Variovorax Enzyme Curation & Module Plan
This document defines the batch curation plan and module architecture for Variovorax (NCBITaxon:34072) enzymes in ai-gene-review, with primary focus on rhizosphere plant–microbe chemical signaling and mineral solubilization and heavy-metal homeostasis.
1. Taxonomic & Proteome Strategy
Following UniProt's 2026_02 reference proteome policy (PROTEOME_REMOVAL), curation is anchored on active UniProtKB reference proteomes and Swiss-Prot reviewed records:
- Variovorax paradoxus S110 (
VARPS,NCBITaxon:543728, ProteomeUP000001552): - Multipartite genome (Chromosome 1
CP001635and Chromosome 2CP001636, locus tagsVapar_0001–Vapar_6257; Han et al. 2011, PMID:21183664) with 234 Swiss-Prot reviewed proteins and 6 retained TrEMBL entries in UniProtKB, notably including the four core proteins of theiadauxin-catabolism locus (Vapar_1489C5CSP2iadR,Vapar_1492C5CSP5iadC,Vapar_1493C5CSP6iadD, andVapar_1494C5CSP7iadE). - Also provides Swiss-Prot reviewed anchors for rhizosphere amide turnover (
amiEC5CWZ4), organosulfonate desulfonation (ssuDC5CNW9), cytosolic YggX-family iron trafficking (fetPC5CNX5), coenzyme PQQ precursor peptide (pqqAC5CPT7), and nickel-dependent urea hydrolysis (ureCC5CY00). - Variovorax paradoxus (
VARPD,NCBITaxon:34073, Reference ProteomeUP000035170/UP000019090): - Hosts experimentally characterized Swiss-Prot entries including 1-aminocyclopropane-1-carboxylate deaminase (
acdS, Q6J256) and 3-sulfinopropanoyl-CoA desulfinase (acd, B9U6P5,VPARA_05440), alongside active reference-proteome entries for PQQ biosynthesis (pqqBA0A0H2M8Q2,pqqCA0A0H2MDI9,pqqDA0A0H2M992,pqqEA0A0H2MPV4), periplasmic PQQ-dependent glucose (gcdA0A0H2LUW4) and alcohol (VPARA_00790A0A0H2MDH4) dehydrogenases, TonB-dependent ferric-siderophore uptake (tonBA0A0H2M2E3,bfrD1A0A0H2M677), polyphosphate kinase (ppkA0A0H2M4T4), theczcCBAIRheavy-metal RND efflux island (czcA3A0A0H2MBF7), and taurine dioxygenase (tauD1A0A0H2MHV8).
2. Tranche 1 Curation Batches (Completed in PR #6000)
Batch 1A: Auxin (IAA) Catabolism (iad Operon) & Root Growth Inhibition Reversal
Variovorax is the keystone genus in plant root microbiomes responsible for degrading excess bacterial and plant indole-3-acetic acid (IAA) to prevent ethylene- and auxin-driven root growth inhibition (Finkel et al. 2020, PMID:32999461; Conway et al. 2022, PMID:36266335; Ma et al. 2023, PMID:37459330).
