EzCatDB: D00515
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DB codeD00515
CATH domainDomain 13.40.640.10 : Aspartate Aminotransferase; domain 2Catalytic domain
Domain 23.90.1150.10 : Aspartate Aminotransferase, domain 1Catalytic domain
E.C.4.4.1.8
CSA1cl1

CATH domainRelated DB codes (homologues)
3.40.640.10 : Aspartate Aminotransferase; domain 2D00085,D00092,D00101,D00102,D00103,D00104,D00107,D00108,D00109,D00255,D00257,D00258,D00265,D00269,M00031,D00279
3.90.1150.10 : Aspartate Aminotransferase, domain 1D00085,D00092,D00101,D00102,D00103,D00104,D00107,D00108,D00109,D00255,D00257,D00258,D00265,D00269,M00031,D00279

Enzyme Name
UniProtKBKEGG

P06721P53780
Protein nameCystathionine beta-lyase MetCCystathionine beta-lyase, chloroplasticcystathionine beta-lyase
beta-cystathionase
cystine lyase
cystathionine L-homocysteine-lyase (deaminating)
L-cystathionine L-homocysteine-lyase (deaminating)
SynonymsCBL
EC 4.4.1.8
Beta-cystathionase
Cysteine lyase
CBL
EC 4.4.1.8
Beta-cystathionase
Cysteine lyase
RefSeqNP_417481.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491201.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_191264.1 (Protein)
NM_115564.3 (DNA/RNA sequence)
NP_850712.1 (Protein)
NM_180381.2 (DNA/RNA sequence)
PfamPF01053 (Cys_Met_Meta_PP)
[Graphical view]
PF01053 (Cys_Met_Meta_PP)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00271Methionine metabolism
MAP00272Cysteine metabolism
MAP00450Selenoamino acid metabolism
MAP00910Nitrogen metabolism
MAP00920Sulfur metabolism

UniProtKB:Accession NumberP06721P53780
Entry nameMETC_ECOLIMETC_ARATH
ActivityL-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate.L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate.
SubunitHomotetramer.Homotetramer.
Subcellular locationCytoplasm.Plastid, chloroplast.
CofactorPyridoxal phosphate.Pyridoxal phosphate.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00018C00542C00001C00155C00014C00022
CompoundPyridoxal phosphateCystathionineH2OL-HomocysteineNH3Pyruvate
Typearomatic ring (with nitrogen atoms),phosphate group/phosphate ionamino acids,sulfide groupH2Oamino acids,sulfhydryl groupamine group,organic ioncarbohydrate,carboxyl group
ChEBI18405
17755
15377
17588
58199
16134
32816

PubChem1051
834
4083111
962
22247451
91552
6971015
222
1060

               
1cl1A01Bound:LLPUnbound UnboundUnboundUnboundUnbound
1cl1B01Bound:LLPUnbound UnboundUnboundUnboundUnbound
1cl2A01Analogue:PPGUnbound UnboundUnboundUnboundIntermediate-analogue:PPG
1cl2B01Analogue:PPGUnbound UnboundUnboundUnboundIntermediate-analogue:PPG
1ibjA01Bound:PLPUnbound UnboundUnboundUnboundUnbound
1ibjC01Bound:PLPUnbound UnboundUnboundUnboundUnbound
1cl1A02UnboundUnbound UnboundUnboundUnboundUnbound
1cl1B02UnboundUnbound UnboundUnboundUnboundUnbound
1cl2A02UnboundUnbound UnboundUnboundUnboundUnbound
1cl2B02UnboundUnbound UnboundUnboundUnboundUnbound
1ibjA02UnboundUnbound UnboundUnboundUnboundUnbound
1ibjC02UnboundUnbound UnboundUnboundUnboundUnbound

Active-site residues
resource
literature [2], [7]
pdbCatalytic residuesCofactor-binding residues
          
1cl1A01TYR  56;TYR 111;ASP 185;LLP 210
LLP 210(PLP binding)
1cl1B01TYR  56;TYR 111;ASP 185;LLP 210
LLP 210(PLP binding)
1cl2A01TYR  56;TYR 111;ASP 185;LYS 210
LYS 210(PLP binding)
1cl2B01TYR  56;TYR 111;ASP 185;LYS 210
LYS 210(PLP binding)
1ibjA01TYR 127;TYR 181;ASP 253;LYS 278
LYS 278(PLP binding)
1ibjC01TYR 127;TYR 181;ASP 253;LYS 278
LYS 278(PLP binding)
1cl1A02SER 339
 
1cl1B02SER 339
 
1cl2A02SER 339
 
1cl2B02SER 339
 
1ibjA02SER 405
 
1ibjC02SER 405
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.13, p.218-2204
[3]Scheme 1, Scheme 3
[4]Scheme 1, Scheme 2, p.323-3264
[7]Fig.7, p.638-6394

references
[1]
PubMed ID8566238
JournalFEBS Lett
Year1996
Volume379
Pages94-6
AuthorsLaber B, Clausen T, Huber R, Messerschmidt A, Egner U, Muller-Fahrnow A, Pohlenz HD
TitleCloning, purification, and crystallization of Escherichia coli cystathionine beta-lyase.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.83 ANGSTROMS)
Medline ID96428687
PubMed ID8831789
JournalJ Mol Biol
Year1996
Volume262
Pages202-24
AuthorsClausen T, Huber R, Laber B, Pohlenz HD, Messerschmidt A
TitleCrystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A.
Related PDB1cl1
Related UniProtKBP06721
[3]
CommentsX-ray crystallography
PubMed ID9376370
JournalBiochemistry
Year1997
Volume36
Pages12633-43
AuthorsClausen T, Huber R, Messerschmidt A, Pohlenz HD, Laber B
TitleSlow-binding inhibition of Escherichia coli cystathionine beta-lyase by L-aminoethoxyvinylglycine: a kinetic and X-ray study.
Related PDB1cl2
[4]
PubMed ID9165088
JournalBiol Chem
Year1997
Volume378
Pages321-6
AuthorsClausen T, Laber B, Messerschmidt A
TitleMode of action of cystathionine beta-lyase.
[5]
PubMed ID10438597
JournalJ Mol Biol
Year1999
Volume290
Pages983-96
AuthorsSteegborn C, Messerschmidt A, Laber B, Streber W, Huber R, Clausen T
TitleThe crystal structure of cystathionine gamma-synthase from Nicotiana tabacum reveals its substrate and reaction specificity.
[6]
PubMed ID10715213
JournalJ Mol Biol
Year2000
Volume297
Pages451-64
AuthorsKaiser JT, Clausen T, Bourenkow GP, Bartunik HD, Steinbacher S, Huber R
TitleCrystal structure of a NifS-like protein from Thermotoga maritima: implications for iron sulphur cluster assembly.
[7]
CommentsX-ray crystallography
PubMed ID11402193
JournalPlant Physiol
Year2001
Volume126
Pages631-42
AuthorsBreitinger U, Clausen T, Ehlert S, Huber R, Laber B, Schmidt F, Pohl E, Messerschmidt A
TitleThe three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity.
Related PDB1ibj

comments
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.)

createdupdated
2004-07-012015-07-28


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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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