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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei23 – 231D-ribose 5-phosphateUniRule annotation
Active sitei80 – 801Schiff-base intermediate with D-ribose 5-phosphateUniRule annotation
Binding sitei152 – 1521D-ribose 5-phosphate; via amide nitrogenUniRule annotation
Binding sitei164 – 1641Glyceraldehyde 3-phosphateUniRule annotation
Binding sitei213 – 2131D-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

BioCyciTTHE300852:GH8R-734-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: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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 293293Pyridoxal 5'-phosphate synthase subunit PdxSPRO_0000109425Add
BLAST

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi300852.TTHA0704.

Structurei

Secondary structure

293
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 88Combined sources
Beta strandi11 – 133Combined sources
Helixi14 – 163Combined sources
Beta strandi19 – 268Combined sources
Helixi27 – 3610Combined sources
Beta strandi39 – 435Combined sources
Helixi48 – 536Combined sources
Helixi63 – 708Combined sources
Beta strandi77 – 826Combined sources
Helixi86 – 949Combined sources
Beta strandi98 – 1036Combined sources
Helixi117 – 1193Combined sources
Beta strandi124 – 1307Combined sources
Helixi131 – 1399Combined sources
Beta strandi143 – 1475Combined sources
Beta strandi151 – 1533Combined sources
Helixi157 – 17519Combined sources
Helixi178 – 1803Combined sources
Helixi181 – 1888Combined sources
Helixi192 – 20110Combined sources
Beta strandi208 – 2103Combined sources
Helixi217 – 2259Combined sources
Beta strandi229 – 2335Combined sources
Helixi235 – 2395Combined sources
Helixi243 – 25513Combined sources
Turni256 – 2583Combined sources
Helixi260 – 2678Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ZBTX-ray1.65A/B/C/D1-293[»]
ProteinModelPortaliQ5SKD9.
SMRiQ5SKD9. Positions 1-274.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SKD9.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni234 – 2352D-ribose 5-phosphate bindingUniRule annotation

Sequence similaritiesi

Belongs to the PdxS/SNZ family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CD9. Bacteria.
COG0214. LUCA.
HOGENOMiHOG000227586.
KOiK06215.
OMAiMVGINES.
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.

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 BAD70527.1 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
EntryMethodResolution (Å)ChainPositionsPDBsum
2ZBTX-ray1.65A/B/C/D1-293[»]
ProteinModelPortaliQ5SKD9.
SMRiQ5SKD9. Positions 1-274.
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.
OMAiMVGINES.
OrthoDBiEOG6W9XBJ.

Enzyme and pathway databases

UniPathwayiUPA00245.
BioCyciTTHE300852:GH8R-734-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ5SKD9.

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. "Complete genome sequence of Thermus thermophilus HB8."
    Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HB8 / ATCC 27634 / DSM 579.
  2. "Crystal structure of pyridoxine biosynthesis protein from Thermus thermophilus HB8."
    Manzoku M., Ebihara A., Fujimoto Y., Yokoyama S., Kuramitsu S.
    Submitted (OCT-2007) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS).

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: March 16, 2016
This is version 85 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.