| Role in Module | Gene Symbol | UniProt / Locus (VARPS) |
Enzyme / Function | Key Cofactors / Chemistry | Target GO Terms |
|---|---|---|---|---|---|
| Catalytic $\alpha$ subunit | iadD |
C5CSP6 (Vapar_1493) |
Indole-3-acetic acid Rieske dioxygenase large subunit | [2Fe-2S] Rieske cluster + mononuclear non-heme Fe(II) |
GO:0016708, GO:0042437 (indoleacetic acid catabolic process) |
| Structural $\beta$ subunit | iadE |
C5CSP7 (Vapar_1494) |
Indole-3-acetic acid dioxygenase small subunit | $\alpha_3\beta_3$ heterohexamer assembly (contributes_to holoenzyme activity) |
GO:0016708 (contributes_to), GO:0042437 |
| Electron transfer | iadC |
C5CSP5 (Vapar_1492) |
Class IA FMN/[2Fe-2S] ferredoxin-$\text{NAD}^+$ reductase |
FMN (GO:0010181) + [2Fe-2S] cluster (GO:0051537) |
GO:0008860 (ferredoxin-NAD+ reductase activity), GO:0042437 |
| Transcriptional sensor | iadR |
C5CSP2 (Vapar_1489) |
MarR-family IAA-sensing transcriptional repressor | Direct IAA binding pocket (derepresses iad transcription) |
GO:0001217, GO:0000976, GO:0045892 |
- Target Module:
modules/bacterial_iad_auxin_catabolism.yaml
Batch 1B: Ethylene Stress Buffering (acdS), Amide Crosstalk (amiE), Mineral Acidolysis (gcd), Iron Trafficking (fetP), PolyP (ppk), RND Efflux (czcA3) & Organosulfur (ssuD, acd)
| Role | Gene Symbol | UniProt / Locus | Enzyme / Function | Key Cofactors / Chemistry | Target GO Terms |
|---|---|---|---|---|---|
| ACC cleavage | acdS |
Q6J256 (VARPD) |
1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) | Pyridoxal 5'-phosphate (GO:0030170); cleaves ACC to 2-oxobutanoate + $\text{NH}_3$ |
GO:0008660, GO:0042217 |
| Amide hydrolysis | amiE |
C5CWZ4 (VARPS, Vapar_0135) |
Aliphatic amidase (EC 3.5.1.4) | Glu59-Lys134-Cys166 catalytic triad | GO:0004040 (amidase activity) |
| Cytosolic Fe(2+) trafficking | fetP |
C5CNX5 (VARPS, Vapar_2982) |
Probable $\text{Fe}^{2+}$-trafficking protein | Cytosolic YggX-family iron-binding protein (HAMAP MF_00686) |
GO:0005506, GO:0006879 |
| Periplasmic PQQ oxidation | gcd |
A0A0H2LUW4 (VARPD, VPARA_65850) |
Quinoprotein glucose dehydrogenase (EC 1.1.5.2) | PQQ + divalent cation cofactor; oxidizes D-glucose to D-glucono-1,5-lactone | GO:0008876, GO:0019521 |
| Intracellular polyP synthesis | ppk |
A0A0H2M4T4 (VARPD, VPARA_28600) |
Polyphosphate kinase (EC 2.7.4.1) | Polymerizes terminal $\gamma$-phosphate of ATP into long-chain polyP polymers | GO:0008976, GO:0006799 |
| RND metal antiporter | czcA3 |
A0A0H2MBF7 (VARPD, VPARA_44890) |
Cobalt/zinc/cadmium efflux RND transporter, CzcA family (CzcA3) | Inner-membrane HME-RND proton/cation antiporter subunit | GO:0008324, GO:0098655 |
| Organosulfur desulfonation | ssuD |
C5CNW9 (VARPS, Vapar_2976) |
Alkanesulfonate monooxygenase (EC 1.14.14.5) | $\text{FMNH}_2$-dependent TIM-barrel monooxygenase | GO:0008726, GO:0046306 |
| 3SP-CoA cleavage | acd |
B9U6P5 (VARPD, VPARA_05440) |
3-sulfinopropanoyl-CoA desulfinase (EC 3.13.1.4) | Acyl-CoA dehydrogenase fold adapted for non-oxidative C–S cleavage | GO:0016846, GO:0044273 (sulfur compound catabolic process) |
- Target Module:
modules/variovorax_metallophore_metal_homeostasis.yaml
