UniProtKB - Q9KQ92 (PDXB_VIBCH)
Protein
Erythronate-4-phosphate dehydrogenase
Gene
pdxB
Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Functioni
Catalyzes the oxidation of erythronate-4-phosphate to 3-hydroxy-2-oxo-4-phosphonooxybutanoate.UniRule annotation
Catalytic activityi
- 4-phospho-D-erythronate + NAD+ = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + H+ + NADHUniRule annotationEC:1.1.1.290UniRule annotation
: pyridoxine 5'-phosphate biosynthesis Pathwayi
This protein is involved in step 2 of the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate.UniRule annotationProteins known to be involved in the 5 steps of the subpathway in this organism are:
- D-erythrose-4-phosphate dehydrogenase (epd)
- Erythronate-4-phosphate dehydrogenase (pdxB)
- Phosphoserine aminotransferase (serC)
- 4-hydroxythreonine-4-phosphate dehydrogenase (pdxA)
- Pyridoxine 5'-phosphate synthase (pdxJ)
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate, the pathway pyridoxine 5'-phosphate biosynthesis and in Cofactor biosynthesis.
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 45 | SubstrateUniRule annotation | 1 | |
Binding sitei | 67 | SubstrateUniRule annotation | 1 | |
Binding sitei | 147 | NADUniRule annotation | 1 | |
Binding sitei | 176 | NAD; via carbonyl oxygenUniRule annotation | 1 | |
Active sitei | 209 | UniRule annotation | 1 | |
Binding sitei | 233 | NADUniRule annotation | 1 | |
Active sitei | 238 | UniRule annotation | 1 | |
Active sitei | 255 | Proton donorUniRule annotation | 1 | |
Binding sitei | 258 | NAD; via amide nitrogenUniRule annotation | 1 | |
Binding sitei | 259 | SubstrateUniRule annotation | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 127 – 128 | NADUniRule annotation | 2 |
GO - Molecular functioni
- 4-phosphoerythronate dehydrogenase activity Source: GO_Central
- NAD binding Source: InterPro
- oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Source: TIGR
- protein dimerization activity Source: InterPro
GO - Biological processi
- 'de novo' pyridoxal 5'-phosphate biosynthetic process Source: GO_Central
- pyridoxine biosynthetic process Source: TIGR
Keywordsi
Molecular function | Oxidoreductase |
Biological process | Pyridoxine biosynthesis |
Ligand | NAD |
Enzyme and pathway databases
UniPathwayi | UPA00244;UER00310 |
Names & Taxonomyi
Protein namesi | Recommended name: Erythronate-4-phosphate dehydrogenaseUniRule annotation (EC:1.1.1.290UniRule annotation) |
Gene namesi | Name:pdxBUniRule annotation Ordered Locus Names:VC_2108 |
Organismi | Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) |
Taxonomic identifieri | 243277 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio › |
Proteomesi |
|
Subcellular locationi
- Cytoplasm UniRule annotation
GO - Cellular componenti
- cytosol Source: GO_Central
Keywords - Cellular componenti
CytoplasmPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000075991 | 1 – 381 | Erythronate-4-phosphate dehydrogenaseAdd BLAST | 381 |
Interactioni
Subunit structurei
Homodimer.UniRule annotation
GO - Molecular functioni
- protein dimerization activity Source: InterPro
Protein-protein interaction databases
STRINGi | 243277.VC2108 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
5DT9 | X-ray | 2.66 | A | 1-381 | [»] | |
ProteinModelPortali | Q9KQ92 | |||||
SMRi | Q9KQ92 | |||||
ModBasei | Search... | |||||
MobiDBi | Search... |
Family & Domainsi
Sequence similaritiesi
Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. PdxB subfamily.UniRule annotation
Phylogenomic databases
eggNOGi | ENOG4105CJ0 Bacteria COG0111 LUCA |
KOi | K03473 |
OMAi | SAPGCNA |
Family and domain databases
CDDi | cd12158 ErythrP_dh, 1 hit |
Gene3Di | 3.30.1370.170, 1 hit |
HAMAPi | MF_01825 PdxB, 1 hit |
InterProi | View protein in InterPro IPR006139 D-isomer_2_OHA_DH_cat_dom IPR029753 D-isomer_DH_CS IPR006140 D-isomer_DH_NAD-bd IPR020921 Erythronate-4-P_DHase IPR024531 Erythronate-4-P_DHase_dimer IPR036291 NAD(P)-bd_dom_sf IPR038251 PdxB_dimer_sf |
PANTHERi | PTHR42938:SF3 PTHR42938:SF3, 1 hit |
Pfami | View protein in Pfam PF00389 2-Hacid_dh, 1 hit PF02826 2-Hacid_dh_C, 1 hit PF11890 DUF3410, 1 hit |
SUPFAMi | SSF51735 SSF51735, 1 hit |
PROSITEi | View protein in PROSITE PS00671 D_2_HYDROXYACID_DH_3, 1 hit |
i Sequence
Sequence statusi: Complete.
