https://doi.org/10.1002/pld3.609, doi:10.1002/pld3.609. This article has 2 citations and is from a peer-reviewed journal.

  19. (scholtysek2024theactivationof pages 15-17): Lisa Scholtysek, Ansgar Poetsch, Eckhard Hofmann, and Anja Hemschemeier. The activation of chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its n‐terminal aspartate kinase–chorismate mutase–tyra (act) domain. Plant Direct, Jun 2024. URL: https://doi.org/10.1002/pld3.609, doi:10.1002/pld3.609. This article has 2 citations and is from a peer-reviewed journal.

  20. (scholtysek2024theactivationof pages 14-15): Lisa Scholtysek, Ansgar Poetsch, Eckhard Hofmann, and Anja Hemschemeier. The activation of chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its n‐terminal aspartate kinase–chorismate mutase–tyra (act) domain. Plant Direct, Jun 2024. URL: https://doi.org/10.1002/pld3.609, doi:10.1002/pld3.609. This article has 2 citations and is from a peer-reviewed journal.

  21. (scholtysek2024theactivationof pages 1-2): Lisa Scholtysek, Ansgar Poetsch, Eckhard Hofmann, and Anja Hemschemeier. The activation of chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its n‐terminal aspartate kinase–chorismate mutase–tyra (act) domain. Plant Direct, Jun 2024. URL: https://doi.org/10.1002/pld3.609, doi:10.1002/pld3.609. This article has 2 citations and is from a peer-reviewed journal.

  22. (scholtysek2024theactivationof pages 19-20): Lisa Scholtysek, Ansgar Poetsch, Eckhard Hofmann, and Anja Hemschemeier. The activation of chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its n‐terminal aspartate kinase–chorismate mutase–tyra (act) domain. Plant Direct, Jun 2024. URL: https://doi.org/10.1002/pld3.609, doi:10.1002/pld3.609. This article has 2 citations and is from a peer-reviewed journal.

  23. (naz2023insightintoderegulation pages 25-25): Sadia Naz, Pi Liu, Umar Farooq, and Hongwu Ma. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microbial Cell Factories, Aug 2023. URL: https://doi.org/10.1186/s12934-023-02178-z, doi:10.1186/s12934-023-02178-z. This article has 20 citations and is from a peer-reviewed journal.

  24. (miao2021chromosomescaleassemblyand pages 2-4): Jiashun Miao, Qi Feng, Yan Li, Qiang Zhao, Congcong Zhou, Hengyun Lu, Danlin Fan, Juan Yan, Yiqi Lu, Qilin Tian, Wenjun Li, Qijun Weng, Lei S. Zhang, Yan Zhao, Tao Huang, Laigeng Li, Xuehui Huang, T. Sang, and B. Han. Chromosome-scale assembly and analysis of biomass crop miscanthus lutarioriparius genome. Nature Communications, Apr 2021. URL: https://doi.org/10.1038/s41467-021-22738-4, doi:10.1038/s41467-021-22738-4. This article has 51 citations and is from a highest quality peer-reviewed journal.

  25. (masdroux2006anovelorganization media dc47af90): Corine Mas-Droux, Gilles Curien, Mylène Robert-Genthon, Mathieu Laurencin, Jean-Luc Ferrer, and Renaud Dumas. A novel organization of act domains in allosteric enzymes revealed by the crystal structure of arabidopsis aspartate kinase. The Plant Cell, 18:1681-1692, May 2006. URL: https://doi.org/10.1105/tpc.105.040451, doi:10.1105/tpc.105.040451. This article has 74 citations.

  26. (jander2009aspartatederivedaminoacid pages 10-11): Georg Jander and Vijay Joshi. Aspartate-derived amino acid biosynthesis in arabidopsis thaliana. The arabidopsis book, 7:e0121, Jun 2009. URL: https://doi.org/10.1199/tab.0121, doi:10.1199/tab.0121. This article has 114 citations and is from a peer-reviewed journal.