3. Tranche 2 Curation Batches (Coenzyme PQQ Biosynthesis, Periplasmic Alcohol Dehydrogenase, TonB-Dependent Siderophore Import, Nickel Urease & Taurine Dioxygenase)
Batch 2A: De Novo PQQ Biosynthesis (pqqABCDE) & Periplasmic Quinoprotein Dehydrogenase (VPARA_00790)
Variovorax paradoxus synthesizes coenzyme PQQ via the conserved five-gene pqqABCDE pathway to supply periplasmic quinoprotein dehydrogenases (gcd and VPARA_00790) that drive organic-acid mineral weathering and alcohol/volatile organic compound oxidation in the rhizosphere:
| Role in Pathway | Gene Symbol | UniProt / Locus | Enzyme / Function | Key Cofactors / Chemistry | Target GO Terms |
|---|---|---|---|---|---|
| Precursor peptide | pqqA |
C5CPT7 (VARPS, Vapar_3057) |
Coenzyme PQQ synthesis protein A (24 aa) | Ribosomally synthesized precursor supplying Glu15 and Tyr19 (ETSY) |
GO:0018189 (pyrroloquinoline quinone biosynthetic process), GO:0005829 (cytosol) |
| Oxygenase / hydroxylase | pqqB |
A0A0H2M8Q2 (VARPD, VPARA_00950) |
Coenzyme PQQ synthesis protein B (307 aa) | Non-heme Fe(II)-dependent $\text{O}_2$ hydroxylase + structural $\text{Zn}^{2+}$ site | GO:0016705, GO:0005506, GO:0008270, GO:0018189 |
| Ring-closing oxidase | pqqC |
A0A0H2MDI9 (VARPD, VPARA_00940) |
Pyrroloquinoline-quinone synthase (EC 1.3.3.11, 254 aa) | Cofactorless 8-electron oxidation and ring cyclization of AHQQ to PQQ | GO:0008986 (pyrroloquinoline-quinone synthase activity), GO:0018189 |
| Peptide chaperone | pqqD |
A0A0H2M992 (VARPD, VPARA_00930) |
PQQ biosynthesis peptide chaperone PqqD (98 aa) | Binds PqqA leader peptide (GO:0042277) and presents it to PqqE |
GO:0042277 (peptide binding), GO:0018189 |
| Radical SAM cyclase | pqqE |
A0A0H2MPV4 (VARPD, VPARA_00920) |
PqqA peptide cyclase (EC 1.21.98.4, 383 aa) | Catalytic + auxiliary [4Fe-4S] clusters (GO:0051539) + SAM (GO:1904047) |
GO:0009975 (cyclase activity), GO:0051539, GO:1904047, GO:0018189 |
| Periplasmic quinoprotein | VPARA_00790 |
A0A0H2MDH4 (VARPD, VPARA_00790) |
PQQ-dependent alcohol/methanol dehydrogenase (EC 1.1.2.7, 608 aa) | Periplasmic 8-bladed $\beta$-propeller binding PQQ + active-site $\text{Ca}^{2+}$/$\text{Ln}^{3+}$ | GO:0052882 (methanol dehydrogenase (cytochrome c) activity), GO:0070968, GO:0046872, GO:0042597 |
- Linked Module:
modules/pqq_biosynthesis.yaml(MODULE:pqq_biosynthesis)
Batch 2B: TonB-Dependent Ferric-Siderophore Import (tonB, bfrD1), Nickel Urease (ureC) & Taurine Dioxygenase (tauD1)
| Role | Gene Symbol | UniProt / Locus | Enzyme / Function | Key Cofactors / Chemistry | Target GO Terms |
|---|---|---|---|---|---|
| Outer-membrane TBDT | bfrD1 |
A0A0H2M677 (VARPD, VPARA_25830) |
Outer-membrane TonB-dependent ferric-siderophore receptor BfrD1 (739 aa) | 22-stranded $\beta$-barrel (PF00593) + N-terminal plug domain (PF07715) |
GO:0015344 (siderophore uptake transmembrane transporter activity), GO:0033214, GO:0009279 |
| Inner-membrane energy transducer | tonB |
A0A0H2M2E3 (VARPD, VPARA_25820) |
Inner-membrane proton-motive-force energy transducer TonB (232 aa) | N-terminal TM helix + proline-rich periplasmic linker + C-terminal TonB domain (PF03544) |
GO:0031992 (energy transducer activity), GO:0015891 (siderophore transport), GO:0005886, GO:0030288, GO:0098797 |
