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UniProtKB - P0A6D5 (YDIB_ECOLI)
Protein
Quinate/shikimate dehydrogenase
Gene
ydiB
Organism
Escherichia coli (strain K12)
Status
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 annotation3 PublicationsCatalytic activityi
- EC:1.1.1.282UniRule annotation2 Publications
- EC:1.1.1.282UniRule annotation2 Publications
- EC:1.1.1.282UniRule annotation2 Publications
- EC:1.1.1.282UniRule annotation2 Publications
Kineticsi
kcat is 91 sec(-1) for dehydrogenase activity with shikimate (at pH 9 and 20 degrees Celsius). kcat is 113 sec(-1) for dehydrogenase activity with quinate (at pH 9 and 20 degrees Celsius). kcat is 105 sec(-1) for dehydrogenase activity with NAD (with shikinate at pH 9 and 20 degrees Celsius). kcat is 142 sec(-1) for dehydrogenase activity with NAD (with quinate at pH 9 and 20 degrees Celsius).
- KM=2.9 µM for shikimate (at pH 9 and 20 degrees Celsius)1 Publication
- KM=9.1 µM for quinate (at pH 9 and 20 degrees Celsius)1 Publication
- KM=12.2 µM for NAD (with shikimate at pH 9 and 20 degrees Celsius)1 Publication
- KM=18.4 µM for NAD (with quinate at pH 9 and 20 degrees Celsius)1 Publication
- KM=20 µM for shikimate (with NAD at pH 9 and 20 degrees Celsius)1 Publication
- KM=41 µM for quinate (with NAD at pH 9 and 20 degrees Celsius)1 Publication
- KM=87 µM for NAD (with shikimate at pH 9 and 20 degrees Celsius)1 Publication
- KM=100 µM for NADP (with shikimate at pH 9 and 20 degrees Celsius)1 Publication
- KM=116 µM for NAD (with quinate at pH 9 and 20 degrees Celsius)1 Publication
- KM=120 µM for shikimate (with NADP at pH 9 and 20 degrees Celsius)1 Publication
- KM=500 µM for NADP (with quinate at pH 9 and 20 degrees Celsius)1 Publication
- KM=555 µM for quinate (with NADP at pH 9 and 20 degrees Celsius)1 Publication
: chorismate biosynthesis Pathwayi
This protein is involved in step 4 of the subpathway that synthesizes chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate.UniRule annotation 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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 71 | SubstrateUniRule annotation | 1 | |
Binding sitei | 107 | SubstrateUniRule annotation | 1 | |
Binding sitei | 205 | NAD; via amide nitrogenUniRule annotation3 Publications | 1 | |
Binding sitei | 255 | NAD; via carbonyl oxygenUniRule annotation3 Publications | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 132 – 135 | NADUniRule annotation3 Publications | 4 | |
Nucleotide bindingi | 155 – 158 | NADUniRule annotation3 Publications | 4 | |
Nucleotide bindingi | 232 – 235 | NADUniRule annotation3 Publications | 4 |
GO - Molecular functioni
- quinate 3-dehydrogenase (NAD+) activity Source: EcoCyc
- quinate 3-dehydrogenase (NADP+) activity Source: UniProtKB-EC
- shikimate 3-dehydrogenase (NAD+) activity Source: EcoCyc
- shikimate 3-dehydrogenase (NADP+) activity Source: EcoCyc
GO - Biological processi
- aromatic amino acid family biosynthetic process Source: UniProtKB-UniRule
- cellular amino acid biosynthetic process Source: UniProtKB-KW
- chorismate biosynthetic process Source: GO_Central
- shikimate metabolic process Source: GO_Central
Keywordsi
Molecular function | Oxidoreductase |
Biological process | Amino-acid biosynthesis, Aromatic amino acid biosynthesis |
Ligand | NAD, NADP |
Enzyme and pathway databases
BioCyci | EcoCyc:EG11234-MONOMER |
BRENDAi | 1.1.1.282, 2026 |
SABIO-RKi | P0A6D5 |
UniPathwayi | UPA00053;UER00087 |
Names & Taxonomyi
Protein namesi | Recommended name: Quinate/shikimate dehydrogenase1 PublicationUniRule annotation (EC:1.1.1.282UniRule annotation2 Publications)Alternative name(s): NAD-dependent shikimate 5-dehydrogenase1 PublicationUniRule annotation |
Gene namesi | Name:ydiB1 PublicationUniRule annotation |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 22 | S → A: Kinetically unchanged as compared with the wild-type. 1 Publication | 1 | |
Mutagenesisi | 39 | Y → F: Kinetically unchanged as compared with the wild-type. 1 Publication | 1 | |
Mutagenesisi | 67 | S → A: Reduces activity towards quinate about 6-fold, but has a little effect on shikimate conversion. 1 Publication | 1 | |
Mutagenesisi | 71 | K → A: 3200-fold decrease in the affinity for quinate. 170-fold decrease in the affinity for shikimate. 1 Publication | 1 | |
Mutagenesisi | 71 | K → G: 10-fold greater reduction in catalytic efficiency is observed with quinate than with shikimate. 1 Publication | 1 | |
Mutagenesisi | 92 | N → A: Alters protein structure. Loss of activity for both substrates. 1 Publication | 1 | |
Mutagenesisi | 106 | T → A: 2000-fold decrease in the affinity for quinate. 70-fold decrease in the affinity for shikimate. 10-fold greater reduction in catalytic efficiency is observed with quinate than with shikimate. 1 Publication | 1 | |
Mutagenesisi | 107 | D → A: Loss of activity towards quinate. 20000-fold decrease in the affinity for shikimate. 1 Publication | 1 | |
Mutagenesisi | 262 | Q → A: 3-fold reduction in catalytic efficiency for both substrates. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | Removed1 Publication | |||
ChainiPRO_0000136069 | 2 – 288 | Quinate/shikimate dehydrogenaseAdd BLAST | 287 |
Proteomic databases
PaxDbi | P0A6D5 |
PRIDEi | P0A6D5 |
Expressioni
Inductioni
Induced under carbon limitation but not under phosphate limitation.1 Publication
Interactioni
Subunit structurei
Homodimer.