Citations

  1. clark2015analysisoflossoffunction pages 1-2
  2. masdroux2006anovelorganization pages 9-10
  3. masdroux2006anovelorganization pages 2-4
  4. rinder2008regulationofaspartatederived pages 1-2
  5. naz2023insightintoderegulation pages 22-23
  6. scholtysek2024theactivationof pages 17-18
  7. scholtysek2024theactivationof pages 1-2
  8. jander2010recentprogressin pages 1-2
  9. miao2021chromosomescaleassemblyand pages 2-4
  10. jander2009aspartatederivedaminoacid pages 3-4
  11. jander2009aspartatederivedaminoacid pages 10-11
  12. miao2021chromosomescaleassemblyand pages 10-11
  13. jander2009aspartatederivedaminoacid pages 1-3
  14. masdroux2006anovelorganization pages 1-2
  15. masdroux2006anovelorganization pages 10-11
  16. naz2023insightintoderegulation pages 23-24
  17. naz2023insightintoderegulation pages 15-19
  18. naz2023insightintoderegulation pages 9-11
  19. scholtysek2024theactivationof pages 10-11
  20. scholtysek2024theactivationof pages 15-17
  21. scholtysek2024theactivationof pages 14-15
  22. scholtysek2024theactivationof pages 19-20
  23. naz2023insightintoderegulation pages 25-25
  24. open
  25. https://doi.org/10.1186/s12934-023-02178-z
  26. https://doi.org/10.1002/pld3.609
  27. https://doi.org/10.1038/s41467-021-22738-4
  28. https://doi.org/10.1105/tpc.105.040451
  29. https://doi.org/10.1199/tab.0121
  30. https://doi.org/10.1104/pp.15.00364
  31. https://doi.org/10.1093/mp/ssp104
  32. https://doi.org/10.1074/jbc.m207379200
  33. https://doi.org/10.1007/s00726-007-0504-5
  34. https://doi.org/10.1199/tab.0121,
  35. https://doi.org/10.1038/s41467-021-22738-4,
  36. https://doi.org/10.1093/mp/ssp104,
  37. https://doi.org/10.1104/pp.15.00364,
  38. https://doi.org/10.1105/tpc.105.040451,
  39. https://doi.org/10.1002/pld3.609,
  40. https://doi.org/10.1007/s00726-007-0504-5,
  41. https://doi.org/10.1186/s12934-023-02178-z,

📚 Additional Documentation

Notes

(NCGR_LOCUS29329-notes.md)

NCGR_LOCUS29329 - Bifunctional Aspartate Kinase / Homoserine Dehydrogenase

Gene Summary

  • UniProt ID: A0A811PKG6 (TrEMBL, unreviewed)
  • Organism: Miscanthus lutarioriparius (taxon 422564, Poaceae/grasses)
  • Protein: Bifunctional aspartokinase/homoserine dehydrogenase (AK-HSD)
  • Size: 920 amino acids
  • Domains: N-terminal aspartate kinase (AA_kinase, Pfam PF00696), C-terminal homoserine dehydrogenase (Homoserine_dh, PF00742), NAD-binding domain (NAD_binding_3, PF03447), two ACT regulatory domains (positions 416-491 and 497-574)
  • EC numbers: EC 2.7.2.4 (aspartate kinase), EC 1.1.1.3 (homoserine dehydrogenase)
  • Localization: Chloroplast/plastid

Functional Context

Bifunctional AK-HSD enzymes catalyze the first (AK) and third (HSD) steps in the aspartate-derived amino acid biosynthetic pathway, which produces lysine, threonine, and methionine from L-aspartate. This is a conserved pathway in plants and bacteria.

Reactions catalyzed:

  1. Aspartate kinase (EC 2.7.2.4): L-aspartate + ATP -> 4-phospho-L-aspartate + ADP
  2. Homoserine dehydrogenase (EC 1.1.1.3): L-aspartate 4-semialdehyde + NAD(P)H + H+ -> L-homoserine + NAD(P)+

Pathway involvement:

  • L-lysine biosynthesis via DAP pathway (step 1)
  • L-threonine biosynthesis (steps 1 and 3)
  • L-methionine biosynthesis via de novo pathway (steps 1 and 3)
  • L-homoserine biosynthesis (catalyzes the HSD step directly)