| Nickel urease $\alpha$ subunit | ureC |
C5CY00 (VARPS, Vapar_4243) |
Urease catalytic subunit alpha (EC 3.5.1.5, 572 aa) | Dinuclear $\text{Ni}^{2+}$ center bridged by N6-carboxylysine (Lys222) in $(\text{UreABC})_3$ complex | GO:0009039 (urease activity), GO:0016151 (nickel cation binding), GO:0043419, GO:0035550, GO:0005829 |
| Taurine dioxygenase | tauD1 |
A0A0H2MHV8 (VARPD, VPARA_23370) |
Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17, 302 aa) | Mononuclear non-heme Fe(II) (GO:0005506) + 2-oxoglutarate + $\text{O}_2$ |
GO:0000908 (taurine dioxygenase activity), GO:0005506, GO:0019529 (taurine catabolic process), GO:0005829 |
- Target & Linked Modules:
modules/bacterial_tonb_siderophore_import.yaml(MODULE:bacterial_tonb_siderophore_import— new module anchored ontonBandbfrD1)modules/urease_biogenesis_urea_hydrolysis.yaml(MODULE:urease_biogenesis_urea_hydrolysis— linked toureC)modules/taurine_uptake_and_desulfonation.yaml(MODULE:taurine_uptake_and_desulfonation— linked totauD1)
4. Tranche 3 Curation Batches (Nickel Urease Structural & Maturation Complex, ExbB-ExbD Siderophore-Import Stator, Tripartite CzcCBA & CzcD Heavy-Metal Efflux, and Exopolyphosphatase Ppx)
Batch 3A: Nickel-Dependent Urease Structural (ureA, ureB) & Maturation Accessory Complex (ureD, ureE, ureF, ureG)
Completes the cytoplasmic bacterial urease holoenzyme ((UreABC)3) and UreD-UreF-UreG/UreE metallocenter activation machinery around ureC (C5CY00, Vapar_4243):
| Role in Complex | Gene Symbol | UniProt / Locus | Protein / Function | Key Cofactors / Chemistry | Target GO Terms |
|---|---|---|---|---|---|
| Gamma structural chain | ureA |
C5CXZ7 (VARPS, Vapar_4240) |
Urease subunit gamma (100 aa, HAMAP MF_00739) |
Trimer-interface structural subunit of (UreABC)3 |
GO:0005198 (structural molecule activity), GO:0035550, GO:0043419, GO:0005737 |
| Beta structural chain | ureB |
C5CXZ9 (VARPS, Vapar_4242) |
Urease subunit beta (101 aa, HAMAP MF_01954) |
Non-catalytic beta chain of (UreABC)3 |
GO:0005198, GO:0035550, GO:0043419, GO:0005737 |
| Apoprotein scaffold | ureD |
C5CVT2 (VARPS, Vapar_3971) |
Urease accessory protein UreD (276 aa, HAMAP MF_01384) |
Binds apo-UreABC and recruits UreF/UreG | GO:0018237 (urease activator activity), GO:0044183, GO:0043419, GO:0005737 |
| Nickel metallochaperone | ureE |
A0A0H2LU38 (VARPD, VPARA_50940) |
Urease accessory protein UreE (200 aa, HAMAP MF_00822) |
Dimeric Ni(2+) donor with 15-His C-terminal tail (residues 148-200) | GO:0016151 (nickel cation binding), GO:0051604 (protein maturation), GO:0043419, GO:0005737 |
| GTPase-gating scaffold | ureF |
A0A0H2LZ72 (VARPD, VPARA_50930) |
Urease accessory protein UreF (223 aa, HAMAP MF_01385) |
Docks UreG onto UreD-apourease and gates GTP hydrolysis | GO:0018237, GO:0030695 (GTPase regulator activity), GO:0043419, GO:0005737 |
| SIMIBI G3E GTPase | ureG |
C5CY05 (VARPS, Vapar_4248) |
Urease accessory protein UreG (216 aa, HAMAP MF_01389) |
P-loop (24-GPVGSGKT-31) + Cys72-Pro73-His74 Ni(2+)-binding site |
GO:0003924 (GTPase activity), GO:0016151, GO:0005525, GO:0043419, GO:0005737 |
- Linked Module:
modules/urease_biogenesis_urea_hydrolysis.yaml(MODULE:urease_biogenesis_urea_hydrolysis)
