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Protein

Pyridoxal 5'-phosphate synthase subunit PdxS

Gene

pdxS

Organism
Geobacillus kaustophilus (strain HTA426)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively.UniRule annotation

Catalytic activityi

D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate.UniRule annotation

Pathwayi: pyridoxal 5'-phosphate biosynthesis

This protein is involved in the pathway pyridoxal 5'-phosphate biosynthesis, which is part of Cofactor biosynthesis.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway pyridoxal 5'-phosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei24D-ribose 5-phosphateUniRule annotation1 Publication1
Active sitei81Schiff-base intermediate with D-ribose 5-phosphateUniRule annotation1 Publication1
Binding sitei153D-ribose 5-phosphate; via amide nitrogenUniRule annotation1
Binding sitei165Glyceraldehyde 3-phosphateUniRule annotation1
Binding sitei214D-ribose 5-phosphate; via amide nitrogenUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Pyridoxal phosphate, Schiff base

Enzyme and pathway databases

UniPathwayiUPA00245.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal 5'-phosphate synthase subunit PdxSUniRule annotation (EC:4.3.3.6UniRule annotation)
Short name:
PLP synthase subunit PdxSUniRule annotation
Alternative name(s):
Pdx1UniRule annotation
Gene namesi
Name:pdxSUniRule annotation
Ordered Locus Names:GK0011
OrganismiGeobacillus kaustophilus (strain HTA426)
Taxonomic identifieri235909 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus
Proteomesi
  • UP000001172 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001093951 – 294Pyridoxal 5'-phosphate synthase subunit PdxSAdd BLAST294

Interactioni

Subunit structurei

Homohexamer and homododecamer. In the presence of PdxT, forms a dodecamer of heterodimers.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi235909.GK0011.

Structurei

Secondary structure

1294
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi7 – 14Combined sources8
Turni16 – 19Combined sources4
Beta strandi20 – 27Combined sources8
Helixi28 – 37Combined sources10
Beta strandi40 – 44Combined sources5
Helixi49 – 55Combined sources7
Helixi64 – 73Combined sources10
Beta strandi78 – 83Combined sources6
Helixi87 – 96Combined sources10
Beta strandi99 – 104Combined sources6
Helixi118 – 120Combined sources3
Beta strandi125 – 131Combined sources7
Helixi132 – 140Combined sources9
Beta strandi144 – 148Combined sources5
Beta strandi151 – 154Combined sources4
Helixi158 – 176Combined sources19
Helixi179 – 181Combined sources3
Helixi182 – 189Combined sources8
Helixi193 – 202Combined sources10
Beta strandi206 – 214Combined sources9
Helixi218 – 226Combined sources9
Beta strandi230 – 234Combined sources5
Helixi236 – 240Combined sources5
Helixi244 – 256Combined sources13
Turni257 – 259Combined sources3
Helixi261 – 267Combined sources7
Turni268 – 270Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZNNX-ray2.20A/B/C/D/E/F1-294[»]
4WXYX-ray2.70A/C/E/G/I/K1-294[»]
4WXZX-ray2.70A/B/C/D/E/F1-294[»]
4WY0X-ray2.30A/B/C/D/E/F/G/H/I/J/K/L1-294[»]
ProteinModelPortaliQ5L3Y2.
SMRiQ5L3Y2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5L3Y2.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni235 – 236D-ribose 5-phosphate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the PdxS/SNZ family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CD9. Bacteria.
COG0214. LUCA.
HOGENOMiHOG000227586.
KOiK06215.
OMAiKVRIGHV.
OrthoDBiPOG091H0A28.

Family and domain databases

CDDicd04727. pdxS. 1 hit.
Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR001852. PdxS/SNZ.
IPR033755. PdxS/SNZ_N.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF01680. SOR_SNZ. 1 hit.
[Graphical view]
PIRSFiPIRSF029271. Pdx1. 1 hit.
SUPFAMiSSF51366. SSF51366. 1 hit.
TIGRFAMsiTIGR00343. TIGR00343. 1 hit.
PROSITEiPS01235. PDXS_SNZ_1. 1 hit.
PS51129. PDXS_SNZ_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5L3Y2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALTGTDRVK RGMAEMQKGG VIMDVVNAEQ AKIAEAAGAV AVMALERVPA
60 70 80 90 100
DIRAAGGVAR MADPTVIEEV MNAVSIPVMA KVRIGHYVEA RVLEALGVDY
110 120 130 140 150
IDESEVLTPA DEEFHIDKRQ FTVPFVCGCR DLGEAARRIA EGASMLRTKG
160 170 180 190 200
EPGTGNIVEA VRHMRKVNAQ IRKVVNMSED ELVAEAKQLG APVEVLREIK
210 220 230 240 250
RLGRLPVVNF AAGGVATPAD AALMMHLGAD GVFVGSGIFK SENPEKYARA
260 270 280 290
IVEATTHYED YELIAHLSKG LGGAMRGIDI ATLLPEHRMQ ERGW
Length:294
Mass (Da):31,652
Last modified:February 1, 2005 - v1
Checksum:i3427A52A7DE63F50
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000043 Genomic DNA. Translation: BAD74296.1.
RefSeqiWP_011229527.1. NC_006510.1.

Genome annotation databases

EnsemblBacteriaiBAD74296; BAD74296; GK0011.
GeneIDi3185318.
KEGGigka:GK0011.
PATRICi21961027. VBIGeoKau81518_0056.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000043 Genomic DNA. Translation: BAD74296.1.
RefSeqiWP_011229527.1. NC_006510.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZNNX-ray2.20A/B/C/D/E/F1-294[»]
4WXYX-ray2.70A/C/E/G/I/K1-294[»]
4WXZX-ray2.70A/B/C/D/E/F1-294[»]
4WY0X-ray2.30A/B/C/D/E/F/G/H/I/J/K/L1-294[»]
ProteinModelPortaliQ5L3Y2.
SMRiQ5L3Y2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi235909.GK0011.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD74296; BAD74296; GK0011.
GeneIDi3185318.
KEGGigka:GK0011.
PATRICi21961027. VBIGeoKau81518_0056.

Phylogenomic databases

eggNOGiENOG4105CD9. Bacteria.
COG0214. LUCA.
HOGENOMiHOG000227586.
KOiK06215.
OMAiKVRIGHV.
OrthoDBiPOG091H0A28.

Enzyme and pathway databases

UniPathwayiUPA00245.

Miscellaneous databases

EvolutionaryTraceiQ5L3Y2.

Family and domain databases

CDDicd04727. pdxS. 1 hit.
Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR001852. PdxS/SNZ.
IPR033755. PdxS/SNZ_N.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF01680. SOR_SNZ. 1 hit.
[Graphical view]
PIRSFiPIRSF029271. Pdx1. 1 hit.
SUPFAMiSSF51366. SSF51366. 1 hit.
TIGRFAMsiTIGR00343. TIGR00343. 1 hit.
PROSITEiPS01235. PDXS_SNZ_1. 1 hit.
PS51129. PDXS_SNZ_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDXS_GEOKA
AccessioniPrimary (citable) accession number: Q5L3Y2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: February 1, 2005
Last modified: November 30, 2016
This is version 85 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.