DB code: D00515

CATH domain 3.40.640.10 : Aspartate Aminotransferase; domain 2 Catalytic domain
3.90.1150.10 : Aspartate Aminotransferase, domain 1 Catalytic domain
E.C. 4.4.1.8
CSA 1cl1
M-CSA 1cl1
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P06721 Cystathionine beta-lyase MetC
CBL
EC 4.4.1.8
Beta-cystathionase
Cysteine lyase
NP_417481.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491201.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01053 (Cys_Met_Meta_PP)
[Graphical View]
P53780 Cystathionine beta-lyase, chloroplastic
CBL
EC 4.4.1.8
Beta-cystathionase
Cysteine lyase
NP_191264.1 (Protein)
NM_115564.3 (DNA/RNA sequence)
NP_850712.1 (Protein)
NM_180381.2 (DNA/RNA sequence)
PF01053 (Cys_Met_Meta_PP)
[Graphical View]

KEGG enzyme name
cystathionine beta-lyase
beta-cystathionase
cystine lyase
cystathionine L-homocysteine-lyase (deaminating)
L-cystathionine L-homocysteine-lyase (deaminating)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P06721 METC_ECOLI L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate. Homotetramer. Cytoplasm. Pyridoxal phosphate.
P53780 METC_ARATH L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate. Homotetramer. Plastid, chloroplast. Pyridoxal phosphate.

KEGG Pathways
Map code Pathways E.C.
MAP00271 Methionine metabolism
MAP00272 Cysteine metabolism
MAP00450 Selenoamino acid metabolism
MAP00910 Nitrogen metabolism
MAP00920 Sulfur metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00018 C00542 C00001 C00155 C00014 C00022
E.C.
Compound Pyridoxal phosphate Cystathionine H2O L-Homocysteine NH3 Pyruvate
Type aromatic ring (with nitrogen atoms),phosphate group/phosphate ion amino acids,sulfide group H2O amino acids,sulfhydryl group amine group,organic ion carbohydrate,carboxyl group
ChEBI 18405
17755
15377
17588
58199
16134
32816
PubChem 1051
4083111
834
22247451
962
6971015
91552
222
1060
1cl1A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound Unbound
1cl1B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound Unbound
1cl2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PPG Unbound Unbound Unbound Unbound Intermediate-analogue:PPG
1cl2B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PPG Unbound Unbound Unbound Unbound Intermediate-analogue:PPG
1ibjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1ibjC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound
1cl1A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1cl1B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1cl2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1cl2B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ibjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ibjC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [2], [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1cl1A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 56;TYR 111;ASP 185;LLP 210 LLP 210(PLP binding)
1cl1B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 56;TYR 111;ASP 185;LLP 210 LLP 210(PLP binding)
1cl2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 56;TYR 111;ASP 185;LYS 210 LYS 210(PLP binding)
1cl2B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 56;TYR 111;ASP 185;LYS 210 LYS 210(PLP binding)
1ibjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 127;TYR 181;ASP 253;LYS 278 LYS 278(PLP binding)
1ibjC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 127;TYR 181;ASP 253;LYS 278 LYS 278(PLP binding)
1cl1A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 339
1cl1B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 339
1cl2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 339
1cl2B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 339
1ibjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 405
1ibjC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 405

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig.13, p.218-220 4
[3]
Scheme 1, Scheme 3
[4]
Scheme 1, Scheme 2, p.323-326 4
[7]
Fig.7, p.638-639 4

References
[1]
Resource
Comments
Medline ID
PubMed ID 8566238
Journal FEBS Lett
Year 1996
Volume 379
Pages 94-6
Authors Laber B, Clausen T, Huber R, Messerschmidt A, Egner U, Muller-Fahrnow A, Pohlenz HD
Title Cloning, purification, and crystallization of Escherichia coli cystathionine beta-lyase.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.83 ANGSTROMS)
Medline ID 96428687
PubMed ID 8831789
Journal J Mol Biol
Year 1996
Volume 262
Pages 202-24
Authors Clausen T, Huber R, Laber B, Pohlenz HD, Messerschmidt A
Title Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A.
Related PDB 1cl1
Related UniProtKB P06721
[3]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9376370
Journal Biochemistry
Year 1997
Volume 36
Pages 12633-43
Authors Clausen T, Huber R, Messerschmidt A, Pohlenz HD, Laber B
Title Slow-binding inhibition of Escherichia coli cystathionine beta-lyase by L-aminoethoxyvinylglycine: a kinetic and X-ray study.
Related PDB 1cl2
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9165088
Journal Biol Chem
Year 1997
Volume 378
Pages 321-6
Authors Clausen T, Laber B, Messerschmidt A
Title Mode of action of cystathionine beta-lyase.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10438597
Journal J Mol Biol
Year 1999
Volume 290
Pages 983-96
Authors Steegborn C, Messerschmidt A, Laber B, Streber W, Huber R, Clausen T
Title The crystal structure of cystathionine gamma-synthase from Nicotiana tabacum reveals its substrate and reaction specificity.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 10715213
Journal J Mol Biol
Year 2000
Volume 297
Pages 451-64
Authors Kaiser JT, Clausen T, Bourenkow GP, Bartunik HD, Steinbacher S, Huber R
Title Crystal structure of a NifS-like protein from Thermotoga maritima: implications for iron sulphur cluster assembly.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11402193
Journal Plant Physiol
Year 2001
Volume 126
Pages 631-42
Authors Breitinger U, Clausen T, Ehlert S, Huber R, Laber B, Schmidt F, Pohl E, Messerschmidt A
Title The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity.
Related PDB 1ibj
Related UniProtKB

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.)

Created Updated
2004-07-01 2015-07-28