T00414
type: Enzyme
rlcp: p118
cath: http://ezcatdb.cbrc.jp/EzCatDB/cath/-.-.-.-
cath: Leucine Dehydrogenase; Chain A, domain 1
cath: Rossmann fold
ec: https://purl.uniprot.org/enzyme/5.4.99.5
ec: https://purl.uniprot.org/enzyme/1.1.1.25
uniprot: Q97KM0
kegg enzyme: Chorismate mutase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/5.4.99.5
kegg enzyme: Hydroxyphenylpyruvate synthase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/5.4.99.5
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: Chorismate
kegg substrate: shikimate
kegg substrate: NADP+
kegg product: Prephenate
kegg product: 3-dehydroshikimate
kegg product: NADPH
kegg product: H+
pdb: 3fbtA01
pdb: 3fbtB01
pdb: 3fbtC01
pdb: 3fbtD01
pdb: 3fbtA02
pdb: 3fbtB02
pdb: 3fbtC02
pdb: 3fbtD02
pdb bound state: Unbound
  compound: Chorismate
  pdb: 3fbtA01
pdb bound state: Unbound
  compound: Chorismate
  pdb: 3fbtB01
pdb bound state: Unbound
  compound: Chorismate
  pdb: 3fbtC01
pdb bound state: Unbound
  compound: Chorismate
  pdb: 3fbtD01
pdb bound state: Unbound
  compound: Chorismate
  pdb: 3fbtA02
pdb bound state: Unbound
  compound: Chorismate
  pdb: 3fbtB02
pdb bound state: Unbound
  compound: Chorismate
  pdb: 3fbtC02
pdb bound state: Unbound
  compound: Chorismate
  pdb: 3fbtD02
pdb bound state: Unbound
  compound: shikimate
  pdb: 3fbtA01
pdb bound state: Unbound
  compound: shikimate
  pdb: 3fbtB01
pdb bound state: Unbound
  compound: shikimate
  pdb: 3fbtC01
pdb bound state: Unbound
  compound: shikimate
  pdb: 3fbtD01
pdb bound state: Unbound
  compound: shikimate
  pdb: 3fbtA02
pdb bound state: Unbound
  compound: shikimate
  pdb: 3fbtB02
pdb bound state: Unbound
  compound: shikimate
  pdb: 3fbtC02
pdb bound state: Unbound
  compound: shikimate
  pdb: 3fbtD02
pdb bound state: Unbound
  compound: NADP+
  pdb: 3fbtA01
pdb bound state: Unbound
  compound: NADP+
  pdb: 3fbtB01
pdb bound state: Unbound
  compound: NADP+
  pdb: 3fbtC01
pdb bound state: Unbound
  compound: NADP+
  pdb: 3fbtD01
pdb bound state: Unbound
  compound: NADP+
  pdb: 3fbtA02
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 is composed of N-terminal chorismate mutase domain (EC 5.4.99.5) and C-terminal shikimate dehydrogenase domains (EC 1.1.1.25). Although the tertiary structure of the C-terminal shikimate dehydrogenase domains have been solved, that of the N-terminal domain has not been elucidated. The C-terminal 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]). The C-terminal domain corresponds to AroE, which has a similar active site as that of the homologous enzyme (D00845 in EzCatDB). 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

Chorismate
type: KeggSubstrate
references: KEGG:C00251
ec: https://purl.uniprot.org/enzyme/5.4.99.5
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:17333
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

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

NADP+
type: KeggSubstrate
references: KEGG:C00006
ec: https://purl.uniprot.org/enzyme/1.1.1.25
compound type: amide group
compound type: amine group
compound type: nucleotide
references: CHEBI:18009
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Prephenate
type: KeggProduct
references: KEGG:C00254
ec: https://purl.uniprot.org/enzyme/5.4.99.5
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:84387

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

NADPH
type: KeggProduct
references: KEGG:C00005
ec: https://purl.uniprot.org/enzyme/1.1.1.25
compound type: amide group
compound type: amine group
compound type: nucleotide
references: CHEBI:16474
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

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

3fbtA01
type: Pdb
references: 3fbt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3fbt
catalytic residue: LYS 162;ASP 198
comment: (EC 1.1.1.25)

3fbtB01
type: Pdb
references: 3fbt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3fbt
catalytic residue: LYS 162;ASP 198
comment: (EC 1.1.1.25)

3fbtC01
type: Pdb
references: 3fbt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3fbt
catalytic residue: LYS 162;ASP 198
comment: (EC 1.1.1.25)

3fbtD01
type: Pdb
references: 3fbt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3fbt
catalytic residue: LYS 162;ASP 198
comment: (EC 1.1.1.25)

3fbtA02
type: Pdb
references: 3fbt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3fbt
comment: (EC 1.1.1.25)

3fbtB02
type: Pdb
references: 3fbt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3fbt
comment: (EC 1.1.1.25)

3fbtC02
type: Pdb
references: 3fbt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3fbt
comment: (EC 1.1.1.25)

3fbtD02
type: Pdb
references: 3fbt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:3fbt
comment: (EC 1.1.1.25)

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