Plant AK-HSD Biology

In plants like Arabidopsis, bifunctional AK-HSD enzymes (AK-HSDH I and II) are well-characterized PMID:26175505. Key features:

  • All aspartate pathway steps (except final methionine methylation) occur in the chloroplast
  • AK-HSD enzymes are subject to feedback inhibition by threonine via ACT domains
  • The ACT domains serve as allosteric regulatory sensors for threonine
  • Plants typically have both monofunctional AK (lysine-sensitive) and bifunctional AK-HSD (threonine-sensitive) forms

Genome Context

The M. lutarioriparius genome was assembled at chromosome scale (2.07 Gb, 57,710 genes) PMID:33911077. This is a C4 grass used as a biomass energy crop. The NCGR_LOCUS29329 sequence is from WGS preliminary data.

Notes on Annotation Quality

  • All 11 existing GO annotations are IEA (electronic) - no experimental evidence
  • The protein is unreviewed (TrEMBL) and from WGS preliminary data
  • Domain architecture is highly consistent with bifunctional AK-HSD: the InterPro signatures (IPR001341, IPR018042, IPR011147, IPR001342, IPR005106) are all diagnostic
  • PANTHER classification (PTHR43070:SF5) confirms homoserine dehydrogenase subfamily
  • CDD domain cd04257 (AAK_AK-HSDH) is specific to the bifunctional enzyme