Batch 3B: ExbB-ExbD Proton-Channel Motor (exbB4, exbD5), Tripartite CzcCBA & CzcD Heavy-Metal Efflux (czcB, czcC, czcD), and Exopolyphosphatase (ppx)
| Role | Gene Symbol | UniProt / Locus | Protein / Function | Key Cofactors / Chemistry | Target GO Terms |
|---|---|---|---|---|---|
| ExbB pentameric stator | exbB4 |
A0A0H2MHH3 (VARPD, VPARA_25810) |
Biopolymer transport protein ExbB4 (238 aa, Pfam PF01618) |
3-TM inner-membrane proton-channel pore (exbD5-exbB4-tonB-bfrD1 operon) |
GO:0015078 (proton transmembrane transporter activity), GO:1902600, GO:0015891, GO:0005886, GO:0098797 |
| ExbD proton-coupling rotor | exbD5 |
A0A0H2M1F3 (VARPD, VPARA_25800) |
Biopolymer transport protein ExbD5 (137 aa, Pfam PF02472) |
Single-pass type II inner-membrane dimer with conserved TM Asp23 |
GO:0015078, GO:1902600, GO:0015891, GO:0005886, GO:0030288, GO:0098797 |
| RND periplasmic adaptor | czcB |
A0A0H2LX82 (VARPD, VPARA_44900) |
Cobalt-zinc-cadmium resistance protein CzcB (455 aa, TIGR01730) |
N-terminal 10-His region (41-121) + 4 CzcB/CusB adaptor domains | GO:0005198 (structural molecule activity), GO:0015562 (contributes_to), GO:0098655, GO:0030288, GO:0005886 |
| Outer-membrane efflux duct | czcC |
A0A0H2M0U4 (VARPD, VPARA_44910) |
Outer membrane protein CzcC (445 aa, Pfam PF02321, PTHR30203) |
Sec signal peptide (1-20) + two OEP repeats forming trimeric outer-membrane tunnel | GO:0015562, GO:0008324, GO:0098655, GO:0009279 (cell outer membrane) |
| Inner-membrane CDF pump | czcD |
A0A0H2M558 (VARPD, VPARA_15480) |
Cadmium, cobalt and zinc/H(+)-K(+) antiporter CzcD (320 aa, TIGR01297) |
6-TM CDF antiporter with Site A (His59, His62, His188, Asp192) + 15-His loop (152-179) |
GO:0005385 (zinc ion transmembrane transporter activity), GO:0071577, GO:0006882, GO:0005886 |
| PolyP depolymerization | ppx |
A0A0H2MBK5 (VARPD, VPARA_10490) |
Exopolyphosphatase Ppx (EC 3.6.1.11, 506 aa, PTHR30005:SF14) |
ASKHA catalytic domain (PF02541, P1 11-DLGSNSFR-18, P2 142-DIGGRSTE-149) + C-terminal polyP-binding domain (PF21447) |
GO:0004309 (exopolyphosphatase activity), GO:0006798 (polyphosphate catabolic process), GO:0005829 |
- Updated Modules:
modules/bacterial_tonb_siderophore_import.yaml(MODULE:bacterial_tonb_siderophore_import— expanded withexbB4andexbD5proton-channel motor step)modules/variovorax_metallophore_metal_homeostasis.yaml(MODULE:variovorax_metallophore_metal_homeostasis— expanded withppxpolyP turnover andczcB,czcC,czcDheavy-metal efflux)
5. Tranche 4 Curation Batches (SsuABC-SsuE Alkanesulfonate Import & Reductase, TauABC Taurine Import, CzcI/CzcR/CusS/CadA2 Heavy-Metal Island Completion, and Fur1 Iron Regulation)
Batch 4A: Alkanesulfonate ABC Importer & FMN Reductase (ssuA2, ssuB2, ssuC5, ssuE) and Taurine ABC Importer (tauA, tauB1, tauC)
Completes the organosulfonate and taurine assimilation pathways around ssuD (C5CNW9) and tauD1 (A0A0H2MHV8):
| Role in Complex / Pathway | Gene Symbol | UniProt / Locus (VARPD) |
Protein / Function | Key Cofactors / Chemistry | Target GO Terms |
|---|---|---|---|---|---|
| Periplasmic sulfonate SBP | ssuA2 |
A0A0H2M784 (VPARA_09270) |
Aliphatic sulfonate-binding protein SsuA2 (319 aa, TIGR01728, IPR010067) |
