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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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei24 – 241D-ribose 5-phosphateUniRule annotation1 Publication
Active sitei81 – 811Schiff-base intermediate with D-ribose 5-phosphateUniRule annotation1 Publication
Binding sitei153 – 1531D-ribose 5-phosphate; via amide nitrogenUniRule annotation
Binding sitei165 – 1651Glyceraldehyde 3-phosphateUniRule annotation
Binding sitei214 – 2141D-ribose 5-phosphate; via amide nitrogenUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Pyridoxal phosphate, Schiff base

Enzyme and pathway databases

BioCyciGKAU235909:GJO7-16-MONOMER.
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
ProteomesiUP000001172 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 294294Pyridoxal 5'-phosphate synthase subunit PdxSPRO_0000109395Add
BLAST

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

1
294
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 159Combined sources
Turni16 – 194Combined sources
Beta strandi20 – 278Combined sources
Helixi28 – 3710Combined sources
Beta strandi40 – 445Combined sources
Helixi49 – 557Combined sources
Helixi64 – 7310Combined sources
Beta strandi78 – 836Combined sources
Helixi87 – 9610Combined sources
Beta strandi99 – 1046Combined sources
Helixi118 – 1203Combined sources
Beta strandi125 – 1317Combined sources
Helixi132 – 1409Combined sources
Beta strandi144 – 1485Combined sources
Beta strandi151 – 1544Combined sources
Helixi158 – 17619Combined sources
Helixi179 – 1813Combined sources
Helixi182 – 1898Combined sources
Helixi193 – 20210Combined sources
Beta strandi206 – 2149Combined sources
Helixi218 – 2269Combined sources
Beta strandi230 – 2345Combined sources
Helixi236 – 2405Combined sources
Helixi244 – 25613Combined sources
Turni257 – 2593Combined sources
Helixi261 – 2677Combined sources
Turni268 – 2703Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 18-271.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5L3Y2.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni235 – 2362D-ribose 5-phosphate bindingUniRule annotation

Sequence similaritiesi

Belongs to the PdxS/SNZ family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0214.
HOGENOMiHOG000227586.
KOiK06215.
OMAiIGVDMID.
OrthoDBiEOG6W9XBJ.

Family and domain databases

Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS.
InterProiIPR013785. Aldolase_TIM.
IPR001852. PdxS/SNZ.
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.
YP_145864.1. 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.
YP_145864.1. NC_006510.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 18-271.
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

eggNOGiCOG0214.
HOGENOMiHOG000227586.
KOiK06215.
OMAiIGVDMID.
OrthoDBiEOG6W9XBJ.

Enzyme and pathway databases

UniPathwayiUPA00245.
BioCyciGKAU235909:GJO7-16-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ5L3Y2.

Family and domain databases

Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS.
InterProiIPR013785. Aldolase_TIM.
IPR001852. PdxS/SNZ.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus."
    Takami H., Takaki Y., Chee G.-J., Nishi S., Shimamura S., Suzuki H., Matsui S., Uchiyama I.
    Nucleic Acids Res. 32:6292-6303(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HTA426.
  2. "A new arrangement of (beta/alpha)8 barrels in the synthase subunit of PLP synthase."
    Zhu J., Burgner J.W., Harms E., Belitsky B.R., Smith J.L.
    J. Biol. Chem. 280:27914-27923(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SUBUNIT.

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: May 27, 2015
This is version 76 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

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.