Q9KQ92-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MKILIDENMP YAQALFSQLG EVILKPGRTL TADDLIDVDA LMIRSVTKVN
60 70 80 90 100
DALLAKANRL KFVGTATAGM DHVDQALLRE RGIFFTAAPG CNKVGVAEYV
110 120 130 140 150
FSVLMVLAQQ QGFSVFDKTV GIIGAGQVGS YLAKCLSGIG MKVLLNDPPK
160 170 180 190 200
QAQGDEREFT ELETLLKQAD VITLHTPITR GGEWPTHHLI DAAILEQLRS
210 220 230 240 250
DQILINAARG PVVDNAALKA RLQQGDGFTA VLDVFEFEPQ VDMELLPLLA
260 270 280 290 300
FATPHIAGYG LEGKARGTTM IFNSYCEFLG SAHCANPASL LPKAPVPKVY
310 320 330 340 350
LERAWDEETL RTLTQIIYDV RKDDAQFRRE IHQPGAFDLM RKHYWDRREY
360 370 380
SAVTLAGGAD CHLAPLAKLG FQVEVCDEPT I
Sequence cautioni
The sequence AAF95254 differs from that shown. Reason: Erroneous initiation.Curated
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AE003852 Genomic DNA Translation: AAF95254.1 Different initiation. |
PIRi | C82118 |
RefSeqi | NP_231740.1, NC_002505.1 |
Genome annotation databases
EnsemblBacteriai | AAF95254; AAF95254; VC_2108 |
GeneIDi | 2613364 |
KEGGi | vch:VC2108 |
PATRICi | fig|243277.26.peg.2014 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AE003852 Genomic DNA Translation: AAF95254.1 Different initiation. |
PIRi | C82118 |
RefSeqi | NP_231740.1, NC_002505.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
5DT9 | X-ray | 2.66 | A | 1-381 | [»] | |
ProteinModelPortali | Q9KQ92 | |||||
SMRi | Q9KQ92 | |||||
ModBasei | Search... | |||||
MobiDBi | Search... |
Protein-protein interaction databases
STRINGi | 243277.VC2108 |
Protocols and materials databases
DNASUi | 2613364 |
Structural Biology Knowledgebase | Search... |
Genome annotation databases
EnsemblBacteriai | AAF95254; AAF95254; VC_2108 |
GeneIDi | 2613364 |
KEGGi | vch:VC2108 |
PATRICi | fig|243277.26.peg.2014 |
Phylogenomic databases
eggNOGi | ENOG4105CJ0 Bacteria COG0111 LUCA |
KOi | K03473 |
OMAi | SAPGCNA |
Enzyme and pathway databases
UniPathwayi | UPA00244;UER00310 |
Family and domain databases
CDDi | cd12158 ErythrP_dh, 1 hit |
Gene3Di | 3.30.1370.170, 1 hit |
HAMAPi | MF_01825 PdxB, 1 hit |
InterProi | View protein in InterPro IPR006139 D-isomer_2_OHA_DH_cat_dom IPR029753 D-isomer_DH_CS IPR006140 D-isomer_DH_NAD-bd IPR020921 Erythronate-4-P_DHase IPR024531 Erythronate-4-P_DHase_dimer IPR036291 NAD(P)-bd_dom_sf IPR038251 PdxB_dimer_sf |
PANTHERi | PTHR42938:SF3 PTHR42938:SF3, 1 hit |
Pfami | View protein in Pfam PF00389 2-Hacid_dh, 1 hit PF02826 2-Hacid_dh_C, 1 hit PF11890 DUF3410, 1 hit |
SUPFAMi | SSF51735 SSF51735, 1 hit |
PROSITEi | View protein in PROSITE PS00671 D_2_HYDROXYACID_DH_3, 1 hit |
ProtoNeti | Search... |
Entry informationi
Entry namei | PDXB_VIBCH | |
Accessioni | Q9KQ92Primary (citable) accession number: Q9KQ92 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | April 13, 2004 |
Last sequence update: | April 13, 2004 | |
Last modified: | January 16, 2019 | |
This is version 113 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Complete proteome, Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - PATHWAY comments
Index of metabolic and biosynthesis pathways