Tat signal peptide (1-29, PS51318) + periplasmic SsuA fold (PTHR30024:SF42) |
GO:0042918 (alkanesulfonate transmembrane transport), GO:0042959 (contributes_to), GO:0030288, GO:0055052 |
| Sulfonate import ATPase | ssuB2 |
A0A0H2MBB8 (VPARA_09230) |
Aliphatic sulfonates import ATP-binding protein SsuB2 (276 aa, PTHR42788:SF17) |
ABC ATPase (PS50893) with Walker A (51-GRSGCGKS-58) |
GO:0042959 (contributes_to), GO:0005524, GO:0016887, GO:0042918, GO:0005886, GO:0055052 |
| Sulfonate permease | ssuC5 |
A0A0H2M6G6 (VPARA_09240) |
Aliphatic sulfonates transport permease protein SsuC5 (284 aa, NF008470, PTHR30151:SF38) |
5-TM ABC transmembrane type-1 domain (PS50928, residues 80-264) |
GO:0042918, GO:0042959 (contributes_to), GO:0005886, GO:0055052 |
| NAD(P)H-FMN reductase | ssuE |
A0A0H2M6H0 (VPARA_09290) |
FMN reductase SsuE (EC 1.5.1.38, 194 aa, TIGR03567, PTHR43408:SF1) |
Flavodoxin-like fold (PF03358, residues 1-142) supplying $\text{FMNH}_2$ to SsuD |
GO:0008752 (FMN reductase [NAD(P)H] activity), GO:0046306, GO:0005829 |
| Periplasmic taurine SBP | tauA |
A0A0H2M727 (VPARA_03650) |
Taurine-binding periplasmic protein TauA (340 aa, TIGR01729) |
Sec signal peptide (1-30) + periplasmic TauA fold (PTHR30024:SF47) |
GO:0030977 (taurine binding), GO:0015734, GO:0015411 (contributes_to), GO:0030288, GO:0055052 |
| Taurine import ATPase | tauB1 |
A0A0H2MNF8 (VPARA_03660) |
Taurine import ATP-binding protein TauB1 (262 aa, PTHR42788:SF18) |
ABC ATPase (PS50893) with Walker A (40-GASGCGKT-47) |
GO:0015411 (contributes_to), GO:0005524, GO:0016887, GO:0015734, GO:0005886, GO:0055052 |
| Taurine permease | tauC |
A0A0H2M7Y1 (VPARA_03670) |
Taurine transport system permease protein TauC (294 aa, PTHR30151:SF25) |
6-TM ABC transmembrane type-1 domain (PS50928, residues 100-280) |
GO:0015734, GO:0015411 (contributes_to), GO:0005886, GO:0055052 |
- Linked Module:
modules/taurine_uptake_and_desulfonation.yaml(MODULE:taurine_uptake_and_desulfonation— expanded withtauA,tauB1, andtauC)
Batch 4B: Heavy-Metal Resistance Island Completion (czcI, czcR, cusS, cadA2) and Ferric Uptake Regulator (fur1)
| Role | Gene Symbol | UniProt / Locus (VARPD) |
Protein / Function | Key Cofactors / Chemistry | Target GO Terms |
|---|---|---|---|---|---|
| Periplasmic Czc modulator | czcI |
A0A0H2LVR9 (VPARA_44920) |
Cobalt-zinc-cadmium resistance protein CzcI (123 aa, NF045614) |
Histidine-rich cluster (36-HWGHHEHE-43) + 71-CAVCH-75 motif |
GO:0046686 (response to cadmium ion), GO:0010043 (response to zinc ion), GO:0030288 (outer membrane-bounded periplasmic space) |
| Heavy-metal response regulator | czcR |
A0A0H2LVW5 (VPARA_44930) |
Two-component response regulator CzcR (225 aa, TIGR01387) |
Receiver domain (Asp51) + OmpR/PhoB winged-helix DNA-binding domain (PS51755) |
GO:0000156, GO:0003700, GO:0000976, GO:0000160, GO:0006355, GO:0010043, GO:0005829 |
| Heavy-metal sensor kinase | cusS |
A0A0H2MBG2 (VPARA_44940) |
Sensor protein CusS/CzcS (EC 2.7.13.3, 443 aa, TIGR01386) |
2 TM helices + HAMP (PS50885) + HisKA/HATPase_c (PS50109, His233) |
GO:0000155 (phosphorelay sensor kinase activity), GO:0005524, GO:0000160, GO:0046777, GO:0010043, GO:0005886 |
| P1B-2-type heavy-metal ATPase | cadA2 |
A0A0H2LVW9 (VPARA_44980) |