📄 View Raw YAML

 
id: A0A811PKG6
gene_symbol: NCGR_LOCUS29329
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:422564
  label: Miscanthus lutarioriparius
description: >-
  Bifunctional aspartate kinase / homoserine dehydrogenase (AK-HSD) that catalyzes
  the first and third steps in the aspartate-derived amino acid biosynthetic pathway,
  leading to the production of lysine (via DAP pathway), threonine, and methionine
  from L-aspartate. The N-terminal domain has aspartate kinase activity (EC 2.7.2.4)
  and the C-terminal domain has homoserine dehydrogenase activity (EC 1.1.1.3).
  Contains two ACT regulatory domains for allosteric feedback inhibition by threonine.
  Localized to the chloroplast where the aspartate pathway operates in plants.
  Unreviewed TrEMBL entry from whole genome shotgun data.
references:
- id: UniProt:A0A811PKG6
  title: UniProt entry for NCGR_LOCUS29329
- id: PMID:33911077
  title: Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome
- id: PMID:8507831
  title: Identification and expression of a cDNA from Daucus carota encoding a bifunctional aspartokinase-homoserine dehydrogenase
- id: file:9POAL/NCGR_LOCUS29329/NCGR_LOCUS29329-notes.md
  title: Notes file for NCGR_LOCUS29329
- id: file:9POAL/NCGR_LOCUS29329/NCGR_LOCUS29329-deep-research-falcon.md
  title: Deep research for NCGR_LOCUS29329 (Falcon)
- id: GO_REF:0000120
  title: Phylogenomic-based GO annotation by ARBA and InterPro
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
- id: GO_REF:0000117
  title: Automatic Gene Ontology annotation by ARBA
- id: GO_REF:0000118
  title: TreeGrafter annotation based on PANTHER
- id: GO_REF:0000041
  title: UniPathway-based Gene Ontology annotation
- id: GO_REF:0000044
  title: UniProtKB-SubCell based Gene Ontology annotation
existing_annotations:
- term:
    id: GO:0004072
    label: aspartate kinase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Aspartate kinase activity is the core N-terminal enzymatic function of this
      bifunctional AK-HSD enzyme. The protein contains a well-defined AA_kinase domain
      (Pfam PF00696), aspartate kinase signature (PROSITE PS00324), and specific CDD
      domain cd04257 (AAK_AK-HSDH). Multiple InterPro signatures (IPR001341, IPR018042)
      confirm the aspartate kinase classification. EC 2.7.2.4 is the correct enzyme
      commission number for this activity.
    action: ACCEPT
    reason: >-
      Strong domain evidence from multiple databases (InterPro, PROSITE, CDD, Pfam)
      consistently supports aspartate kinase activity. This is a core catalytic function
      of the bifunctional enzyme, catalyzing L-aspartate + ATP -> 4-phospho-L-aspartate + ADP.
    supported_by:
    - reference_id: UniProt:A0A811PKG6
      supporting_text: Belongs to the aspartokinase family (N-terminal section)
    - reference_id: PMID:8507831
      supporting_text: the isolated carrot cDNA appears to encode a bifunctional aspartokinase-homoserine dehydrogenase enzyme
- term:
    id: GO:0004412
    label: homoserine dehydrogenase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Homoserine dehydrogenase activity is the core C-terminal enzymatic function.
      The protein contains a Homoserine_dh domain (Pfam PF00742), HSD catalytic site
      (PROSITE PS01042), NAD-binding domain (PF03447), and the bifunctional-specific
      InterPro signature IPR011147. PANTHER subfamily PTHR43070:SF5 specifically
      classifies this as homoserine dehydrogenase. EC 1.1.1.3 is correct.
    action: ACCEPT
    reason: >-
      Strong domain evidence from multiple databases. This is the second core catalytic
      function of the bifunctional enzyme, catalyzing L-aspartate 4-semialdehyde + NAD(P)H
      -> L-homoserine + NAD(P)+. The reaction is the third step in the aspartate pathway.
    supported_by:
    - reference_id: UniProt:A0A811PKG6
      supporting_text: Belongs to the homoserine dehydrogenase family (C-terminal section)
    - reference_id: PMID:8507831
      supporting_text: the isolated carrot cDNA appears to encode a bifunctional aspartokinase-homoserine dehydrogenase enzyme
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Oxidoreductase activity is a parent term of homoserine dehydrogenase activity
      (GO:0004412). While technically correct, it is redundant with the more specific
      GO:0004412 annotation already present.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      This is a true but overly general annotation. The more specific GO:0004412
      (homoserine dehydrogenase activity) already captures this function precisely.
      Annotating both the parent and child term is redundant.
- term:
    id: GO:0050661
    label: NADP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      The homoserine dehydrogenase domain uses NAD(P)+ as cofactor. The protein
      contains a NAD-binding Rossmann-fold domain (Pfam PF03447, InterPro IPR005106).
      The enzyme can use both NAD+ and NADP+ as cofactors based on the UniProt
      catalytic activity annotations.
    action: ACCEPT
    reason: >-
      NADP binding is supported by the NAD(P)-binding Rossmann-fold domain and is
      functionally relevant to the homoserine dehydrogenase activity. The enzyme
      uses NADP+ as an alternative cofactor to NAD+.
    supported_by:
    - reference_id: UniProt:A0A811PKG6
      supporting_text: L-homoserine + NADP(+) = L-aspartate 4-semialdehyde + NADPH + H(+)
- term:
    id: GO:0006520
    label: amino acid metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Amino acid metabolic process is a high-level parent of the more specific
      biosynthetic process annotations already present (GO:0009067, GO:0009088,
      GO:0009090). While technically correct, it adds no additional information.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Redundant with the more specific biological process annotations. The protein
