D00858
type: Enzyme
rlcp: p118
cath: Leucine Dehydrogenase; Chain A, domain 1
cath: Rossmann fold
ec: https://purl.uniprot.org/enzyme/1.1.1.24
ec: https://purl.uniprot.org/enzyme/1.1.1.25
uniprot: Q9X5C9
kegg enzyme: Quinate dehydrogenase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.24
kegg enzyme: Quinic dehydrogenase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.24
kegg enzyme: Quinate:NAD oxidoreductase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.24
kegg enzyme: Quinate 5-dehydrogenase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.24
kegg enzyme: Quinate:NAD+ 5-oxidoreductase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.24
kegg enzyme: Shikimate dehydrogenase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.25
kegg enzyme: Dehydroshikimic reductase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.25
kegg enzyme: Shikimate oxidoreductase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.25
kegg enzyme: Shikimate:NADP+ oxidoreductase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.25
kegg enzyme: 5-Dehydroshikimate reductase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.25
kegg enzyme: Shikimate 5-dehydrogenase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.25
kegg enzyme: 5-Dehydroshikimic reductase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.25
kegg enzyme: DHS reductase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.25
kegg enzyme: Shikimate:NADP+ 5-oxidoreductase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.25
kegg enzyme: AroE
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/1.1.1.25
kegg pathway: Phenylalanine, tyrosine and tryptophan biosynthesis
kegg substrate: L-quinate
kegg substrate: shikimate
kegg substrate: NAD+
kegg product: 3-dehydroquinate
kegg product: 3-dehydroshikimate
kegg product: NADH
kegg product: H+
pdb: 2ez3A01
pdb: 2nloA01
pdb: 3jyoA01
pdb: 3jypA01
pdb: 3jyqA01
pdb: 2ez3A02
pdb: 2nloA02
pdb: 3jyoA02
pdb: 3jypA02
pdb: 3jyqA02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 2ez3A01
pdb bound state: Analogue
  compound: L-quinate
  pdb: 2nloA01
  ligand het code: GOL
pdb bound state: Unbound
  compound: L-quinate
  pdb: 3jyoA01
pdb bound state: Unbound
  compound: L-quinate
  pdb: 3jyqA01
pdb bound state: Unbound
  compound: L-quinate
  pdb: 2ez3A02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 2nloA02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 3jyoA02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 3jypA02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 3jyqA02
pdb bound state: Unbound
  compound: shikimate
  pdb: 2ez3A01
pdb bound state: Unbound
  compound: shikimate
  pdb: 2nloA01
pdb bound state: Unbound
  compound: shikimate
  pdb: 3jyoA01
pdb bound state: Unbound
  compound: shikimate
  pdb: 3jypA01
pdb bound state: Unbound
  compound: shikimate
  pdb: 2ez3A02
pdb bound state: Unbound
  compound: shikimate
  pdb: 2nloA02
pdb bound state: Unbound
  compound: shikimate
  pdb: 3jyoA02
pdb bound state: Unbound
  compound: shikimate
  pdb: 3jypA02
active site residues resources: Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution.
active site residues resources: Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae.
active site residues resources: Structural analysis of a set of proteins resulting from a bacterial genomics project.
active site residues resources: Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism.
active site residues resources: Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism.
active site residues resources: 1.6 angstroms structure of an NAD+-dependent quinate dehydrogenase from Corynebacterium glutamicum.
active site residues resources: X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis.
references: The crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode.
references: 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.
references: Structures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities.
references: Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution.
references: Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli.
references: Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae.
references: Structural analysis of a set of proteins resulting from a bacterial genomics project.
references: Structure of Arabidopsis dehydroquinate dehydratase-shikimate dehydrogenase and implications for metabolic channeling in the shikimate pathway.
references: Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism.
references: Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism.
references: 1.6 angstroms structure of an NAD+-dependent quinate dehydrogenase from Corynebacterium glutamicum.
references: A phylogenomic analysis of the shikimate dehydrogenases reveals broadscale functional diversification and identifies one functionally distinct subclass.
references: The conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis shikimate dehydrogenase.
references: X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis.
references: Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP.
comment: 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 belongs to the subfamily of AroE, which has activity towards both quinate and shikimate. (The catalytic efficiency with quinate seems to be higher than that with shikimate.) This enzyme is homologous to AroE (D00845 in EzCatDB), sharing a similar active site with the homologous enzyme. Thus, its catalytic mechanism must be also similar to that of the homologue.