P-type Zn(2+)/Cd(2+) transporter CadA2 (EC 7.2.2.12, 759 aa, TIGR01512) |
N-terminal HMA domain (IPR006121) + intramembrane 410-CPC-412 + Asp454 phosphorylation site |
GO:0016463 (P-type zinc transporter activity), GO:0015086 (cadmium ion transmembrane transporter activity), GO:0005524, GO:0008270, GO:0046870, GO:0071577, GO:0070574, GO:0005886 |
| Ferric uptake repressor | fur1 |
A0A0H2M8T9 (VPARA_18200) |
Ferric uptake regulation protein Fur1 (139 aa, NF006999) |
Structural $\text{Zn}^{2+}$ site (Cys92, Cys95, Cys132, Cys135) + regulatory $\text{Fe}^{2+}$ site (His86, Asp88, Glu107, His124) |
GO:0001217 (DNA-binding transcription repressor activity), GO:0000976, GO:0008198 (ferrous iron binding), GO:0045892, GO:0006879, GO:0005829 |
- Updated Modules:
modules/variovorax_metallophore_metal_homeostasis.yaml(MODULE:variovorax_metallophore_metal_homeostasis— expanded withfur1,cadA2,czcI,czcR, andcusS)modules/bacterial_tonb_siderophore_import.yaml(MODULE:bacterial_tonb_siderophore_import— evidence updated withfur1)
6. Tranche 5 Curation Batches (TDP/3MP Organosulfur Catabolism, High-Affinity PstSCAB-PhoU-PhoBR Phosphate Acquisition & Regulon, and CopA2/Zur Copper & Zinc Homeostasis)
Batch 5A: 3,3'-Thiodipropionic Acid & 3-Mercaptopropionate Catabolism (fox, mdo, act) and High-Affinity PstSCAB-PhoU-PhoBR Phosphate System (pstS, pstC, pstA, pstB, phoU, phoB1, phoR1)
Completes the Variovorax paradoxus TBEA6 (VARPD) 3,3'-thiodipropionic acid (TDP) catabolic pathway around acd (B9U6P5, VPARA_05440) on contig JZWI01000003 and the high-affinity phosphate transport/signaling cluster (VPARA_10420-VPARA_10480) immediately adjacent to ppx (VPARA_10490) on contig JZWI01000005:
| Role in Pathway / Complex | Gene Symbol | UniProt / Locus (VARPD) |
Protein / Function | Key Cofactors / Chemistry | Target GO Terms |
|---|---|---|---|---|---|
Flavoprotein near mdo |
fox |
A0A0H2M811 (VPARA_05580) |
FAD-dependent oxidoreductase Fox (EC 1.-.-.-, 474 aa, PS51387, PF01565/PF02913) |
N-terminal PCMH-type FAD-binding domain (residues 36-217) | GO:0016491 (oxidoreductase activity), GO:0071949 (FAD binding), GO:0005829 (cytosol) |
| 3MP dioxygenase | mdo |
B9U5L8 (VPARA_05600) |
3-Mercaptopropionate dioxygenase Mdo (EC 1.13.11.66, 195 aa, cd10548, IPR010300) |
Cupin 3-His mononuclear $\text{Fe}^{2+}$ triad (His90, His92, His143); oxygenates 3MP to 3SP |
GO:0016702, GO:0008198 (ferrous iron binding), GO:0044273, GO:0005829 |
| 3SP CoA-transferase | act |
B9U6P4 (VPARA_05450) |
Family III acyl-CoA-transferase Act (398 aa, PF02515, IPR003673, MONOMER-18547) |
Transfers CoA to 3-sulfinopropionate to form 3-sulfinopropionyl-CoA for Acd | GO:0008410 (CoA-transferase activity), GO:0044273, GO:0005829 |
| Periplasmic Pi SBP | pstS |
A0A0H2M7F6 (VPARA_10480) |
Periplasmic phosphate-binding protein PstS (345 aa, TIGR00975, PTHR42996:SF1) |
Sec signal peptide (1-24) + periplasmic PBP domain (PF12849, residues 26-304) |
GO:0042301 (phosphate ion binding), GO:0015415 (contributes_to), GO:0035435, GO:0030288, GO:0055052 |
| Pi transmembrane permease | pstC |
A0A0H2MMT5 (VPARA_10470) |
Phosphate transport system permease protein PstC (359 aa, TIGR02138, PTHR30425:SF1) |
