Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei30 – 301D-ribose 5-phosphate1 PublicationUniRule annotation
Active sitei87 – 871Schiff-base intermediate with D-ribose 5-phosphate1 PublicationUniRule annotation
Binding sitei159 – 1591D-ribose 5-phosphate; via amide nitrogen1 PublicationUniRule annotation
Binding sitei171 – 1711Glyceraldehyde 3-phosphateUniRule annotation
Binding sitei257 – 2571D-ribose 5-phosphate; via amide nitrogen1 PublicationUniRule annotation

GO - Molecular functioni

  1. 2-iminoacetate synthase activity Source: InterPro

GO - Biological processi

  1. pyridoxal phosphate biosynthetic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Pyridoxal phosphate, Schiff base

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-1361-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:PH1355
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000000752: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 335335Pyridoxal 5'-phosphate synthase subunit PdxSPRO_0000109445Add
BLAST

Interactioni

Subunit structurei

Homohexamer. In the presence of PdxT, forms a dodecamer of heterodimers.1 PublicationUniRule annotation

Protein-protein interaction databases

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

Structurei

Secondary structure

1
335
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 2119Combined sources
Turni22 – 254Combined sources
Beta strandi26 – 338Combined sources
Helixi34 – 4310Combined sources
Beta strandi46 – 505Combined sources
Helixi55 – 606Combined sources
Helixi70 – 778Combined sources
Beta strandi84 – 896Combined sources
Helixi93 – 10210Combined sources
Beta strandi105 – 1139Combined sources
Helixi124 – 1263Combined sources
Beta strandi131 – 1377Combined sources
Helixi138 – 14710Combined sources
Beta strandi150 – 1545Combined sources
Helixi164 – 18118Combined sources
Helixi185 – 19511Combined sources
Helixi197 – 2004Combined sources
Helixi201 – 2099Combined sources
Beta strandi221 – 2233Combined sources
Helixi228 – 24518Combined sources
Beta strandi249 – 2546Combined sources
Helixi261 – 2699Combined sources
Beta strandi273 – 2775Combined sources
Helixi279 – 2824Combined sources
Beta strandi283 – 2853Combined sources
Helixi287 – 29913Combined sources
Turni300 – 3023Combined sources
Helixi304 – 3129Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4FIQX-ray2.70A/B/C/D/E/F1-335[»]
4FIRX-ray3.10A/B/C/D/E/F1-335[»]
ProteinModelPortaliO59080.
SMRiO59080. Positions 12-320.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni278 – 2792D-ribose 5-phosphate binding1 PublicationUniRule annotation

Sequence similaritiesi

Belongs to the PdxS/SNZ family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0214.
HOGENOMiHOG000227586.
KOiK06215.
OMAiIGVDMID.

Family and domain databases

Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS.
InterProiIPR013785. Aldolase_TIM.
IPR011060. RibuloseP-bd_barrel.
IPR001852. Snz1p/Sor1.
IPR008867. ThiG.
[Graphical view]
PfamiPF01680. SOR_SNZ. 1 hit.
PF05690. ThiG. 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.
RefSeqiNP_143237.1. NC_000961.1.
WP_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.
RefSeqiNP_143237.1. NC_000961.1.
WP_010885443.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4FIQX-ray2.70A/B/C/D/E/F1-335[»]
4FIRX-ray3.10A/B/C/D/E/F1-335[»]
ProteinModelPortaliO59080.
SMRiO59080. Positions 12-320.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG0214.
HOGENOMiHOG000227586.
KOiK06215.
OMAiIGVDMID.

Enzyme and pathway databases

UniPathwayiUPA00245.
BioCyciPHOR70601:GJWR-1361-MONOMER.

Family and domain databases

Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS.
InterProiIPR013785. Aldolase_TIM.
IPR011060. RibuloseP-bd_barrel.
IPR001852. Snz1p/Sor1.
IPR008867. ThiG.
[Graphical view]
PfamiPF01680. SOR_SNZ. 1 hit.
PF05690. ThiG. 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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
  2. "Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii."
    Matsuura A., Yoon J.Y., Yoon H.J., Lee H.H., Suh S.W.
    Mol. Cells 34:407-412(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH RIBOSE 5-PHOSPHATE, ACTIVE SITE, SUBUNIT.

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: February 4, 2015
This is version 90 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

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.