D00515
type: Enzyme
cath: Aspartate Aminotransferase; domain 2
cath: Aspartate Aminotransferase, domain 1
ec: https://purl.uniprot.org/enzyme/4.4.1.8
csa: 1cl1
uniprot: P06721
uniprot: P53780
kegg enzyme: cystathionine beta-lyase
kegg enzyme: beta-cystathionase
kegg enzyme: cystine lyase
kegg enzyme: cystathionine L-homocysteine-lyase (deaminating)
kegg enzyme: L-cystathionine L-homocysteine-lyase (deaminating)
kegg pathway: Methionine metabolism
kegg pathway: Cysteine metabolism
kegg pathway: Selenoamino acid metabolism
kegg pathway: Nitrogen metabolism
kegg pathway: Sulfur metabolism
kegg cofactor: Pyridoxal phosphate
kegg substrate: Cystathionine
kegg substrate: H2O
kegg product: L-Homocysteine
kegg product: NH3
kegg product: Pyruvate
pdb: 1cl1A01
pdb: 1cl1B01
pdb: 1cl2A01
pdb: 1cl2B01
pdb: 1ibjA01
pdb: 1ibjC01
pdb: 1cl1A02
pdb: 1cl1B02
pdb: 1cl2A02
pdb: 1cl2B02
pdb: 1ibjA02
pdb: 1ibjC02
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1cl1A01
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1cl1B01
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1cl2A01
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1cl2B01
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1ibjA01
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1ibjC01
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1cl1A02
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1cl1B02
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1cl2A02
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1cl2B02
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1ibjA02
pdb bound state: Unbound
  compound: Cystathionine
  pdb: 1ibjC02
pdb bound state: Analogue
  compound: Pyridoxal phosphate
  pdb: 1cl2A01
  ligand het code: PPG
pdb bound state: Analogue
  compound: Pyridoxal phosphate
  pdb: 1cl2B01
  ligand het code: PPG
pdb bound state: Unbound
  compound: Pyridoxal phosphate
  pdb: 1cl1A02
pdb bound state: Unbound
  compound: Pyridoxal phosphate
  pdb: 1cl1B02
pdb bound state: Unbound
  compound: Pyridoxal phosphate
  pdb: 1cl2A02
pdb bound state: Unbound
  compound: Pyridoxal phosphate
  pdb: 1cl2B02
pdb bound state: Unbound
  compound: Pyridoxal phosphate
  pdb: 1ibjA02
pdb bound state: Unbound
  compound: Pyridoxal phosphate
  pdb: 1ibjC02
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1cl1A01
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1cl1B01
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1cl2A01
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1cl2B01
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1ibjA01
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1ibjC01
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1cl1A02
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1cl1B02
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1cl2A02
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1cl2B02
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1ibjA02
pdb bound state: Unbound
  compound: L-Homocysteine
  pdb: 1ibjC02
pdb bound state: Unbound
  compound: NH3
  pdb: 1cl1A01
pdb bound state: Unbound
  compound: NH3
  pdb: 1cl1B01
pdb bound state: Unbound
  compound: NH3
  pdb: 1cl2A01
active site residues resources: Slow-binding inhibition of Escherichia coli cystathionine beta-lyase by L-aminoethoxyvinylglycine: a kinetic and X-ray study.
active site residues resources: http://ezcatdb.cbrc.jp/EzCatDB/reference/D00515#8
references: Cloning, purification, and crystallization of Escherichia coli cystathionine beta-lyase.
references: Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A.
references: Slow-binding inhibition of Escherichia coli cystathionine beta-lyase by L-aminoethoxyvinylglycine: a kinetic and X-ray study.
references: Mode of action of cystathionine beta-lyase.
references: The crystal structure of cystathionine gamma-synthase from Nicotiana tabacum reveals its substrate and reaction specificity.
references: Crystal structure of a NifS-like protein from Thermotoga maritima: implications for iron sulphur cluster assembly.
references: The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity.
comment: Although the residues 85-131 of 1ibj (PDB) are included in the first domain, the region seems to correspond to the first domain of 1cl1 and 1cl2. According to the literature [2], [4] & [7], this enzyme catalyzes the following reactions: (A) Formation of external aldimine (transaldimine), (B) Elimination of homocysteine, (C) Formation of internal aldimine (transaldimine), (D) Hydration of iminopropionate, to form pyruvate and ammonia, outside the enzyme. (This hydration might involve Schiff-base deforming reaction.)

Aspartate Aminotransferase; domain 2
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.640.10
catalytic domain: index.html

Aspartate Aminotransferase, domain 1
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.90.1150.10
catalytic domain: index.html

Methionine metabolism
type: KeggPathway
references: KEGG:MAP00271

Cysteine metabolism
type: KeggPathway
references: KEGG:MAP00272

Selenoamino acid metabolism
type: KeggPathway
references: KEGG:MAP00450

Nitrogen metabolism
type: KeggPathway
references: KEGG:MAP00910

Sulfur metabolism
type: KeggPathway
references: KEGG:MAP00920

Pyridoxal phosphate
type: KeggCofactor
references: KEGG:C00018
compound type: aromatic ring (with nitrogen atoms)
compound type: phosphate group/phosphate ion
references: CHEBI:18405
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Cystathionine
type: KeggSubstrate
references: KEGG:C00542
compound type: amino acids
compound type: sulfide group
references: CHEBI:17755
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