6-TM ABC permease (PS50928, residues 114-344, Arg276/Glu280) forming heterodimeric pore with PstA |
GO:0015415 (contributes_to), GO:0035435, GO:0005886, GO:0055052 |
| Pi transmembrane permease | pstA |
A0A0H2M6I3 (VPARA_10460) |
Phosphate transport system permease protein PstA (294 aa, TIGR00974, NF008430, PTHR42922:SF1) |
6-TM ABC permease (PS50928, residues 83-286, Arg220/Glu224) forming heterodimeric pore with PstC |
GO:0015415 (contributes_to), GO:0035435, GO:0005886, GO:0055052 |
| Pi import ABC ATPase | pstB |
A0A0D0L7E0 (VPARA_10450) |
Phosphate import ATP-binding protein PstB (259 aa, TIGR00972, PTHR43423:SF3) |
ABC ATPase (PS50893, Walker A 45-GPSGCGKS-52, Walker B Glu181, switch His212) |
GO:0016887, GO:0015415 (contributes_to), GO:0005524, GO:0035435, GO:0005886, GO:0055052 |
| Pi signaling adaptor | phoU |
A0A0H2MBK2 (VPARA_10440) |
Phosphate transport system regulatory protein PhoU (233 aa, TIGR02135, PTHR42930:SF3) |
Tandem PhoU 3-helix bundles (PF01895, 22-108 & 129-210, Glu96/Arg97 & Glu198/Arg199) bridging PstB and PhoR1 PAS domain |
GO:0030145 (manganese ion binding), GO:0000287 (magnesium ion binding), GO:0030643, GO:0045936, GO:0005737 |
| Pho regulon activator | phoB1 |
A0A0H2M7F4 (VPARA_10430) |
Phosphate regulon response regulator PhoB1 (230 aa, TIGR02154, PTHR48111:SF40) |
Receiver domain (PS50110, residues 5-121, Asp54) + OmpR/PhoB winged-helix (PS51755, residues 130-226) |
GO:0000156, GO:0001216, GO:0000976, GO:0000160, GO:0016036, GO:0045893, GO:0005829 |
| Pho regulon sensor kinase | phoR1 |
A0A0H2MMT2 (VPARA_10420) |
Phosphate regulon sensor histidine kinase PhoR1 (EC 2.7.13.3, 464 aa, TIGR02966, PTHR45453:SF1) |
N-terminal TM (PF11808, 29-45) + PAS (PF00989) + HisKA/HATPase_c (PS50109, residues 216-436, His219) |
GO:0000155, GO:0004721 (phosphoprotein phosphatase activity), GO:0000160, GO:0016036, GO:0005886 |
- Related Module:
modules/bacterial_pst_phosphate_uptake.yaml(MODULE:bacterial_pst_phosphate_uptake— reusableCOMPLETEbacterial PstSACB phosphate-uptake module;phoU,phoB1, andphoR1encode the cognate phosphate-homeostasis and starvation-signaling regulators)
Batch 5B: Copper Efflux P1B-1 ATPase (copA2) and Zinc Uptake Repressor (zur)
| Role | Gene Symbol | UniProt / Locus (VARPD) |
Protein / Function | Key Cofactors / Chemistry | Target GO Terms |
|---|---|---|---|---|---|
| P1B-1 Cu(+) efflux ATPase | copA2 |
A0A0H2M2H3 (VPARA_21930) |
P-type Cu(+) transporter CopA2 (EC 7.2.2.8, 747 aa, TIGR01511, PTHR43520:SF8) |
N-terminal HMA (PS50846, 22-MTCASCV-28) + TM6 390-CPC-392 + Asp434 (434-DKTGTLT-440) phosphorylation site |
GO:0140581 (P-type monovalent copper transporter activity), GO:0005507, GO:0005524, GO:0060003, GO:0055070, GO:0005886 |
| Zinc uptake repressor | zur |
A0A0H2LYR2 (VPARA_33720) |
Fur-family zinc uptake transcriptional repressor Zur (149 aa, PTHR33202, PF01475) |
Structural 4-Cys $\text{Zn}^{2+}$ site (Cys96, Cys99, Cys133, Cys136) + regulatory His90/His125 site |
GO:0001217 (DNA-binding transcription repressor activity), GO:0000976, GO:0008270, GO:0045892, GO:0006882, GO:0005829 |
- Updated Module:
modules/variovorax_metallophore_metal_homeostasis.yaml(MODULE:variovorax_metallophore_metal_homeostasis— expanded withcopA2andzur)