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Protein

Pyridoxal 5'-phosphate synthase subunit PdxS

Gene

pdxS

Organism
Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei24 – 241D-ribose 5-phosphateUniRule annotation
Active sitei81 – 811Schiff-base intermediate with D-ribose 5-phosphateUniRule annotation
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

BioCyciBLIC279010:GJ2P-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:BLi00016, BL02353
OrganismiBacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46)
Taxonomic identifieri279010 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000000606 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 294294Pyridoxal 5'-phosphate synthase subunit PdxSPRO_0000109381Add
BLAST

Interactioni

Subunit structurei

In the presence of PdxT, forms a dodecamer of heterodimers.UniRule annotation

Protein-protein interaction databases

STRINGi279010.BLi00016.

Structurei

3D structure databases

ProteinModelPortaliQ65PL2.
SMRiQ65PL2. Positions 2-272.
ModBaseiSearch...
MobiDBiSearch...

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

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

Family and domain databases

Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS. 1 hit.
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.

Q65PL2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQTGTDRVK RGMAEMQKGG VIMDVVNAEQ AKIAEEAGAV AVMALERVPA
60 70 80 90 100
DIRAAGGVAR MADPTIVEEV MNAVSIPVMA KARIGHIVEA RVLEALGVDY
110 120 130 140 150
IDESEVLTPA DEEFHLNKNE FTVPFVCGCR DLGEATRRIA EGASMLRTKG
160 170 180 190 200
EPGTGNIVEA VRHMRKVNAQ VRKVVGMSDD ELMTEAKNLG APYELLKEIK
210 220 230 240 250
AEGRLPVVNF AAGGVATPAD AALMMQLGAD GVFVGSGIFK SDNPAKFAKA
260 270 280 290
IVEATTHFTD YKLIAELSKE LGTAMKGIEI SNLLPEQRMQ ERGW
Length:294
Mass (Da):31,522
Last modified:October 25, 2004 - v1
Checksum:i8266E6714FBCA79D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017333 Genomic DNA. Translation: AAU39002.1.
CP000002 Genomic DNA. Translation: AAU21655.1.
RefSeqiWP_003178108.1. NC_006322.1.

Genome annotation databases

EnsemblBacteriaiAAU21655; AAU21655; BL02353.
AAU39002; AAU39002; BLi00016.
GeneIDi3028791.
KEGGibld:BLi00016.
bli:BL02353.
PATRICi18945503. VBIBacLic203714_0011.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017333 Genomic DNA. Translation: AAU39002.1.
CP000002 Genomic DNA. Translation: AAU21655.1.
RefSeqiWP_003178108.1. NC_006322.1.

3D structure databases

ProteinModelPortaliQ65PL2.
SMRiQ65PL2. Positions 2-272.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi279010.BLi00016.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAU21655; AAU21655; BL02353.
AAU39002; AAU39002; BLi00016.
GeneIDi3028791.
KEGGibld:BLi00016.
bli:BL02353.
PATRICi18945503. VBIBacLic203714_0011.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00245.
BioCyciBLIC279010:GJ2P-16-MONOMER.

Family and domain databases

Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS. 1 hit.
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...

Entry informationi

Entry nameiPDXS_BACLD
AccessioniPrimary (citable) accession number: Q65PL2
Secondary accession number(s): Q630A3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: October 25, 2004
Last modified: September 7, 2016
This is version 89 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.