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Protein

Quinate/shikimate dehydrogenase

Gene

ydiB

Organism
Escherichia coli (strain K12 / MC4100 / BW2952)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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

Pathway:ichorismate 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. no protein annotated in this organism
  2. 3-dehydroquinate synthase (aroB)
  3. 3-dehydroquinate dehydratase (aroD)
  4. Shikimate dehydrogenase (NADP(+)) (aroE), Quinate/shikimate dehydrogenase (ydiB)
  5. Shikimate kinase 2 (aroL)
  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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei71 – 711SubstrateUniRule annotation
Binding sitei107 – 1071SubstrateUniRule annotation
Binding sitei205 – 2051NAD; via amide nitrogenUniRule annotation
Binding sitei255 – 2551NAD; via carbonyl oxygenUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi132 – 1354NADUniRule annotation
Nucleotide bindingi155 – 1584NADUniRule annotation
Nucleotide bindingi232 – 2354NADUniRule annotation

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

BioCyciECOL595496:GI18-1556-MONOMER.
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:BWG_1506
OrganismiEscherichia coli (strain K12 / MC4100 / BW2952)
Taxonomic identifieri595496 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 288288Quinate/shikimate dehydrogenasePRO_1000215614Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliC4ZYF4.
SMRiC4ZYF4. Positions 5-288.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the shikimate dehydrogenase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0169.
HOGENOMiHOG000237875.
KOiK05887.
OMAiINGMGML.
OrthoDBiEOG64R67G.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00222. Shikimate_DH_AroE.
MF_01578. Shikimate_DH_YdiB.
InterProiIPR016040. NAD(P)-bd_dom.
IPR022872. Quinate/Shikimate_DH.
IPR013708. Shikimate_DH-bd_N.
IPR022893. Shikimate_DH_fam.
IPR006151. Shikm_DH/Glu-tRNA_Rdtase.
[Graphical view]
PfamiPF01488. Shikimate_DH. 1 hit.
PF08501. Shikimate_dh_N. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

C4ZYF4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDVTAKYELI GLMAYPIRHS LSPEMQNKAL EKAGLPFTYM AFEVDNDSFP
60 70 80 90 100
GAIEGLKALK MRGTGVSMPN KQLACEYVDE LTPAAKLVGA INTIVNDDGY
110 120 130 140 150
LRGYNTDGTG HIRAIKESGF DIKGKTMVLL GAGGASTAIG AQGAIEGLKE
160 170 180 190 200
IKLFNRRDEF FDKALAFAQR VNENTDCVVT VTDLADQQAF AEALASADIL
210 220 230 240 250
TNGTKVGMKP LENESLVNDI SLLHPGLLVT ECVYNPHMTK LLQQAQQAGC
260 270 280
KTIDGYGMLL WQGAEQFTLW TGKDFPLEYV KQVMGFGA
Length:288
Mass (Da):31,228
Last modified:July 28, 2009 - v1
Checksum:iC3D1415E03820A5A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001396 Genomic DNA. Translation: ACR65393.1.
RefSeqiWP_000383469.1. NC_012759.1.

Genome annotation databases

EnsemblBacteriaiACR65393; ACR65393; BWG_1506.
KEGGiebw:BWG_1506.
PATRICi18272239. VBIEscCol60876_1652.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001396 Genomic DNA. Translation: ACR65393.1.
RefSeqiWP_000383469.1. NC_012759.1.

3D structure databases

ProteinModelPortaliC4ZYF4.
SMRiC4ZYF4. Positions 5-288.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACR65393; ACR65393; BWG_1506.
KEGGiebw:BWG_1506.
PATRICi18272239. VBIEscCol60876_1652.

Phylogenomic databases

eggNOGiCOG0169.
HOGENOMiHOG000237875.
KOiK05887.
OMAiINGMGML.
OrthoDBiEOG64R67G.

Enzyme and pathway databases

UniPathwayiUPA00053; UER00087.
BioCyciECOL595496:GI18-1556-MONOMER.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00222. Shikimate_DH_AroE.
MF_01578. Shikimate_DH_YdiB.
InterProiIPR016040. NAD(P)-bd_dom.
IPR022872. Quinate/Shikimate_DH.
IPR013708. Shikimate_DH-bd_N.
IPR022893. Shikimate_DH_fam.
IPR006151. Shikm_DH/Glu-tRNA_Rdtase.
[Graphical view]
PfamiPF01488. Shikimate_DH. 1 hit.
PF08501. Shikimate_dh_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12."
    Ferenci T., Zhou Z., Betteridge T., Ren Y., Liu Y., Feng L., Reeves P.R., Wang L.
    J. Bacteriol. 191:4025-4029(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MC4100 / BW2952.

Entry informationi

Entry nameiYDIB_ECOBW
AccessioniPrimary (citable) accession number: C4ZYF4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 28, 2009
Last modified: July 22, 2015
This is version 43 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.