EzCatDB: D00605
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DB codeD00605
RLCP classification9.1050.439970.118 : Hydride transfer
9.5010.536170.118 : Hydride transfer
CATH domainDomain 13.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1Catalytic domain
Domain 23.40.50.720 : Rossmann fold
E.C.1.1.1.282

CATH domainRelated DB codes (homologues)
3.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1D00458,D00032,D00033,D00035,D00845,D00857,D00858,M00210,T00010,T00011,T00414
3.40.50.720 : Rossmann foldS00543,S00551,S00552,S00553,S00602,S00604,S00605,S00608,S00610,S00625,S00319,S00328,S00329,S00330,S00331,S00332,D00456,D00457,D00458,S00324,S00320,S00325,S00326,S00327,D00459,S00335,S00336,S00334,T00219,S00339,D00513,D00001,D00002,D00003,D00005,D00007,D00008,D00010,D00012,D00017,D00018,D00023,D00027,D00028,D00031,D00032,D00033,D00034,D00035,D00037,D00048,D00071,D00476,D00481,D00482,D00490,D00492,D00494,D00545,D00601,D00603,D00604,D00615,D00845,D00857,D00858,M00161,M00171,M00210,T00002,T00010,T00011,T00015,T00227,T00247,T00408,T00414,D00827,D00262,D00274,D00275,M00035,T00109

Enzyme Name
UniProtKBKEGG

P0A6D5
Protein nameQuinate/shikimate dehydrogenaseQuinate/shikimate dehydrogenase
YdiB
SynonymsEC 1.1.1.282
NAD-dependent shikimate 5-dehydrogenase 2
RefSeqNP_416207.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489954.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00400Phenylalanine, tyrosine and tryptophan biosynthesis

UniProtKB:Accession NumberP0A6D5
Entry nameYDIB_ECOLI
ActivityL-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H.,Shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H.
SubunitHomodimer.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00296C00003C00006C00493C00944C00004C00005C00080C02637
CompoundL-quinateNAD+NADP+shikimate3-dehydroquinateNADHNADPHH+3-dehydroshikimate
Typecarbohydrate,carboxyl groupamide group,amine group,nucleotideamide group,amine group,nucleotidecarbohydrate,carboxyl groupcarbohydrate,carboxyl groupamide group,amine group,nucleotideamide group,amine group,nucleotideotherscarbohydrate,carboxyl group
ChEBI17521
15846
18009
16119
17947
16908
16474
15378
30918
PubChem
5893
5886
8742
439351
439153
5884
1038
439774
                 
1npdA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound Unbound
1npdB01UnboundUnboundUnboundUnboundUnboundUnboundUnbound Unbound
1o9bA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound Unbound
1o9bB01UnboundUnboundUnboundUnboundUnboundUnboundUnbound Unbound
1vi2A01UnboundUnboundUnboundUnboundUnboundUnboundUnbound Unbound
1vi2B01UnboundUnboundUnboundUnboundUnboundUnboundUnbound Unbound
1npdA02UnboundBound:NADUnboundUnboundUnboundUnboundUnbound Unbound
1npdB02UnboundBound:NADUnboundUnboundUnboundUnboundUnbound Unbound
1o9bA02UnboundBound:NADUnboundUnboundUnboundUnboundUnbound Unbound
1o9bB02UnboundBound:NADUnboundUnboundUnboundUnboundUnbound Unbound
1vi2A02UnboundBound:NADUnboundUnboundUnboundUnboundUnbound Unbound
1vi2B02UnboundBound:NADUnboundUnboundUnboundUnboundUnbound Unbound

Active-site residues
resource
literature [2], [3], [5], [13]
pdbCatalytic residues
         
1npdA01LYS 71;ASP 107
1npdB01LYS 71;ASP 107
1o9bA01LYS 71;ASP 107
1o9bB01LYS 71;ASP 107
1vi2A01LYS 71;ASP 107
1vi2B01LYS 71;ASP 107
1npdA02 
1npdB02 
1o9bA02 
1o9bB02 
1vi2A02 
1vi2B02 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.19181
[3]p.19470-19471
[5]Fig.5, p.7168-7169
[9]Fig.4, p.9519-9521
[10]Fig.8, p.432-435
[13]p.4-6