L-Homocysteine
type: KeggProduct
references: KEGG:C00155
compound type: amino acids
compound type: sulfhydryl group
references: CHEBI:17588
references: CHEBI:58199
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

NH3
type: KeggProduct
references: KEGG:C00014
compound type: amine group
compound type: organic ion
references: CHEBI:16134
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Pyruvate
type: KeggProduct
references: KEGG:C00022
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:32816
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1cl1A01
type: Pdb
references: 1cl1
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1cl1
catalytic residue: TYR 56;TYR 111;ASP 185;LLP 210
cofactor binding residue: LLP 210(PLP binding)

1cl1B01
type: Pdb
references: 1cl1
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1cl1
catalytic residue: TYR 56;TYR 111;ASP 185;LLP 210
cofactor binding residue: LLP 210(PLP binding)

1cl2A01
type: Pdb
references: 1cl2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1cl2
catalytic residue: TYR 56;TYR 111;ASP 185;LYS 210
cofactor binding residue: LYS 210(PLP binding)

1cl2B01
type: Pdb
references: 1cl2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1cl2
catalytic residue: TYR 56;TYR 111;ASP 185;LYS 210
cofactor binding residue: LYS 210(PLP binding)

1ibjA01
type: Pdb
references: 1ibj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ibj
catalytic residue: TYR 127;TYR 181;ASP 253;LYS 278
cofactor binding residue: LYS 278(PLP binding)

1ibjC01
type: Pdb
references: 1ibj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ibj
catalytic residue: TYR 127;TYR 181;ASP 253;LYS 278
cofactor binding residue: LYS 278(PLP binding)

1cl1A02
type: Pdb
references: 1cl1
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1cl1
catalytic residue: SER 339

1cl1B02
type: Pdb
references: 1cl1
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1cl1
catalytic residue: SER 339

1cl2A02
type: Pdb
references: 1cl2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1cl2
catalytic residue: SER 339

1cl2B02
type: Pdb
references: 1cl2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1cl2
catalytic residue: SER 339

1ibjA02
type: Pdb
references: 1ibj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ibj
catalytic residue: SER 405

1ibjC02
type: Pdb
references: 1ibj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ibj
catalytic residue: SER 405

Cloning, purification, and crystallization of Escherichia coli cystathionine beta-lyase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8566238
journal: FEBS Lett
volume: 379
pages: 94-6
published year: 1996
authors:
  item: Laber B
  item: Clausen T
  item: Huber R
  item: Messerschmidt A
  item: Egner U
  item: Muller-Fahrnow A
  item: Pohlenz HD

Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.83 ANGSTROMS)
medline id: 96428687
references: http://www.ncbi.nlm.nih.gov/pubmed/8831789
journal: J Mol Biol
volume: 262
pages: 202-24
published year: 1996
authors:
  item: Clausen T
  item: Huber R
  item: Laber B
  item: Pohlenz HD
  item: Messerschmidt A
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P06721

Slow-binding inhibition of Escherichia coli cystathionine beta-lyase by L-aminoethoxyvinylglycine: a kinetic and X-ray study.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/9376370
journal: Biochemistry
volume: 36
pages: 12633-43
published year: 1997
authors:
  item: Clausen T
  item: Huber R
  item: Messerschmidt A
  item: Pohlenz HD
  item: Laber B
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Mode of action of cystathionine beta-lyase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9165088
journal: Biol Chem
volume: 378
pages: 321-6
published year: 1997
authors:
  item: Clausen T
  item: Laber B
  item: Messerschmidt A

The crystal structure of cystathionine gamma-synthase from Nicotiana tabacum reveals its substrate and reaction specificity.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10438597
journal: J Mol Biol
volume: 290
pages: 983-96
published year: 1999
authors:
  item: Steegborn C
  item: Messerschmidt A
  item: Laber B
  item: Streber W
  item: Huber R
  item: Clausen T

Crystal structure of a NifS-like protein from Thermotoga maritima: implications for iron sulphur cluster assembly.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10715213
journal: J Mol Biol
volume: 297
pages: 451-64
published year: 2000
authors:
  item: Kaiser JT
  item: Clausen T
  item: Bourenkow GP
  item: Bartunik HD
  item: Steinbacher S
  item: Huber R

The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/11402193
journal: Plant Physiol
volume: 126
pages: 631-42
published year: 2001
authors:
  item: Breitinger U
  item: Clausen T
  item: Ehlert S
  item: Huber R
  item: Laber B
  item: Schmidt F
  item: Pohl E
  item: Messerschmidt A
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

IntermediateAnalogue
pdb: 1cl2A01
ligand het code: PPG

IntermediateAnalogue
pdb: 1cl2B01
ligand het code: PPG

ReferenceForCatalyticMechanism
reference index: 2
reference section: Fig.13, p.218-220
reference step: 4

ReferenceForCatalyticMechanism
reference index: 3
reference section: Scheme 1, Scheme 3

ReferenceForCatalyticMechanism
reference index: 4
reference section: Scheme 1, Scheme 2, p.323-326
reference step: 4

ReferenceForCatalyticMechanism
reference index: 7
reference section: Fig.7, p.638-639
reference step: 4