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Protein

4-hydroxythreonine-4-phosphate dehydrogenase

Gene

pdxA

Organism
Yersinia pestis
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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 Zn2+, Mg2+ or Co2+.UniRule annotation

Pathwayi: 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), D-erythrose-4-phosphate dehydrogenase (gapA)
  2. Erythronate-4-phosphate dehydrogenase (pdxB)
  3. Phosphoserine aminotransferase (serC), Phosphoserine aminotransferase (serC)
  4. 4-hydroxythreonine-4-phosphate dehydrogenase (pdxA), 4-hydroxythreonine-4-phosphate dehydrogenase (pdxA)
  5. Pyridoxine 5'-phosphate synthase (pdxJ), 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)DescriptionActionsGraphical viewLength
Binding sitei137SubstrateUniRule annotation1
Binding sitei138SubstrateUniRule annotation1
Metal bindingi167Divalent metal cation; shared with dimeric partnerUniRule annotation1
Metal bindingi212Divalent metal cation; shared with dimeric partnerUniRule annotation1
Metal bindingi267Divalent metal cation; shared with dimeric partnerUniRule annotation1
Binding sitei275SubstrateUniRule annotation1
Binding sitei284SubstrateUniRule annotation1
Binding sitei293SubstrateUniRule annotation1

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

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:YPO0493, y3682, YP_3686
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesYersiniaceaeYersinia
Proteomesi
  • UP000000815 Componenti: Chromosome
  • UP000001019 Componenti: Chromosome
  • UP000002490 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001888411 – 3314-hydroxythreonine-4-phosphate dehydrogenaseAdd BLAST331

Proteomic databases

PRIDEiP58719.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi187410.y3682.

Structurei

Secondary structure

1331
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 11Combined sources6
Helixi19 – 26Combined sources8
Beta strandi32 – 39Combined sources8
Helixi41 – 50Combined sources10
Beta strandi56 – 59Combined sources4
Beta strandi73 – 78Combined sources6
Helixi92 – 94Combined sources3
Helixi95 – 111Combined sources17
Beta strandi112 – 115Combined sources4
Beta strandi117 – 119Combined sources3
Helixi124 – 129Combined sources6
Helixi137 – 145Combined sources9
Beta strandi151 – 156Combined sources6
Beta strandi159 – 165Combined sources7
Helixi170 – 172Combined sources3
Helixi173 – 176Combined sources4
Helixi179 – 195Combined sources17
Beta strandi204 – 207Combined sources4
Helixi211 – 217Combined sources7
Helixi222 – 225Combined sources4
Helixi227 – 236Combined sources10
Beta strandi241 – 245Combined sources5
Helixi247 – 250Combined sources4
Helixi253 – 256Combined sources4
Beta strandi260 – 266Combined sources7
Helixi267 – 278Combined sources12
Beta strandi283 – 291Combined sources9
Beta strandi293 – 298Combined sources6
Helixi302 – 304Combined sources3
Turni305 – 307Combined sources3
Helixi313 – 328Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3LXYX-ray1.70A1-331[»]
ProteinModelPortaliP58719.
SMRiP58719.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP58719.

Family & Domainsi

Sequence similaritiesi

Belongs to the PdxA family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CEZ. Bacteria.
COG1995. LUCA.
HOGENOMiHOG000221592.
KOiK00097.
OMAiYVWDTPL.

Family and domain databases

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

Sequencei

Sequence statusi: Complete.

P58719-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHNHNNRLVI TPGEPAGVGP DLAITLAQQD WPVELVVCAD PALLLARASQ
60 70 80 90 100
LNLPLQLREY QADQPAIAQQ AGSLTILPVK TAVNVVPGKL DVGNSHYVVE
110 120 130 140 150
TLAKACDGAI SGEFAALVTG PVQKSIINDA GIPFIGHTEF FADRSHCQRV
160 170 180 190 200
VMMLATEELR VALATTHLPL LAVPGAITQA SLHEVITILD NDLKTKFGIT
210 220 230 240 250
QPQIYVCGLN PHAGEGGHMG HEEIDTIIPA LNTLRQQGIN LIGPLPADTL
260 270 280 290 300
FQPKYLQHAD AVLAMYHDQG LPVLKYQGFG RAVNITLGLP FIRTSVDHGT
310 320 330
ALELAATGTA DVGSFITALN LAIKMINNSN E
Length:331
Mass (Da):35,270
Last modified:January 31, 2002 - v1
Checksum:i9E7675F0F7D64349
GO

Sequence cautioni

The sequence AAM87230 differs from that shown. Reason: Erroneous initiation.Curated
The sequence AAS63834 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL19173.1.
AE009952 Genomic DNA. Translation: AAM87230.1. Different initiation.
AE017042 Genomic DNA. Translation: AAS63834.1. Different initiation.
PIRiAC0061.
RefSeqiWP_002210489.1. NZ_LQBA01000109.1.
YP_002345566.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM87230; AAM87230; y3682.
AAS63834; AAS63834; YP_3686.
GeneIDi1173338.
KEGGiype:YPO0493.
ypk:y3682.
ypm:YP_3686.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL19173.1.
AE009952 Genomic DNA. Translation: AAM87230.1. Different initiation.
AE017042 Genomic DNA. Translation: AAS63834.1. Different initiation.
PIRiAC0061.
RefSeqiWP_002210489.1. NZ_LQBA01000109.1.
YP_002345566.1. NC_003143.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3LXYX-ray1.70A1-331[»]
ProteinModelPortaliP58719.
SMRiP58719.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi187410.y3682.

Proteomic databases

PRIDEiP58719.

Protocols and materials databases

DNASUi1148629.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM87230; AAM87230; y3682.
AAS63834; AAS63834; YP_3686.
GeneIDi1173338.
KEGGiype:YPO0493.
ypk:y3682.
ypm:YP_3686.

Phylogenomic databases

eggNOGiENOG4105CEZ. Bacteria.
COG1995. LUCA.
HOGENOMiHOG000221592.
KOiK00097.
OMAiYVWDTPL.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00312.

Miscellaneous databases

EvolutionaryTraceiP58719.

Family and domain databases

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

Entry informationi

Entry nameiPDXA_YERPE
AccessioniPrimary (citable) accession number: P58719
Secondary accession number(s): Q0WJH2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 31, 2002
Last sequence update: January 31, 2002
Last modified: November 2, 2016
This is version 113 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.