DB code: D00845

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. 1.1.1.25
CSA 1nvt
M-CSA 1nvt
MACiE

CATH domain Related DB codes (homologues)
3.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1 D00458 D00032 D00033 D00035 D00605 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 D00605 D00615 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
Q58484 Shikimate dehydrogenase
EC 1.1.1.25
NP_248077.1 (Protein)
NC_000909.1 (DNA/RNA sequence)
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical View]
O67049 Shikimate dehydrogenase
EC 1.1.1.25
NP_213611.1 (Protein)
NC_000918.1 (DNA/RNA sequence)
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical View]
P15770 Shikimate dehydrogenase
EC 1.1.1.25
NP_417740.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492151.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical View]
P43876 Shikimate dehydrogenase
EC 1.1.1.25
NP_438815.1 (Protein)
NC_000907.1 (DNA/RNA sequence)
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical View]
Q5HNV1 Shikimate dehydrogenase
EC 1.1.1.25
YP_188739.1 (Protein)
NC_002976.3 (DNA/RNA sequence)
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical View]
Q5KWX7
Shikimate 5-dehydrogenase
EC 1.1.1.25
YP_148377.1 (Protein)
NC_006510.1 (DNA/RNA sequence)
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical View]
Q5SJF8 Shikimate dehydrogenase
EC 1.1.1.25
YP_144316.1 (Protein)
NC_006461.1 (DNA/RNA sequence)
PF01488 (Shikimate_DH)
PF08501 (Shikimate_dh_N)
[Graphical View]

KEGG enzyme name
Shikimate dehydrogenase
Dehydroshikimic reductase
Shikimate oxidoreductase
Shikimate:NADP+ oxidoreductase
5-Dehydroshikimate reductase
Shikimate 5-dehydrogenase
5-Dehydroshikimic reductase
DHS reductase
Shikimate:NADP+ 5-oxidoreductase
AroE

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q58484 AROE_METJA Shikimate + NADP+ = 3-dehydroshikimate + NADPH. Homodimer.
O67049 AROE_AQUAE Shikimate + NADP+ = 3-dehydroshikimate + NADPH.
P15770 AROE_ECOLI Shikimate + NADP+ = 3-dehydroshikimate + NADPH. Monomer.
P43876 AROE_HAEIN Shikimate + NADP+ = 3-dehydroshikimate + NADPH. Monomer.
Q5HNV1 AROE_STAEQ Shikimate + NADP+ = 3-dehydroshikimate + NADPH.
Q5KWX7 Q5KWX7_GEOKA Shikimate + NADP+ = 3-dehydroshikimate + NADPH.
Q5SJF8 AROE_THET8 Shikimate + NADP+ = 3-dehydroshikimate + NADPH.

