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Protein

4-hydroxythreonine-4-phosphate dehydrogenase

Gene

pdxA

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the NAD(P)-dependent oxidation of 4-(phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP).UniRule annotation

Catalytic activityi

4-phosphonooxy-L-threonine + NAD+ = 3-amino-2-oxopropyl phosphate + CO2 + NADH.

Cofactori

Zn2+UniRule annotation, Mg2+UniRule annotation, Co2+UniRule annotationNote: Binds 1 divalent metal cation per subunit. Can use ions such as Zn(2+), Mg(2+) or Co2+.UniRule annotation

Pathway: pyridoxine 5'-phosphate biosynthesis

This protein is involved in step 4 of the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate.UniRule annotation
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. D-erythrose-4-phosphate dehydrogenase (epd)
  2. Erythronate-4-phosphate dehydrogenase (pdxB)
  3. Phosphoserine aminotransferase (serC)
  4. 4-hydroxythreonine-4-phosphate dehydrogenase (pdxA)
  5. Pyridoxine 5'-phosphate synthase (pdxJ)
This subpathway is part of the pathway pyridoxine 5'-phosphate biosynthesis, which is itself part of Cofactor biosynthesis.
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 keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei138 – 1381SubstrateUniRule annotation
Binding sitei139 – 1391SubstrateUniRule annotation
Metal bindingi168 – 1681Divalent metal cation; shared with dimeric partnerUniRule annotation
Metal bindingi213 – 2131Divalent metal cation; shared with dimeric partnerUniRule annotation
Metal bindingi269 – 2691Divalent metal cation; shared with dimeric partnerUniRule annotation
Binding sitei277 – 2771SubstrateUniRule annotation
Binding sitei286 – 2861SubstrateUniRule annotation
Binding sitei295 – 2951SubstrateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Cobalt, Magnesium, Metal-binding, NAD, NADP, Zinc

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-348-MONOMER.
UniPathwayiUPA00244; UER00312.

Names & Taxonomyi

Protein namesi
Recommended name:
4-hydroxythreonine-4-phosphate dehydrogenaseUniRule annotation (EC:1.1.1.262UniRule annotation)
Alternative name(s):
4-(phosphohydroxy)-L-threonine dehydrogenaseUniRule annotation
Gene namesi
Name:pdxAUniRule annotation
Ordered Locus Names:VP0337
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002493 Componenti: Chromosome 1

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 3323324-hydroxythreonine-4-phosphate dehydrogenasePRO_0000188834Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi223926.VP0337.

Structurei

3D structure databases

ProteinModelPortaliQ87ST5.
SMRiQ87ST5. Positions 5-332.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the PdxA family.UniRule annotation

Phylogenomic databases

eggNOGiCOG1995.
HOGENOMiHOG000221592.
KOiK00097.
OMAiDTLFQDK.
OrthoDBiEOG6GN6ZC.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
HAMAPiMF_00536. PdxA.
InterProiIPR024084. IsoPropMal-DH-like_dom.
IPR005255. PdxA.
[Graphical view]
PfamiPF04166. PdxA. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00557. pdxA. 1 hit.

Sequencei

Sequence statusi: Complete.

Q87ST5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTTNSIRRIV VTAGEPAGIG PDLVLALSKE DWAHQIVVCA DKNMLLERAK
60 70 80 90 100
MLGIDVQLFD YNPEEAPKAQ KAGTLIVDHV EIAENAIAGQ LNEANGHYVL
110 120 130 140 150
KTLERAALGC MNDEFDAIVT GPVHKGVINR AGVAFSGHTE FFAEKSNTPL
160 170 180 190 200
VVMMLATEGL RVALVTTHIP LAYVSKAVTE ERLEKIIDIL HKDLVEKFAI
210 220 230 240 250
AEPNIYVCGL NPHAGEDGCL GREEIETITP TLEKIQKEKG IKLIGPLPAD
260 270 280 290 300
TIFNEKYLND ADAVLGMYHD QVLPVLKYKG FGRSVNITLG LPFIRTSVDH
310 320 330
GTALELAGTG QADTGSFRTA LTHAIELVEK KQ
Length:332
Mass (Da):36,067
Last modified:May 30, 2003 - v1
Checksum:i614012482F81B45A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC58600.1.
RefSeqiNP_796716.1. NC_004603.1.
WP_005459624.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC58600; BAC58600; BAC58600.
GeneIDi1187804.
KEGGivpa:VP0337.
PATRICi20138898. VBIVibPar50997_0324.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC58600.1.
RefSeqiNP_796716.1. NC_004603.1.
WP_005459624.1. NC_004603.1.

3D structure databases

ProteinModelPortaliQ87ST5.
SMRiQ87ST5. Positions 5-332.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VP0337.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC58600; BAC58600; BAC58600.
GeneIDi1187804.
KEGGivpa:VP0337.
PATRICi20138898. VBIVibPar50997_0324.

Phylogenomic databases

eggNOGiCOG1995.
HOGENOMiHOG000221592.
KOiK00097.
OMAiDTLFQDK.
OrthoDBiEOG6GN6ZC.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00312.
BioCyciVPAR223926:GHK4-348-MONOMER.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
HAMAPiMF_00536. PdxA.
InterProiIPR024084. IsoPropMal-DH-like_dom.
IPR005255. PdxA.
[Graphical view]
PfamiPF04166. PdxA. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00557. pdxA. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae."
    Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.
    Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry nameiPDXA_VIBPA
AccessioniPrimary (citable) accession number: Q87ST5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2003
Last sequence update: May 30, 2003
Last modified: May 27, 2015
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The active site is located at the dimer interface.UniRule annotation

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.