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT.
PubMed ID12837789
JournalJ Bacteriol
Year2003
Volume185
Pages4144-51
AuthorsYe S, Von Delft F, Brooun A, Knuth MW, Swanson RV, McRee DE
TitleThe crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode.
Related PDB1p74,1p77
Related UniProtKBP43876
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH NAD, FUNCTION, SUBUNIT.
PubMed ID12624088
JournalJ Biol Chem
Year2003
Volume278
Pages19176-82
AuthorsBenach J, Lee I, Edstrom W, Kuzin AP, Chiang Y, Acton TB, Montelione GT, Hunt JF
TitleThe 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase.
Related PDB1npd
Related UniProtKBP0A6D5
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT. , X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH NAD, CATALYTIC ACTIVITY, SUBUNIT.
PubMed ID12637497
JournalJ Biol Chem
Year2003
Volume278
Pages19463-72
AuthorsMichel G, Roszak AW, Sauve V, Maclean J, Matte A, Coggins JR, Cygler M, Lapthorn AJ
TitleStructures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities.
Related PDB1nyt,1o9b
Related UniProtKBP15770,P0A6D5
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT.
PubMed ID12906831
JournalStructure
Year2003
Volume11
Pages1005-13
AuthorsPadyana AK, Burley SK
TitleCrystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution.
Related PDB1nvt
Related UniProtKBQ58484
[5]
PubMed ID15596430
JournalJ Biol Chem
Year2005
Volume280
Pages7162-9
AuthorsLindner HA, Nadeau G, Matte A, Michel G, Menard R, Cygler M
TitleSite-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), FUNCTION, MUTAGENESIS OF LYS-67 AND ASP-103, SUBUNIT.
PubMed ID15735308
JournalJ Biol Chem
Year2005
Volume280
Pages17101-8
AuthorsSingh S, Korolev S, Koroleva O, Zarembinski T, Collart F, Joachimiak A, Christendat D
TitleCrystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae.
Related PDB1npy
Related UniProtKBP44774
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 2-288 IN COMPLEX WITH NAD.
PubMed ID16021622
JournalProteins
Year2005
Volume60
Pages787-96
AuthorsBadger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ
TitleStructural analysis of a set of proteins resulting from a bacterial genomics project.
Related PDB1vi2
Related UniProtKBP0A6D5
[8]
CommentsX-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 90-603 IN COMPLEX WITH SHIKIMATE AND TARTRATE, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF SER-336; SER-338; LYS-385; ASP-423 AND TYR-550.
PubMed ID16784230
JournalBiochemistry
Year2006
Volume45
Pages7787-96
AuthorsSingh SA, Christendat D
TitleStructure of Arabidopsis dehydroquinate dehydratase-shikimate dehydrogenase and implications for metabolic channeling in the shikimate pathway.
Related PDB2gpt
Related UniProtKBQ9SQT8
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
PubMed ID17649975
JournalBiochemistry
Year2007
Volume46
Pages9513-22
AuthorsGan J, Wu Y, Prabakaran P, Gu Y, Li Y, Andrykovitch M, Liu H, Gong Y, Yan H, Ji X
TitleStructural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism.
Related PDB2hk7,2hk8,2hk9
[10]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
PubMed ID17825835
JournalJ Mol Biol
Year2007
Volume373
Pages424-38
AuthorsBagautdinov B, Kunishima N
TitleCrystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism.
Related PDB1wxd,2cy0,2d5c,2ev9
Related UniProtKBQ5SJF8
[11]
CommentsX-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS), FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, REACTION MECHANISM.
PubMed ID18566515
JournalActa Crystallogr D Biol Crystallogr
Year2008
VolumeD64
Pages803-9
AuthorsSchoepe J, Niefind K, Schomburg D
Title1.6 angstroms structure of an NAD+-dependent quinate dehydrogenase from Corynebacterium glutamicum.
Related PDB2ez3,2nlo
Related UniProtKBQ9X5C9
[12]
PubMed ID18669580
JournalMol Biol Evol
Year2008
Volume25
Pages2221-32
AuthorsSingh S, Stavrinides J, Christendat D, Guttman DS
TitleA phylogenomic analysis of the shikimate dehydrogenases reveals broadscale functional diversification and identifies one functionally distinct subclass.
[13]
PubMed ID19917104
JournalBMC Res Notes
Year2009
Volume2
Pages227
AuthorsRodrigues VS Jr, Breda A, Santos DS, Basso LA
TitleThe conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis shikimate dehydrogenase.
[14]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
PubMed ID19215302
JournalFEBS J
Year2009
Volume276
Pages1125-39
AuthorsHan C, Hu T, Wu D, Qu S, Zhou J, Ding J, Shen X, Qu D, Jiang H
TitleX-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis.
Related PDB3don,3doo
[15]
PubMed ID19043750
JournalJ Mol Model
Year2009
Volume15
Pages147-55
AuthorsBarcellos GB, Caceres RA, de Azevedo WF Jr
TitleStructural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP.

comments
This enzyme belongs to the superfamily of NAD(P)H-dependent shikimate dehydrogenase. This superfamily had been previously subdivided into four groups (1) AroE, EC=1.1.1.25, Shikimate dehydrogenases; (2) YdiB, EC=1.1.1.282, Shikimate/quinate dehydrogenases; (3) SdhL;EC=1.1.1.25, Shikimate dehydrogenase-like protein; (4) RifI, EC=1.1.1.25, Shikimate dehydrogenase (literature [12]).
This enzyme corresponds to YdiB, which is a bifunctional enzyme that can catalyze the reversible reduction to produce both quinate and shikimate.
Although this enzyme was proposed to have different catalytic mechanism from that of its homologue, AroE (D00845 in EzCatDB), according to the literature [2] and [5], it has a similar active site, suggesting that it must have the same catalytic mechanism as that of its homologue. Thus, the catalytic mechanism of this enzyme has been categorized in the same group with the homologous enzyme (D00845).

createdupdated
2010-08-262011-08-03


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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