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Protein

Pyridoxal 5'-phosphate synthase subunit PdxS

Gene

pdxS

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 4 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 sitei30D-ribose 5-phosphateUniRule annotation1 Publication1
Active sitei87Schiff-base intermediate with D-ribose 5-phosphateUniRule annotation1 Publication1
Binding sitei159D-ribose 5-phosphate; via amide nitrogenUniRule annotation1 Publication1
Binding sitei171Glyceraldehyde 3-phosphateUniRule annotation1
Binding sitei257D-ribose 5-phosphate; via amide nitrogenUniRule annotation1 Publication1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Pyridoxal phosphate, Schiff base

Enzyme and pathway databases

BRENDAi4.3.3.6. 5244.
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:PH1355
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001094451 – 335Pyridoxal 5'-phosphate synthase subunit PdxSAdd BLAST335

Interactioni

Subunit structurei

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

Protein-protein interaction databases

IntActiO59080. 1 interactor.
MINTiMINT-1501312.
STRINGi70601.PH1355.

Structurei

Secondary structure

1335
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 21Combined sources19
Turni22 – 25Combined sources4
Beta strandi26 – 33Combined sources8
Helixi34 – 43Combined sources10
Beta strandi46 – 50Combined sources5
Helixi55 – 60Combined sources6
Helixi70 – 77Combined sources8
Beta strandi84 – 89Combined sources6
Helixi93 – 102Combined sources10
Beta strandi105 – 113Combined sources9
Helixi124 – 126Combined sources3
Beta strandi131 – 137Combined sources7
Helixi138 – 147Combined sources10
Beta strandi150 – 154Combined sources5
Helixi164 – 181Combined sources18
Helixi185 – 195Combined sources11
Helixi197 – 200Combined sources4
Helixi201 – 209Combined sources9
Beta strandi221 – 223Combined sources3
Helixi228 – 245Combined sources18
Beta strandi249 – 254Combined sources6
Helixi261 – 269Combined sources9
Beta strandi273 – 277Combined sources5
Helixi279 – 282Combined sources4
Beta strandi283 – 285Combined sources3
Helixi287 – 299Combined sources13
Turni300 – 302Combined sources3
Helixi304 – 312Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4FIQX-ray2.70A/B/C/D/E/F1-335[»]
4FIRX-ray3.10A/B/C/D/E/F1-335[»]
ProteinModelPortaliO59080.
SMRiO59080.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni278 – 279D-ribose 5-phosphate bindingUniRule annotation1 Publication2

Sequence similaritiesi

Belongs to the PdxS/SNZ family.UniRule annotation

Phylogenomic databases

eggNOGiarCOG04075. Archaea.
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. 2 hits.
TIGRFAMsiTIGR00343. TIGR00343. 1 hit.
PROSITEiPS01235. PDXS_SNZ_1. 1 hit.
PS51129. PDXS_SNZ_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O59080-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDKLKIIMEK GTERLKRGFA KMVKGGVIMD VTNAEQARIA EEAGAVAVMA
60 70 80 90 100
LHKVPADIRK AGGVARMAPV EKIQEIMDAV TIPVMAKCRI GHEAEARILE
110 120 130 140 150
ALGVDMIDES EVLTPADPFF HIYKKKFTAP FVCGARNLGE AVRRIWEGAA
160 170 180 190 200
MIRTKGEAGT GNIIEAVRHV RLVNENIRLI QRMTDEEIYG VAEKFAEPYL
210 220 230 240 250
RLAFSVKEIS GLPKRVLENE PIYEGFTYRE IVEDIYKILL EIKKLGRLPV
260 270 280 290 300
VNFAAGGVAT PADAALMMAM GMDGVFVGSG IFKSSNPPKM ARAIVEAVNH
310 320 330
WDEPDVLAEI SREIGEPMRG QAIEELQVRM EERGI
Length:335
Mass (Da):37,014
Last modified:August 1, 1998 - v1
Checksum:iD5E178BB654E5196
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30461.1.
PIRiE71007.
RefSeqiWP_010885443.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA30461; BAA30461; BAA30461.
GeneIDi1443680.
KEGGipho:PH1355.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30461.1.
PIRiE71007.
RefSeqiWP_010885443.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4FIQX-ray2.70A/B/C/D/E/F1-335[»]
4FIRX-ray3.10A/B/C/D/E/F1-335[»]
ProteinModelPortaliO59080.
SMRiO59080.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO59080. 1 interactor.
MINTiMINT-1501312.
STRINGi70601.PH1355.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA30461; BAA30461; BAA30461.
GeneIDi1443680.
KEGGipho:PH1355.

Phylogenomic databases

eggNOGiarCOG04075. Archaea.
COG0214. LUCA.
HOGENOMiHOG000227586.
KOiK06215.
OMAiKVRIGHV.

Enzyme and pathway databases

UniPathwayiUPA00245.
BRENDAi4.3.3.6. 5244.

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. 2 hits.
TIGRFAMsiTIGR00343. TIGR00343. 1 hit.
PROSITEiPS01235. PDXS_SNZ_1. 1 hit.
PS51129. PDXS_SNZ_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDXS_PYRHO
AccessioniPrimary (citable) accession number: O59080
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 13, 2004
Last sequence update: August 1, 1998
Last modified: November 30, 2016
This is version 102 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

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.