D00605
type: Enzyme
rlcp: p118
cath: Leucine Dehydrogenase; Chain A, domain 1
cath: Rossmann fold
ec: https://purl.uniprot.org/enzyme/1.1.1.282
uniprot: P0A6D5
kegg enzyme: Quinate/shikimate dehydrogenase
kegg enzyme: YdiB
kegg pathway: Phenylalanine, tyrosine and tryptophan biosynthesis
kegg substrate: L-quinate
kegg substrate: NAD+
kegg substrate: NADP+
kegg substrate: shikimate
kegg product: 3-dehydroquinate
kegg product: NADH
kegg product: NADPH
kegg product: H+
kegg product: 3-dehydroshikimate
pdb: 1npdA01
pdb: 1npdB01
pdb: 1o9bA01
pdb: 1o9bB01
pdb: 1vi2A01
pdb: 1vi2B01
pdb: 1npdA02
pdb: 1npdB02
pdb: 1o9bA02
pdb: 1o9bB02
pdb: 1vi2A02
pdb: 1vi2B02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1npdA01
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1npdB01
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1o9bA01
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1o9bB01
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1vi2A01
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1vi2B01
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1npdA02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1npdB02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1o9bA02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1o9bB02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1vi2A02
pdb bound state: Unbound
  compound: L-quinate
  pdb: 1vi2B02
pdb bound state: Unbound
  compound: NAD+
  pdb: 1npdA01
pdb bound state: Unbound
  compound: NAD+
  pdb: 1npdB01
pdb bound state: Unbound
  compound: NAD+
  pdb: 1o9bA01
pdb bound state: Unbound
  compound: NAD+
  pdb: 1o9bB01
pdb bound state: Unbound
  compound: NAD+
  pdb: 1vi2A01
pdb bound state: Unbound
  compound: NAD+
  pdb: 1vi2B01
pdb bound state: Unbound
  compound: NADP+
  pdb: 1npdA01
pdb bound state: Unbound
  compound: NADP+
  pdb: 1npdB01
pdb bound state: Unbound
  compound: NADP+
  pdb: 1o9bA01
pdb bound state: Unbound
  compound: NADP+
  pdb: 1o9bB01
pdb bound state: Unbound
  compound: NADP+
  pdb: 1vi2A01
pdb bound state: Unbound
  compound: NADP+
  pdb: 1vi2B01
pdb bound state: Unbound
  compound: NADP+
  pdb: 1npdA02
pdb bound state: Unbound
  compound: NADP+
  pdb: 1npdB02
pdb bound state: Unbound
  compound: NADP+
  pdb: 1o9bA02
pdb bound state: Unbound
  compound: NADP+
  pdb: 1o9bB02
pdb bound state: Unbound
  compound: NADP+
  pdb: 1vi2A02
pdb bound state: Unbound
  compound: NADP+
  pdb: 1vi2B02
active site residues resources: Structures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities.
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: 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 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).

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
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:17521

NAD+
type: KeggSubstrate
references: KEGG:C00003
compound type: amide group
compound type: amine group
compound type: nucleotide
references: CHEBI:15846
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

NADP+
type: KeggSubstrate
references: KEGG:C00006
compound type: amide group
compound type: amine group
compound type: nucleotide
references: CHEBI:18009
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

shikimate
type: KeggSubstrate
references: KEGG:C00493
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:16119
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

3-dehydroquinate
type: KeggProduct
references: KEGG:C00944
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:17947
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

NADH
type: KeggProduct
references: KEGG:C00004
compound type: amide group
compound type: amine group
compound type: nucleotide
references: CHEBI:16908
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

NADPH
type: KeggProduct
references: KEGG:C00005
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
compound type: others
references: CHEBI:15378
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

3-dehydroshikimate
type: KeggProduct
references: KEGG:C02637
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:30918
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1npdA01
type: Pdb
references: 1npd
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1npd
catalytic residue: LYS 71;ASP 107

1npdB01
type: Pdb
references: 1npd
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1npd
catalytic residue: LYS 71;ASP 107

1o9bA01
type: Pdb
references: 1o9b
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1o9b
catalytic residue: LYS 71;ASP 107

1o9bB01
type: Pdb
references: 1o9b
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1o9b
catalytic residue: LYS 71;ASP 107

1vi2A01
type: Pdb
references: 1vi2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1vi2
catalytic residue: LYS 71;ASP 107

1vi2B01
type: Pdb
references: 1vi2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1vi2
catalytic residue: LYS 71;ASP 107

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: 2
reference section: p.19181

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

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

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