      is specifically involved in aspartate family amino acid biosynthesis (GO:0009067),
      threonine biosynthesis (GO:0009088), and homoserine biosynthesis (GO:0009090),
      all of which are children of this term.
- term:
    id: GO:0006531
    label: aspartate metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      The aspartate kinase domain directly uses L-aspartate as substrate, phosphorylating
      it to 4-phospho-L-aspartate. This is the committed first step in aspartate-derived
      amino acid biosynthesis.
    action: ACCEPT
    reason: >-
      Correct and informative. The enzyme directly metabolizes aspartate via the
      aspartate kinase reaction. While the downstream pathway annotations (GO:0009067
      etc.) are more specific about the biosynthetic outcome, this term correctly
      captures the substrate utilization aspect.
    supported_by:
    - reference_id: UniProt:A0A811PKG6
      supporting_text: L-aspartate + ATP = 4-phospho-L-aspartate + ADP
- term:
    id: GO:0008652
    label: amino acid biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      Amino acid biosynthetic process is a parent term of the more specific
      aspartate family amino acid biosynthetic process (GO:0009067) already annotated.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Redundant with GO:0009067 (aspartate family amino acid biosynthetic process),
      which is a more specific child term that better captures the function.
- term:
    id: GO:0009067
    label: aspartate family amino acid biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: >-
      This term encompasses the biosynthesis of aspartate-derived amino acids
      (lysine, methionine, threonine, asparagine). As a bifunctional AK-HSD,
      this enzyme catalyzes the first step common to all branches and the third
      step in the threonine/methionine branch.
    action: ACCEPT
    reason: >-
      This is the most appropriate level of specificity for the overall pathway role.
      The enzyme acts at the branch point of multiple amino acid biosynthetic pathways
      derived from aspartate. TreeGrafter classification via PANTHER:PTN009166675
      supports this annotation.
    supported_by:
    - reference_id: PMID:8507831
      supporting_text: Aspartokinase (EC 2.7.2.4) and homoserine dehydrogenase (EC 1.1.1.3) catalyze steps in the pathway for the synthesis of lysine, threonine, and methionine from aspartate
- term:
    id: GO:0009088
    label: threonine biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000041
  review:
    summary: >-
      The enzyme catalyzes steps 1 and 3 of the 5-step threonine biosynthetic
      pathway from L-aspartate. Step 1 (AK) phosphorylates aspartate, and step 3
      (HSD) reduces aspartate semialdehyde to homoserine, which is then converted
      to threonine. The ACT domains provide threonine-mediated feedback inhibition,
      indicating a direct regulatory link to threonine levels.
    action: ACCEPT
    reason: >-
      Directly supported by UniPathway annotations (UPA00050) and the enzyme's
      dual catalytic activities. Threonine feedback inhibition of the ACT domains
      further confirms the enzyme's role in threonine biosynthesis.
    supported_by:
    - reference_id: UniProt:A0A811PKG6
      supporting_text: "L-threonine biosynthesis; L-threonine from L-aspartate: step 1/5 and step 3/5"
- term:
    id: GO:0009090
    label: L-homoserine biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: >-
      The homoserine dehydrogenase domain directly produces L-homoserine from
      L-aspartate 4-semialdehyde. This is the most direct product of the HSD
      enzymatic activity.
    action: ACCEPT
    reason: >-
      Directly catalyzed by the HSD domain. L-homoserine is the direct product
      of the enzyme's C-terminal catalytic activity and serves as a precursor
      for both threonine and methionine biosynthesis. TreeGrafter classification
      supports this annotation.
    supported_by:
    - reference_id: UniProt:A0A811PKG6
      supporting_text: "L-methionine biosynthesis via de novo pathway; L-homoserine from L-aspartate: step 3/3"
- term:
    id: GO:0009507
    label: chloroplast
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      Chloroplast localization is expected for plant AK-HSD enzymes. The aspartate-derived
      amino acid biosynthetic pathway operates in the chloroplast/plastid in plants. The
      protein has a predicted N-terminal transit peptide consistent with chloroplast targeting.
    action: ACCEPT
    reason: >-
      Consistent with known biology of plant aspartate pathway enzymes. All steps of the
      pathway except the final methylation of homocysteine to methionine occur in the
      chloroplast. The UniProt subcellular location annotation supports this.
    supported_by:
    - reference_id: UniProt:A0A811PKG6
      supporting_text: "SUBCELLULAR LOCATION: Plastid, chloroplast"
core_functions:
- description: >-
    Catalyzes the phosphorylation of L-aspartate to 4-phospho-L-aspartate (aspartate kinase
    activity, EC 2.7.2.4), the first committed step in aspartate-derived amino acid biosynthesis
  molecular_function:
    id: GO:0004072
    label: aspartate kinase activity
  directly_involved_in:
  - id: GO:0009067
    label: aspartate family amino acid biosynthetic process
  locations:
  - id: GO:0009507
    label: chloroplast
- description: >-
    Catalyzes the reduction of L-aspartate 4-semialdehyde to L-homoserine (homoserine
    dehydrogenase activity, EC 1.1.1.3), the third step in the threonine/methionine
    branch of the aspartate pathway
  molecular_function:
    id: GO:0004412
    label: homoserine dehydrogenase activity
  directly_involved_in:
  - id: GO:0009090
    label: L-homoserine biosynthetic process
  locations:
  - id: GO:0009507
    label: chloroplast