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

Compound table
Substrates Products Intermediates
KEGG-id C00493 C00006 C02637 C00005 C00080
E.C.
Compound shikimate NADP+ 3-dehydroshikimate NADPH H+
Type carbohydrate,carboxyl group amide group,amine group,nucleotide carbohydrate,carboxyl group amide group,amine group,nucleotide others
ChEBI 16119
 16119
 		18009
 18009
 		30918
 30918
 		16474
 16474
 		15378
 15378
PubChem 8742
 8742
 		5886
 5886
 		439774
 439774
 		5884
 5884
 		1038
 1038
1nvtA01 Unbound Unbound Unbound Unbound
1nvtB01 Unbound Unbound Unbound Unbound
2hk7A01 Unbound Unbound Unbound Unbound
2hk7B01 Unbound Unbound Unbound Unbound
2hk8A01 Unbound Unbound Unbound Unbound
2hk8B01 Unbound Unbound Unbound Unbound
2hk8C01 Unbound Unbound Unbound Unbound
2hk8D01 Unbound Unbound Unbound Unbound
2hk8E01 Unbound Unbound Unbound Unbound
2hk8F01 Unbound Unbound Unbound Unbound
2hk8G01 Unbound Unbound Unbound Unbound
2hk8H01 Unbound Unbound Unbound Unbound
2hk9A01 Bound:SKM Unbound Unbound Unbound
2hk9B01 Bound:SKM Unbound Unbound Unbound
2hk9C01 Bound:SKM Unbound Unbound Unbound
2hk9D01 Bound:SKM Unbound Unbound Unbound
1nytA01 Analogue:DTV Unbound Unbound Unbound
1nytB01 Unbound Unbound Unbound Unbound
1nytC01 Unbound Unbound Unbound Unbound
1nytD01 Unbound Unbound Unbound Unbound
1p74A01 Unbound Unbound Unbound Unbound
1p74B01 Unbound Unbound Unbound Unbound
1p77A01 Unbound Unbound Unbound Unbound
3donA01 Unbound Unbound Unbound Unbound
3dooA01 Bound:SKM Unbound Unbound Unbound
2eggA01 Unbound Unbound Unbound Unbound
2eggB01 Unbound Unbound Unbound Unbound
1wxdA01 Unbound Unbound Unbound Unbound
1wxdB01 Unbound Unbound Unbound Unbound
2cy0A01 Unbound Unbound Unbound Unbound
2cy0B01 Unbound Unbound Unbound Unbound
2d5cA01 Bound:SKM Unbound Unbound Unbound
2d5cB01 Bound:SKM Unbound Unbound Unbound
2ev9A01 Bound:SKM Unbound Unbound Unbound
2ev9B01 Bound:SKM Unbound Unbound Unbound
1nvtA02 Unbound Bound:NAP Unbound Unbound
1nvtB02 Unbound Bound:NAP Unbound Unbound
2hk7A02 Unbound Unbound Unbound Unbound
2hk7B02 Unbound Unbound Unbound Unbound
2hk8A02 Unbound Unbound Unbound Unbound
2hk8B02 Unbound Unbound Unbound Unbound
2hk8C02 Unbound Unbound Unbound Unbound
2hk8D02 Unbound Unbound Unbound Unbound
2hk8E02 Unbound Unbound Unbound Unbound
2hk8F02 Unbound Unbound Unbound Unbound
2hk8G02 Unbound Unbound Unbound Unbound
2hk8H02 Unbound Unbound Unbound Unbound
2hk9A02 Unbound Analogue:ATR Unbound Unbound
2hk9B02 Unbound Bound:NAP Unbound Unbound
2hk9C02 Unbound Bound:NAP Unbound Unbound
2hk9D02 Unbound Bound:NAP Unbound Unbound
1nytA02 Unbound Bound:NAP Unbound Unbound
1nytB02 Unbound Bound:NAP Unbound Unbound
1nytC02 Unbound Bound:NAP Unbound Unbound
1nytD02 Unbound Bound:NAP Unbound Unbound
1p74A02 Unbound Unbound Unbound Unbound
1p74B02 Unbound Unbound Unbound Unbound
1p77A02 Unbound Analogue:ATR Unbound Unbound
3donA02 Unbound Unbound Unbound Unbound
3dooA02 Unbound Unbound Unbound Unbound
2eggA02 Unbound Unbound Unbound Unbound
2eggB02 Unbound Unbound Unbound Unbound
1wxdA02 Unbound Unbound Unbound Unbound
1wxdB02 Unbound Unbound Unbound Unbound
2cy0A02 Unbound Bound:NAP Unbound Unbound
2cy0B02 Unbound Unbound Unbound Unbound
2d5cA02 Unbound Unbound Unbound Unbound
2d5cB02 Unbound Unbound Unbound Unbound
2ev9A02 Unbound Bound:NAP Unbound Unbound
2ev9B02 Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [3], [5], [6], [8], [9], [10], [13]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1nvtA01 LYS 75;ASP 111
1nvtB01 LYS 75;ASP 111
2hk7A01 LYS 70;ASP 106
2hk7B01 LYS 70;ASP 106
2hk8A01 LYS 70;ASP 106
2hk8B01 LYS 70;ASP 106
2hk8C01 LYS 70;ASP 106
2hk8D01 LYS 70;ASP 106
2hk8E01 LYS 70;ASP 106
2hk8F01 LYS 70;ASP 106
2hk8G01 LYS 70;ASP 106
2hk8H01 LYS 70;ASP 106
2hk9A01 LYS 70;ASP 106
2hk9B01 LYS 70;ASP 106
2hk9C01 LYS 70;ASP 106
2hk9D01 LYS 70;ASP 106
1nytA01 LYS 65;ASP 102
1nytB01 LYS 65;ASP 102
1nytC01 LYS 65;ASP 102
1nytD01 LYS 65;ASP 102
1p74A01 LYS 65;ASP 102
1p74B01 LYS 65;ASP 102
1p77A01 LYS 65;ASP 102
3donA01 LYS 64;ASP 100
3dooA01 LYS 64;ASP 100
2eggA01 LYS 87;ASP 123
2eggB01 LYS 87;ASP 123
1wxdA01 LYS 64;ASP 100
1wxdB01 LYS 64;ASP 100
2cy0A01 LYS 64;ASP 100
2cy0B01 LYS 64;ASP 100
2d5cA01 LYS 64;ASP 100
2d5cB01 LYS 64;ASP 100
2ev9A01 LYS 64;ASP 100
2ev9B01 LYS 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
References Sections No. 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]
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 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.

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