UniRule annotation4 PublicationsBinary interactionsi
P0A6D5
With | #Exp. | IntAct |
---|---|---|
loiP [P25894] | 2 | EBI-560638,EBI-560654 |
Protein-protein interaction databases
BioGRIDi | 4263505, 7 interactors |
DIPi | DIP-47967N |
IntActi | P0A6D5, 3 interactors |
STRINGi | 511145.b1692 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P0A6D5 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P0A6D5 |
Family & Domainsi
Sequence similaritiesi
Belongs to the shikimate dehydrogenase family.UniRule annotation
Phylogenomic databases
eggNOGi | COG0169, Bacteria |
HOGENOMi | CLU_044063_4_4_6 |
InParanoidi | P0A6D5 |
PhylomeDBi | P0A6D5 |
Family and domain databases
HAMAPi | MF_00222, Shikimate_DH_AroE, 1 hit MF_01578, Shikimate_DH_YdiB, 1 hit |
InterProi | View protein in InterPro IPR036291, NAD(P)-bd_dom_sf IPR022872, Quinate/Shikimate_DH IPR041121, SDH_C IPR013708, Shikimate_DH-bd_N IPR022893, Shikimate_DH_fam |
PANTHERi | PTHR21089, PTHR21089, 1 hit |
Pfami | View protein in Pfam PF18317, SDH_C, 1 hit PF08501, Shikimate_dh_N, 1 hit |
SUPFAMi | SSF51735, SSF51735, 1 hit |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
P0A6D5-1 [UniParc]FASTAAdd to basket
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
Sequence cautioni
The sequence CAA27848 differs from that shown. Reason: Frameshift.Curated
Mass spectrometryi
Molecular mass is 31361 Da. Determined by ESI. 1 Publication
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U00096 Genomic DNA Translation: AAC74762.1 AP009048 Genomic DNA Translation: BAA15449.1 X04306 Genomic DNA Translation: CAA27848.1 Frameshift. |
PIRi | D64927 |
RefSeqi | NP_416207.1, NC_000913.3 WP_000383469.1, NZ_SSZK01000001.1 |
Genome annotation databases
EnsemblBacteriai | AAC74762; AAC74762; b1692 BAA15449; BAA15449; BAA15449 |
GeneIDi | 946200 |
KEGGi | ecj:JW1682 eco:b1692 |
PATRICi | fig|1411691.4.peg.566 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U00096 Genomic DNA Translation: AAC74762.1 AP009048 Genomic DNA Translation: BAA15449.1 X04306 Genomic DNA Translation: CAA27848.1 Frameshift. |
PIRi | D64927 |
RefSeqi | NP_416207.1, NC_000913.3 WP_000383469.1, NZ_SSZK01000001.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1NPD | X-ray | 2.30 | A/B | 1-288 | [»] | |
1O9B | X-ray | 2.50 | A/B | 1-288 | [»] | |
1VI2 | X-ray | 2.10 | A/B | 2-288 | [»] | |
SMRi | P0A6D5 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4263505, 7 interactors |
DIPi | DIP-47967N |
IntActi | P0A6D5, 3 interactors |
STRINGi | 511145.b1692 |
Proteomic databases
PaxDbi | P0A6D5 |
PRIDEi | P0A6D5 |
Genome annotation databases
EnsemblBacteriai | AAC74762; AAC74762; b1692 BAA15449; BAA15449; BAA15449 |
GeneIDi | 946200 |
KEGGi | ecj:JW1682 eco:b1692 |
PATRICi | fig|1411691.4.peg.566 |
Organism-specific databases
EchoBASEi | EB1216 |
Phylogenomic databases
eggNOGi | COG0169, Bacteria |
HOGENOMi | CLU_044063_4_4_6 |
InParanoidi | P0A6D5 |
PhylomeDBi | P0A6D5 |
Enzyme and pathway databases
UniPathwayi | UPA00053;UER00087 |
BioCyci | EcoCyc:EG11234-MONOMER |
BRENDAi | 1.1.1.282, 2026 |
SABIO-RKi | P0A6D5 |
Miscellaneous databases
EvolutionaryTracei | P0A6D5 |
PROi | PR:P0A6D5 |
Family and domain databases
HAMAPi | MF_00222, Shikimate_DH_AroE, 1 hit MF_01578, Shikimate_DH_YdiB, 1 hit |
InterProi | View protein in InterPro IPR036291, NAD(P)-bd_dom_sf IPR022872, Quinate/Shikimate_DH IPR041121, SDH_C IPR013708, Shikimate_DH-bd_N IPR022893, Shikimate_DH_fam |
PANTHERi | PTHR21089, PTHR21089, 1 hit |
Pfami | View protein in Pfam PF18317, SDH_C, 1 hit PF08501, Shikimate_dh_N, 1 hit |
SUPFAMi | SSF51735, SSF51735, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | YDIB_ECOLI | |
Accessioni | P0A6D5Primary (citable) accession number: P0A6D5 Secondary accession number(s): P28244, P77647 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | June 7, 2005 |
Last sequence update: | June 7, 2005 | |
Last modified: | February 23, 2022 | |
This is version 134 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PATHWAY comments
Index of metabolic and biosynthesis pathways - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families