DB code: D00605

RLCP classification 9.1050.439970.118 : Hydride transfer
9.5010.536170.118 : Hydride transfer
CATH domain 3.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1 Catalytic domain
3.40.50.720 : Rossmann fold
E.C. 1.1.1.282
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1 D00458 D00032 D00033 D00035 D00845 D00857 D00858 M00210 T00010 T00011 T00414
3.40.50.720 : Rossmann fold S00543 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0A6D5 Quinate/shikimate dehydrogenase
EC 1.1.1.282
NAD-dependent shikimate 5-dehydrogenase 2
NP_416207.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489954.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical View]

KEGG enzyme name
Quinate/shikimate dehydrogenase
YdiB

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0A6D5 YDIB_ECOLI L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H. Shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H. Homodimer.

KEGG Pathways
Map code Pathways E.C.
MAP00400 Phenylalanine, tyrosine and tryptophan biosynthesis

Compound table
Substrates Products Intermediates
KEGG-id C00296 C00003 C00006 C00493 C00944 C00004 C00005 C00080 C02637
E.C.
Compound L-quinate NAD+ NADP+ shikimate 3-dehydroquinate NADH NADPH H+ 3-dehydroshikimate
Type carbohydrate,carboxyl group amide group,amine group,nucleotide amide group,amine group,nucleotide carbohydrate,carboxyl group carbohydrate,carboxyl group amide group,amine group,nucleotide amide group,amine group,nucleotide others carbohydrate,carboxyl group
ChEBI 17521
15846
18009
16119
17947
16908
16474
15378
30918
PubChem 5893
5886
8742
439351
439153
5884
1038
439774
1npdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1npdB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1o9bA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1o9bB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1vi2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1vi2B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1npdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound Unbound Unbound Unbound
1npdB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound Unbound Unbound Unbound
1o9bA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound Unbound Unbound Unbound
1o9bB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound Unbound Unbound Unbound
1vi2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound Unbound Unbound Unbound
1vi2B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [2], [3], [5], [13]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1npdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 71;ASP 107
1npdB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 71;ASP 107
1o9bA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 71;ASP 107
1o9bB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 71;ASP 107
1vi2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 71;ASP 107
1vi2B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 71;ASP 107
1npdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1npdB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1o9bA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1o9bB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1vi2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1vi2B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT.
Medline ID
PubMed ID 12837789
Journal J Bacteriol
Year 2003
Volume 185
Pages 4144-51
Authors Ye S, Von Delft F, Brooun A, Knuth MW, Swanson RV, McRee DE
Title The crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode.
Related PDB 1p74 1p77
Related UniProtKB P43876
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH NAD, FUNCTION, SUBUNIT.
Medline ID
PubMed ID 12624088
Journal J Biol Chem
Year 2003
Volume 278
Pages 19176-82
Authors Benach J, Lee I, Edstrom W, Kuzin AP, Chiang Y, Acton TB, Montelione GT, Hunt JF
Title The 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 PDB 1npd
Related UniProtKB P0A6D5
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT. , X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH NAD, CATALYTIC ACTIVITY, SUBUNIT.
Medline ID
PubMed ID 12637497
Journal J Biol Chem
Year 2003
Volume 278
Pages 19463-72
Authors Michel G, Roszak AW, Sauve V, Maclean J, Matte A, Coggins JR, Cygler M, Lapthorn AJ
Title Structures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities.
Related PDB 1nyt 1o9b
Related UniProtKB P15770 P0A6D5
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT.
Medline ID
PubMed ID 12906831
Journal Structure
Year 2003
Volume 11
Pages 1005-13
Authors Padyana AK, Burley SK
Title Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution.
Related PDB 1nvt
Related UniProtKB Q58484
[5]
Resource
Comments
Medline ID
PubMed ID 15596430
Journal J Biol Chem
Year 2005
Volume 280
Pages 7162-9
Authors Lindner HA, Nadeau G, Matte A, Michel G, Menard R, Cygler M
Title Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), FUNCTION, MUTAGENESIS OF LYS-67 AND ASP-103, SUBUNIT.
Medline ID
PubMed ID 15735308
Journal J Biol Chem
Year 2005
Volume 280
Pages 17101-8
Authors Singh S, Korolev S, Koroleva O, Zarembinski T, Collart F, Joachimiak A, Christendat D
Title Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae.
Related PDB 1npy
Related UniProtKB P44774
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 2-288 IN COMPLEX WITH NAD.
Medline ID
PubMed ID 16021622
Journal Proteins
Year 2005
Volume 60
Pages 787-96
Authors Badger 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
Title Structural analysis of a set of proteins resulting from a bacterial genomics project.
Related PDB 1vi2
Related UniProtKB P0A6D5
[8]
Resource
Comments X-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.
Medline ID
PubMed ID 16784230
Journal Biochemistry
Year 2006
Volume 45
Pages 7787-96
Authors Singh SA, Christendat D
Title Structure of Arabidopsis dehydroquinate dehydratase-shikimate dehydrogenase and implications for metabolic channeling in the shikimate pathway.
Related PDB 2gpt
Related UniProtKB Q9SQT8
[9]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID
PubMed ID 17649975
Journal Biochemistry
Year 2007
Volume 46
Pages 9513-22
Authors Gan J, Wu Y, Prabakaran P, Gu Y, Li Y, Andrykovitch M, Liu H, Gong Y, Yan H, Ji X
Title Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism.
Related PDB 2hk7 2hk8 2hk9
Related UniProtKB
[10]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID
PubMed ID 17825835
Journal J Mol Biol
Year 2007
Volume 373
Pages 424-38
Authors Bagautdinov B, Kunishima N
Title Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism.
Related PDB 1wxd 2cy0 2d5c 2ev9
Related UniProtKB Q5SJF8
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS), FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, REACTION MECHANISM.
Medline ID
PubMed ID 18566515
Journal Acta Crystallogr D Biol Crystallogr
Year 2008
Volume D64
Pages 803-9
Authors Schoepe J, Niefind K, Schomburg D
Title 1.6 angstroms structure of an NAD+-dependent quinate dehydrogenase from Corynebacterium glutamicum.
Related PDB 2ez3 2nlo
Related UniProtKB Q9X5C9
[12]
Resource
Comments
Medline ID
PubMed ID 18669580
Journal Mol Biol Evol
Year 2008
Volume 25
Pages 2221-32
Authors Singh S, Stavrinides J, Christendat D, Guttman DS
Title A phylogenomic analysis of the shikimate dehydrogenases reveals broadscale functional diversification and identifies one functionally distinct subclass.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 19917104
Journal BMC Res Notes
Year 2009
Volume 2
Pages 227
Authors Rodrigues VS Jr, Breda A, Santos DS, Basso LA
Title The conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis shikimate dehydrogenase.
Related PDB
Related UniProtKB
[14]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID
PubMed ID 19215302
Journal FEBS J
Year 2009
Volume 276
Pages 1125-39
Authors Han C, Hu T, Wu D, Qu S, Zhou J, Ding J, Shen X, Qu D, Jiang H
Title X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis.
Related PDB 3don 3doo
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 19043750
Journal J Mol Model
Year 2009
Volume 15
Pages 147-55
Authors Barcellos GB, Caceres RA, de Azevedo WF Jr
Title Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP.
Related PDB
Related UniProtKB

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).

Created Updated
2010-08-26 2011-08-03