Leucine Dehydrogenase; Chain A, domain 1
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.192.10
catalytic domain: index.html

Rossmann fold
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.50.720

Phenylalanine, tyrosine and tryptophan biosynthesis
type: KeggPathway
references: KEGG:MAP00400

L-quinate
type: KeggSubstrate
references: KEGG:C00296
ec: https://purl.uniprot.org/enzyme/1.1.1.24
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:17521

shikimate
type: KeggSubstrate
references: KEGG:C00493
ec: https://purl.uniprot.org/enzyme/1.1.1.25
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:16119
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

NAD+
type: KeggSubstrate
references: KEGG:C00003
ec: https://purl.uniprot.org/enzyme/1.1.1.24
ec: https://purl.uniprot.org/enzyme/1.1.1.25
compound type: amide group
compound type: amine group
compound type: nucleotide
references: CHEBI:15846
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

3-dehydroquinate
type: KeggProduct
references: KEGG:C00944
ec: https://purl.uniprot.org/enzyme/1.1.1.24
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:17947
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

3-dehydroshikimate
type: KeggProduct
references: KEGG:C02637
ec: https://purl.uniprot.org/enzyme/1.1.1.25
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:30918
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

NADH
type: KeggProduct
references: KEGG:C00004
ec: https://purl.uniprot.org/enzyme/1.1.1.24
ec: https://purl.uniprot.org/enzyme/1.1.1.25
compound type: amide group
compound type: amine group
compound type: nucleotide
references: CHEBI:16908
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

H+
type: KeggProduct
references: KEGG:C00080
ec: https://purl.uniprot.org/enzyme/1.1.1.24
ec: https://purl.uniprot.org/enzyme/1.1.1.25
compound type: others
references: CHEBI:15378
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

2ez3A01
type: Pdb
references: 2ez3
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2ez3
catalytic residue: LYS 92;ASP 129

2nloA01
type: Pdb
references: 2nlo
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2nlo
catalytic residue: LYS 92;ASP 129

3jyoA01
type: Pdb
references: 3jyo
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3jyo
catalytic residue: LYS 73;ASP 110

3jypA01
type: Pdb
references: 3jyp
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3jyp
catalytic residue: LYS 73;ASP 110

3jyqA01
type: Pdb
references: 3jyq
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3jyq
catalytic residue: LYS 73;ASP 110

The crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT.
references: http://www.ncbi.nlm.nih.gov/pubmed/12837789
journal: J Bacteriol
volume: 185
pages: 4144-51
published year: 2003
authors:
  item: Ye S
  item: Von Delft F
  item: Brooun A
  item: Knuth MW
  item: Swanson RV
  item: McRee DE
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P43876

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.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH NAD, FUNCTION, SUBUNIT.
references: http://www.ncbi.nlm.nih.gov/pubmed/12624088
journal: J Biol Chem
volume: 278
pages: 19176-82
published year: 2003
authors:
  item: Benach J
  item: Lee I
  item: Edstrom W
  item: Kuzin AP
  item: Chiang Y
  item: Acton TB
  item: Montelione GT
  item: Hunt JF
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P0A6D5

Structures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT. , X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH NAD, CATALYTIC ACTIVITY, SUBUNIT.
references: http://www.ncbi.nlm.nih.gov/pubmed/12637497
journal: J Biol Chem
volume: 278
pages: 19463-72
published year: 2003
authors:
  item: Michel G
  item: Roszak AW
  item: Sauve V
  item: Maclean J
  item: Matte A
  item: Coggins JR
  item: Cygler M
  item: Lapthorn AJ
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P15770
references: P0A6D5

Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT.
references: http://www.ncbi.nlm.nih.gov/pubmed/12906831
journal: Structure
volume: 11
pages: 1005-13
published year: 2003
authors:
  item: Padyana AK
  item: Burley SK
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q58484

Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/15596430
journal: J Biol Chem
volume: 280
pages: 7162-9
published year: 2005
authors:
  item: Lindner HA
  item: Nadeau G
  item: Matte A
  item: Michel G
  item: Menard R
  item: Cygler M

Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), FUNCTION, MUTAGENESIS OF LYS-67 AND ASP-103, SUBUNIT.
references: http://www.ncbi.nlm.nih.gov/pubmed/15735308
journal: J Biol Chem
volume: 280
pages: 17101-8
published year: 2005
authors:
  item: Singh S
  item: Korolev S
  item: Koroleva O
  item: Zarembinski T
  item: Collart F
  item: Joachimiak A
  item: Christendat D
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P44774

