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Protein

Pyridoxal 5'-phosphate synthase subunit PdxS

Gene

pdxS

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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 sitei23D-ribose 5-phosphateUniRule annotation1
Active sitei80Schiff-base intermediate with D-ribose 5-phosphateUniRule annotation1
Binding sitei152D-ribose 5-phosphate; via amide nitrogenUniRule annotation1
Binding sitei164Glyceraldehyde 3-phosphateUniRule annotation1
Binding sitei213D-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:TTHA0704
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001094251 – 293Pyridoxal 5'-phosphate synthase subunit PdxSAdd BLAST293

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi300852.TTHA0704.

Structurei

Secondary structure

1293
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 8Combined sources8
Beta strandi11 – 13Combined sources3
Helixi14 – 16Combined sources3
Beta strandi19 – 26Combined sources8
Helixi27 – 36Combined sources10
Beta strandi39 – 43Combined sources5
Helixi48 – 53Combined sources6
Helixi63 – 70Combined sources8
Beta strandi77 – 82Combined sources6
Helixi86 – 94Combined sources9
Beta strandi98 – 103Combined sources6
Helixi117 – 119Combined sources3
Beta strandi124 – 130Combined sources7
Helixi131 – 139Combined sources9
Beta strandi143 – 147Combined sources5
Beta strandi151 – 153Combined sources3
Helixi157 – 175Combined sources19
Helixi178 – 180Combined sources3
Helixi181 – 188Combined sources8
Helixi192 – 201Combined sources10
Beta strandi208 – 210Combined sources3
Helixi217 – 225Combined sources9
Beta strandi229 – 233Combined sources5
Helixi235 – 239Combined sources5
Helixi243 – 255Combined sources13
Turni256 – 258Combined sources3
Helixi260 – 267Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2ZBTX-ray1.65A/B/C/D1-293[»]
ProteinModelPortaliQ5SKD9.
SMRiQ5SKD9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SKD9.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni234 – 235D-ribose 5-phosphate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the PdxS/SNZ family.UniRule annotation

Phylogenomic databases

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

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.

Q5SKD9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKGTFQIKT GFAEMFKGGV IMDVTTPEQA VIAEEAGAVA VMALERVPAD
60 70 80 90 100
IRAQGGVARM SDPKIIKEIM AAVSIPVMAK VRIGHFVEAM ILEAIGVDFI
110 120 130 140 150
DESEVLTPAD EEHHIDKWKF KVPFVCGARN LGEALRRIAE GAAMIRTKGE
160 170 180 190 200
AGTGNVVEAV RHARTMWKEI RYVQSLREDE LMAYAKEIGA PFELVKWVHD
210 220 230 240 250
HGRLPVVNFA AGGIATPADA ALMMHLGMDG VFVGSGIFKS GDPRKRARAI
260 270 280 290
VRAVAHYNDP EVLAEVSEDL GEPMVGINLD QLKEEERLAK RGW
Length:293
Mass (Da):32,026
Last modified:July 5, 2005 - v2
Checksum:i50693B1FFEDB777F
GO

Sequence cautioni

The sequence BAD70527 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD70527.1. Different initiation.
RefSeqiWP_011228134.1. NC_006461.1.
YP_143970.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD70527; BAD70527; BAD70527.
GeneIDi3169908.
KEGGittj:TTHA0704.
PATRICi23956385. VBITheThe93045_0698.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD70527.1. Different initiation.
RefSeqiWP_011228134.1. NC_006461.1.
YP_143970.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2ZBTX-ray1.65A/B/C/D1-293[»]
ProteinModelPortaliQ5SKD9.
SMRiQ5SKD9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA0704.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD70527; BAD70527; BAD70527.
GeneIDi3169908.
KEGGittj:TTHA0704.
PATRICi23956385. VBITheThe93045_0698.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00245.

Miscellaneous databases

EvolutionaryTraceiQ5SKD9.

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_THET8
AccessioniPrimary (citable) accession number: Q5SKD9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: July 5, 2005
Last modified: November 30, 2016
This is version 90 of the entry and version 2 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.