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

Quinate/shikimate dehydrogenase

Gene

ydiB

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

The actual biological function of YdiB remains unclear, nor is it known whether 3-dehydroshikimate or quinate represents the natural substrate. Catalyzes the reversible NAD-dependent reduction of both 3-dehydroshikimate (DHSA) and 3-dehydroquinate to yield shikimate (SA) and quinate, respectively. It can use both NAD or NADP for catalysis, however it has higher catalytic efficiency with NAD.UniRule annotation

Catalytic activityi

L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H.UniRule annotation
Shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H.UniRule annotation

Pathwayi: chorismate biosynthesis

This protein is involved in step 4 of the subpathway that synthesizes chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate.UniRule annotation
Proteins known to be involved in the 7 steps of the subpathway in this organism are:
  1. Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive (aroF), Phospho-2-dehydro-3-deoxyheptonate aldolase, Trp-sensitive (aroH), Phospho-2-dehydro-3-deoxyheptonate aldolase (aroG)
  2. 3-dehydroquinate synthase (aroB)
  3. 3-dehydroquinate dehydratase (aroD)
  4. Quinate/shikimate dehydrogenase (ydiB), Shikimate dehydrogenase (NADP(+)) (aroE)
  5. Shikimate kinase 2 (aroL), Shikimate kinase 1 (aroK)
  6. 3-phosphoshikimate 1-carboxyvinyltransferase (aroA)
  7. Chorismate synthase (aroC)
This subpathway is part of the pathway chorismate biosynthesis, which is itself part of Metabolic intermediate biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate, the pathway chorismate biosynthesis and in Metabolic intermediate biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei71SubstrateUniRule annotation1
Binding sitei107SubstrateUniRule annotation1
Binding sitei205NAD; via amide nitrogenUniRule annotation1 Publication1
Binding sitei255NAD; via carbonyl oxygenUniRule annotation1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi132 – 135NADUniRule annotation1 Publication4
Nucleotide bindingi155 – 158NADUniRule annotation1 Publication4
Nucleotide bindingi232 – 235NADUniRule annotation1 Publication4

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Aromatic amino acid biosynthesis

Keywords - Ligandi

NAD, NADP

Enzyme and pathway databases

UniPathwayiUPA00053; UER00087.

Names & Taxonomyi

Protein namesi
Recommended name:
Quinate/shikimate dehydrogenaseUniRule annotation (EC:1.1.1.282UniRule annotation)
Alternative name(s):
NAD-dependent shikimate 5-dehydrogenaseUniRule annotation
Gene namesi
Name:ydiBUniRule annotation
Ordered Locus Names:STM1359
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001360721 – 288Quinate/shikimate dehydrogenaseAdd BLAST288

Proteomic databases

PaxDbiQ8ZPR4.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi99287.STM1359.

Structurei

Secondary structure

1288
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 15Combined sources8
Helixi22 – 33Combined sources12
Beta strandi36 – 43Combined sources8
Turni46 – 48Combined sources3
Helixi49 – 58Combined sources10
Beta strandi63 – 66Combined sources4
Helixi71 – 74Combined sources4
Helixi75 – 77Combined sources3
Beta strandi79 – 81Combined sources3
Helixi83 – 88Combined sources6
Beta strandi92 – 97Combined sources6
Beta strandi100 – 104Combined sources5
Helixi106 – 117Combined sources12
Beta strandi126 – 130Combined sources5
Helixi134 – 145Combined sources12
Beta strandi149 – 155Combined sources7
Helixi160 – 174Combined sources15
Beta strandi178 – 183Combined sources6
Helixi187 – 196Combined sources10
Beta strandi198 – 202Combined sources5
Helixi220 – 222Combined sources3
Beta strandi228 – 231Combined sources4
Beta strandi235 – 238Combined sources4
Helixi240 – 247Combined sources8
Beta strandi251 – 253Combined sources3
Helixi255 – 271Combined sources17
Helixi277 – 283Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3T4EX-ray1.95A/B1-288[»]
ProteinModelPortaliQ8ZPR4.
SMRiQ8ZPR4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the shikimate dehydrogenase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E2X. Bacteria.
COG0169. LUCA.
HOGENOMiHOG000237875.
KOiK05887.
OMAiPFIHNSA.
PhylomeDBiQ8ZPR4.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00222. Shikimate_DH_AroE. 1 hit.
MF_01578. Shikimate_DH_YdiB. 1 hit.
InterProiIPR016040. NAD(P)-bd_dom.
IPR022872. Quinate/Shikimate_DH.
IPR013708. Shikimate_DH-bd_N.
IPR022893. Shikimate_DH_fam.
[Graphical view]
PfamiPF08501. Shikimate_dh_N. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.

Sequencei

Sequence statusi: Complete.

Q8ZPR4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDVTAKYELI GLMAYPIRHS LSPEMQNKAL EKAGLPYTYM AFEVDNTTFA
60 70 80 90 100
SAIEGLKALK MRGTGVSMPN KQLACEYVDE LTPAAKLVGA INTIVNDDGY
110 120 130 140 150
LRGYNTDGTG HIRAIKESGF DMRGKTMVLL GAGGAATAIG AQAAIEGIKE
160 170 180 190 200
IKLFNRKDDF FEKAVAFAKR VNENTDCVVT VTDLADQHAF TEALASADIL
210 220 230 240 250
TNGTKVGMKP LENESLIGDV SLLRPELLVT ECVYNPHMTK LLQQAQQAGC
260 270 280
KTIDGYGMLL WQGAEQFELW TGKAFPLDYV KQVMGFTA
Length:288
Mass (Da):31,337
Last modified:March 1, 2002 - v1
Checksum:i42984154DE6BB962
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL20284.1.
RefSeqiNP_460325.1. NC_003197.1.
WP_000383490.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL20284; AAL20284; STM1359.
GeneIDi1252877.
KEGGistm:STM1359.
PATRICi32381201. VBISalEnt20916_1443.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL20284.1.
RefSeqiNP_460325.1. NC_003197.1.
WP_000383490.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3T4EX-ray1.95A/B1-288[»]
ProteinModelPortaliQ8ZPR4.
SMRiQ8ZPR4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM1359.

Proteomic databases

PaxDbiQ8ZPR4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL20284; AAL20284; STM1359.
GeneIDi1252877.
KEGGistm:STM1359.
PATRICi32381201. VBISalEnt20916_1443.

Phylogenomic databases

eggNOGiENOG4105E2X. Bacteria.
COG0169. LUCA.
HOGENOMiHOG000237875.
KOiK05887.
OMAiPFIHNSA.
PhylomeDBiQ8ZPR4.

Enzyme and pathway databases

UniPathwayiUPA00053; UER00087.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00222. Shikimate_DH_AroE. 1 hit.
MF_01578. Shikimate_DH_YdiB. 1 hit.
InterProiIPR016040. NAD(P)-bd_dom.
IPR022872. Quinate/Shikimate_DH.
IPR013708. Shikimate_DH-bd_N.
IPR022893. Shikimate_DH_fam.
[Graphical view]
PfamiPF08501. Shikimate_dh_N. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiYDIB_SALTY
AccessioniPrimary (citable) accession number: Q8ZPR4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 19, 2002
Last sequence update: March 1, 2002
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, 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.