EzCatDB: D00845
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DB codeD00845
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.1.1.1.25
CSA1nvt

CATH domainRelated DB codes (homologues)
3.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1D00458,D00032,D00033,D00035,D00605,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,D00605,D00615,D00857,D00858,M00161,M00171,M00210,T00002,T00010,T00011,T00015,T00227,T00247,T00408,T00414,D00827,D00262,D00274,D00275,M00035,T00109

Enzyme Name
UniProtKBKEGG

Q58484O67049P15770P43876Q5HNV1Q5KWX7Q5SJF8
Protein nameShikimate dehydrogenaseShikimate dehydrogenaseShikimate dehydrogenaseShikimate dehydrogenaseShikimate dehydrogenase
Shikimate dehydrogenaseShikimate dehydrogenase
Dehydroshikimic reductase
Shikimate oxidoreductase
Shikimate:NADP+ oxidoreductase
5-Dehydroshikimate reductase
Shikimate 5-dehydrogenase
5-Dehydroshikimic reductase
DHS reductase
Shikimate:NADP+ 5-oxidoreductase
AroE
SynonymsEC 1.1.1.25
EC 1.1.1.25
EC 1.1.1.25
EC 1.1.1.25
EC 1.1.1.25
Shikimate 5-dehydrogenase
EC 1.1.1.25
EC 1.1.1.25
RefSeqNP_248077.1 (Protein)
NC_000909.1 (DNA/RNA sequence)
NP_213611.1 (Protein)
NC_000918.1 (DNA/RNA sequence)
NP_417740.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492151.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_438815.1 (Protein)
NC_000907.1 (DNA/RNA sequence)
YP_188739.1 (Protein)
NC_002976.3 (DNA/RNA sequence)
YP_148377.1 (Protein)
NC_006510.1 (DNA/RNA sequence)
YP_144316.1 (Protein)
NC_006461.1 (DNA/RNA sequence)
PfamPF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical view]
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical view]
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical view]
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical view]
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical view]
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical view]
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00400Phenylalanine, tyrosine and tryptophan biosynthesis

UniProtKB:Accession NumberQ58484O67049P15770P43876Q5HNV1Q5KWX7Q5SJF8
Entry nameAROE_METJAAROE_AQUAEAROE_ECOLIAROE_HAEINAROE_STAEQQ5KWX7_GEOKAAROE_THET8
ActivityShikimate + NADP+ = 3-dehydroshikimate + NADPH.Shikimate + NADP+ = 3-dehydroshikimate + NADPH.Shikimate + NADP+ = 3-dehydroshikimate + NADPH.Shikimate + NADP+ = 3-dehydroshikimate + NADPH.Shikimate + NADP+ = 3-dehydroshikimate + NADPH.Shikimate + NADP+ = 3-dehydroshikimate + NADPH.Shikimate + NADP+ = 3-dehydroshikimate + NADPH.
SubunitHomodimer.
Monomer.Monomer.


Subcellular location






Cofactor







Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00493C00006C02637C00005C00080
CompoundshikimateNADP+3-dehydroshikimateNADPHH+
Typecarbohydrate,carboxyl groupamide group,amine group,nucleotidecarbohydrate,carboxyl groupamide group,amine group,nucleotideothers
ChEBI16119
18009
30918
16474
15378
PubChem8742
5886
439774
5884
1038
             
1nvtA01UnboundUnboundUnboundUnbound 
1nvtB01UnboundUnboundUnboundUnbound 
2hk7A01UnboundUnboundUnboundUnbound 
2hk7B01UnboundUnboundUnboundUnbound 
2hk8A01UnboundUnboundUnboundUnbound 
2hk8B01UnboundUnboundUnboundUnbound 
2hk8C01UnboundUnboundUnboundUnbound 
2hk8D01UnboundUnboundUnboundUnbound 
2hk8E01UnboundUnboundUnboundUnbound 
2hk8F01UnboundUnboundUnboundUnbound 
2hk8G01UnboundUnboundUnboundUnbound 
2hk8H01UnboundUnboundUnboundUnbound 
2hk9A01Bound:SKMUnboundUnboundUnbound 
2hk9B01Bound:SKMUnboundUnboundUnbound 
2hk9C01Bound:SKMUnboundUnboundUnbound 
2hk9D01Bound:SKMUnboundUnboundUnbound 
1nytA01Analogue:DTVUnboundUnboundUnbound 
1nytB01UnboundUnboundUnboundUnbound 
1nytC01UnboundUnboundUnboundUnbound 
1nytD01UnboundUnboundUnboundUnbound 
1p74A01UnboundUnboundUnboundUnbound 
1p74B01UnboundUnboundUnboundUnbound 
1p77A01UnboundUnboundUnboundUnbound 
3donA01UnboundUnboundUnboundUnbound 
3dooA01Bound:SKMUnboundUnboundUnbound 
2eggA01UnboundUnboundUnboundUnbound 
2eggB01UnboundUnboundUnboundUnbound 
1wxdA01UnboundUnboundUnboundUnbound 
1wxdB01UnboundUnboundUnboundUnbound 
2cy0A01UnboundUnboundUnboundUnbound 
2cy0B01UnboundUnboundUnboundUnbound 
2d5cA01Bound:SKMUnboundUnboundUnbound 
2d5cB01Bound:SKMUnboundUnboundUnbound 
2ev9A01Bound:SKMUnboundUnboundUnbound 
2ev9B01Bound:SKMUnboundUnboundUnbound 
1nvtA02UnboundBound:NAPUnboundUnbound 
1nvtB02UnboundBound:NAPUnboundUnbound 
2hk7A02UnboundUnboundUnboundUnbound 
2hk7B02UnboundUnboundUnboundUnbound 
2hk8A02UnboundUnboundUnboundUnbound 
2hk8B02UnboundUnboundUnboundUnbound 
2hk8C02UnboundUnboundUnboundUnbound 
2hk8D02UnboundUnboundUnboundUnbound 
2hk8E02UnboundUnboundUnboundUnbound 
2hk8F02UnboundUnboundUnboundUnbound 
2hk8G02UnboundUnboundUnboundUnbound 
2hk8H02UnboundUnboundUnboundUnbound 
2hk9A02UnboundAnalogue:ATRUnboundUnbound 
2hk9B02UnboundBound:NAPUnboundUnbound 
2hk9C02UnboundBound:NAPUnboundUnbound 
2hk9D02UnboundBound:NAPUnboundUnbound 
1nytA02UnboundBound:NAPUnboundUnbound 
1nytB02UnboundBound:NAPUnboundUnbound 
1nytC02UnboundBound:NAPUnboundUnbound 
1nytD02UnboundBound:NAPUnboundUnbound 
1p74A02UnboundUnboundUnboundUnbound 
1p74B02UnboundUnboundUnboundUnbound 
1p77A02UnboundAnalogue:ATRUnboundUnbound 
3donA02UnboundUnboundUnboundUnbound 
3dooA02UnboundUnboundUnboundUnbound 
2eggA02UnboundUnboundUnboundUnbound 
2eggB02UnboundUnboundUnboundUnbound 
1wxdA02UnboundUnboundUnboundUnbound 
1wxdB02UnboundUnboundUnboundUnbound 
2cy0A02UnboundBound:NAPUnboundUnbound 
2cy0B02UnboundUnboundUnboundUnbound 
2d5cA02UnboundUnboundUnboundUnbound 
2d5cB02UnboundUnboundUnboundUnbound 
2ev9A02UnboundBound:NAPUnboundUnbound 
2ev9B02UnboundUnboundUnboundUnbound 