Structural analysis of a set of proteins resulting from a bacterial genomics project.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 2-288 IN COMPLEX WITH NAD.
references: http://www.ncbi.nlm.nih.gov/pubmed/16021622
journal: Proteins
volume: 60
pages: 787-96
published year: 2005
authors:
  item: Badger J
  item: Sauder JM
  item: Adams JM
  item: Antonysamy S
  item: Bain K
  item: Bergseid MG
  item: Buchanan SG
  item: Buchanan MD
  item: Batiyenko Y
  item: Christopher JA
  item: Emtage S
  item: Eroshkina A
  item: Feil I
  item: Furlong EB
  item: Gajiwala KS
  item: Gao X
  item: He D
  item: Hendle J
  item: Huber A
  item: Hoda K
  item: Kearins P
  item: Kissinger C
  item: Laubert B
  item: Lewis HA
  item: Lin J
  item: Loomis K
  item: Lorimer D
  item: Louie G
  item: Maletic M
  item: Marsh CD
  item: Miller I
  item: Molinari J
  item: Muller-Dieckmann HJ
  item: Newman JM
  item: Noland BW
  item: Pagarigan B
  item: Park F
  item: Peat TS
  item: Post KW
  item: Radojicic S
  item: Ramos A
  item: Romero R
  item: Rutter ME
  item: Sanderson WE
  item: Schwinn KD
  item: Tresser J
  item: Winhoven J
  item: Wright TA
  item: Wu L
  item: Xu J
  item: Harris TJ
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P0A6D5

Structure of Arabidopsis dehydroquinate dehydratase-shikimate dehydrogenase and implications for metabolic channeling in the shikimate pathway.
type: BibliographicResource
comment: 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.
references: http://www.ncbi.nlm.nih.gov/pubmed/16784230
journal: Biochemistry
volume: 45
pages: 7787-96
published year: 2006
authors:
  item: Singh SA
  item: Christendat D
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q9SQT8

Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/17649975
journal: Biochemistry
volume: 46
pages: 9513-22
published year: 2007
authors:
  item: Gan J
  item: Wu Y
  item: Prabakaran P
  item: Gu Y
  item: Li Y
  item: Andrykovitch M
  item: Liu H
  item: Gong Y
  item: Yan H
  item: Ji X
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/17825835
journal: J Mol Biol
volume: 373
pages: 424-38
published year: 2007
authors:
  item: Bagautdinov B
  item: Kunishima N
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q5SJF8

1.6 angstroms structure of an NAD+-dependent quinate dehydrogenase from Corynebacterium glutamicum.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS), FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, REACTION MECHANISM.
references: http://www.ncbi.nlm.nih.gov/pubmed/18566515
journal: Acta Crystallogr D Biol Crystallogr
volume: D64
pages: 803-9
published year: 2008
authors:
  item: Schoepe J
  item: Niefind K
  item: Schomburg D
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q9X5C9

A phylogenomic analysis of the shikimate dehydrogenases reveals broadscale functional diversification and identifies one functionally distinct subclass.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/18669580
journal: Mol Biol Evol
volume: 25
pages: 2221-32
published year: 2008
authors:
  item: Singh S
  item: Stavrinides J
  item: Christendat D
  item: Guttman DS

The conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis shikimate dehydrogenase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/19917104
journal: BMC Res Notes
volume: 2
pages: 227
published year: 2009
authors:
  item: Rodrigues VS Jr
  item: Breda A
  item: Santos DS
  item: Basso LA

X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/19215302
journal: FEBS J
volume: 276
pages: 1125-39
published year: 2009
authors:
  item: Han C
  item: Hu T
  item: Wu D
  item: Qu S
  item: Zhou J
  item: Ding J
  item: Shen X
  item: Qu D
  item: Jiang H
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/19043750
journal: J Mol Model
volume: 15
pages: 147-55
published year: 2009
authors:
  item: Barcellos GB
  item: Caceres RA
  item: de Azevedo WF Jr

ReferenceForCatalyticMechanism
reference index: 3
reference section: p.19470-19471

ReferenceForCatalyticMechanism
reference index: 5
reference section: Fig.5, p.7168-7169

ReferenceForCatalyticMechanism
reference index: 6
reference section: p.17105-17107

ReferenceForCatalyticMechanism
reference index: 8
reference section: p.7791-7794

ReferenceForCatalyticMechanism
reference index: 9
reference section: Fig.4, p.9519-9521

ReferenceForCatalyticMechanism
reference index: 10
reference section: Fig.8, p.432-435

ReferenceForCatalyticMechanism
reference index: 13
reference section: p.4-6

ReferenceForCatalyticMechanism
reference index: 14
reference section: Fig.4, p.1130-1132, p.1136