Active-site residues
resource
literature [3], [5], [6], [8], [9], [10], [13]
pdbCatalytic residues
         
1nvtA01LYS  75;ASP 111
1nvtB01LYS  75;ASP 111
2hk7A01LYS  70;ASP 106
2hk7B01LYS  70;ASP 106
2hk8A01LYS  70;ASP 106
2hk8B01LYS  70;ASP 106
2hk8C01LYS  70;ASP 106
2hk8D01LYS  70;ASP 106
2hk8E01LYS  70;ASP 106
2hk8F01LYS  70;ASP 106
2hk8G01LYS  70;ASP 106
2hk8H01LYS  70;ASP 106
2hk9A01LYS  70;ASP 106
2hk9B01LYS  70;ASP 106
2hk9C01LYS  70;ASP 106
2hk9D01LYS  70;ASP 106
1nytA01LYS  65;ASP 102
1nytB01LYS  65;ASP 102
1nytC01LYS  65;ASP 102
1nytD01LYS  65;ASP 102
1p74A01LYS  65;ASP 102
1p74B01LYS  65;ASP 102
1p77A01LYS  65;ASP 102
3donA01LYS  64;ASP 100
3dooA01LYS  64;ASP 100
2eggA01LYS  87;ASP 123
2eggB01LYS  87;ASP 123
1wxdA01LYS  64;ASP 100
1wxdB01LYS  64;ASP 100
2cy0A01LYS  64;ASP 100
2cy0B01LYS  64;ASP 100
2d5cA01LYS  64;ASP 100
2d5cB01LYS  64;ASP 100
2ev9A01LYS  64;ASP 100
2ev9B01LYS  64;ASP 100
1nvtA02               
1nvtB02               
2hk7A02               
2hk7B02               
2hk8A02               
2hk8B02               
2hk8C02               
2hk8D02               
2hk8E02               
2hk8F02               
2hk8G02               
2hk8H02               
2hk9A02               
2hk9B02               
2hk9C02               
2hk9D02               
1nytA02               
1nytB02               
1nytC02               
1nytD02               
1p74A02               
1p74B02               
1p77A02               
3donA02               
3dooA02               
2eggA02               
2eggB02               
1wxdA02               
1wxdB02               
2cy0A02               
2cy0B02               
2d5cA02               
2d5cB02               
2ev9A02               
2ev9B02               

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.19470-19471
[5]Fig.5, p.7168-7169
[6]p.17105-17107
[8]p.7791-7794
[9]Fig.4, p.9519-9521
[10]Fig.8, p.432-435
[13]p.4-6
[14]Fig.4, p.1130-1132, p.1136

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 AroE.
According to the literature [10], this enzyme catalyzes the following reversible reactions:
(A) Hydride transfer from C5 of shikimate to nicotinamide of NADP+; Oxidation or dehydrogenation:
(A0) Asp100 (of 2ev9) modulates the activity of Lys64 by its negative charge.
(A1) Lys64 acts as a general base to deprotonate 5-hydoxyl group, whereas hydride transfer from C5 of shikimate to C4 of NADP+ occurs.
(B) Hydride transfer from nicotinamide of NADPH to C5 of dehydroshikimate; Reduction:
(B0) Asp100 (of 2ev9) modulates the activity of Lys64 by its negative charge.
(B1) Lys64 acts as a general acid to protonate 5-carbonyl group, whereas hydride transfer from C4 of NADPH to C5 of dehydroshikimate occurs.

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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