EzCatDB: D00639
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DB codeD00639
RLCP classification6.30.115000.5080 : Double-bonded atom exchange
3.1187.65790.5550 : Transfer
6.40.500000.5600 : Double-bonded atom exchange
CATH domainDomain 13.40.640.10 : Aspartate Aminotransferase; domain 2Catalytic domain
Domain 23.90.1150.10 : Aspartate Aminotransferase, domain 1
E.C.2.3.1.29
CSA1fc4


Enzyme Name
UniProtKBKEGG

P0AB77Q83F40
Protein name2-amino-3-ketobutyrate coenzyme A ligase
Glycine C-acetyltransferase
2-Amino-3-ketobutyrate CoA ligase
2-Amino-3-ketobutyrate coenzyme A ligase
2-Amino-3-ketobutyrate-CoA ligase
Glycine acetyltransferase
Aminoacetone synthase
SynonymsAKB ligase
EC 2.3.1.29
Glycine acetyltransferase
2-amino-3-ketobutyrate coenzyme A ligase
EC 2.3.1.29
RefSeqNP_418074.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491816.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_819161.1 (Protein)
NC_002971.3 (DNA/RNA sequence)
PfamPF00155 (Aminotran_1_2)
[Graphical view]
PF00155 (Aminotran_1_2)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00260Glycine, serine and threonine metabolism

UniProtKB:Accession NumberP0AB77Q83F40
Entry nameKBL_ECOLIQ83F40_COXBU
ActivityAcetyl-CoA + glycine = CoA + 2-amino-3-oxobutanoate.
SubunitHomodimer.
Subcellular location

CofactorPyridoxal phosphate.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00018C00024C00037C00010C03508I00044I00045I00162I00161
CompoundPyridoxal phosphateacetyl-CoAglycineCoAL-2-amino-3-oxobutanoateExternal aldimine intermediate (PLP-Gly)Quinonoid intermediate (PLP-Gly)External aldimine intermediate (PLP-2-amino-3-ketobutyric acid-CoA-tetrahedral intermediate)External aldimine intermediate (PLP-2-amino-3-ketobutyric acid)
Typearomatic ring (with nitrogen atoms),phosphate group/phosphate ionamine group,carbohydrate,nucleotide,peptide/protein,sulfide groupamino acidsamine group,carbohydrate,nucleotide,peptide/protein,sulfhydryl groupamino acids,carbohydrate



ChEBI18405
15351
15428
57305
15346
40673
78948




PubChem1051
6302
444493
750
5257127
87642
6816
86289686
440033




                 
1fc4A01Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:AKB-PLP
1fc4B01Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:AKB-PLP
3tqxA02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3tqxB02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1fc4A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1fc4B02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3tqxA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3tqxB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature[6]
pdbCatalytic residuesCofactor-binding residues
          
1fc4A01HIS 136;SER 185;ASP 210;HIS 213;LYS 244
LYS 244(PLP binding)
1fc4B01HIS 136;SER 185;ASP 210;HIS 213;LYS 244
LYS 244(PLP binding)
3tqxA02HIS 134;SER 183;ASP 208;HIS 211;LYS 242
LYS 242(PLP binding)
3tqxB02HIS 134;SER 183;ASP 208;HIS 211;LYS 242
LYS 242(PLP binding)
1fc4A02               
 
1fc4B02               
 
3tqxA01               
 
3tqxB01               
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]Fig.8, p.5158-5159

references
[1]
PubMed ID3117785
JournalJ Biol Chem
Year1987
Volume262
Pages14441-7
AuthorsMukherjee JJ, Dekker EE
TitlePurification, properties, and N-terminal amino acid sequence of homogeneous Escherichia coli 2-amino-3-ketobutyrate CoA ligase, a pyridoxal phosphate-dependent enzyme.
[2]
PubMed ID2104756
JournalBiochim Biophys Acta
Year1990
Volume1037
Pages24-9
AuthorsMukherjee JJ, Dekker EE
Title2-Amino-3-ketobutyrate CoA ligase of Escherichia coli: stoichiometry of pyridoxal phosphate binding and location of the pyridoxyllysine peptide in the primary structure of the enzyme.
[3]
PubMed ID1903922
JournalBiochem J
Year1991
Volume275
Pages575-9
AuthorsRay S, Sarkar D, Ray M
TitleAminoacetone synthase from goat liver. Involvement of arginine residue at the active site and on the stability of the enzyme.
[4]
PubMed ID1444446
JournalArch Biochem Biophys
Year1992
Volume299
Pages147-53
AuthorsMukherjee JJ, Dekker EE
TitleInactivation of Escherichia coli 2-amino-3-ketobutyrate CoA ligase by phenylglyoxal and identification of an active-site arginine peptide.
[5]
PubMed ID7880831
JournalBiochemistry
Year1995
Volume34
Pages3362-7
AuthorsTong H, Davis L
Title2-Amino-3-ketobutyrate-CoA ligase from beef liver mitochondria: an NMR spectroscopic study of low-barrier hydrogen bonds of a pyridoxal 5'-phosphate-dependent enzyme.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND PYRIDOXAL PHOSPHATE, REACTION MECHANISM, SUBUNIT.
PubMed ID11318637
JournalBiochemistry
Year2001
Volume40
Pages5151-60
AuthorsSchmidt A, Sivaraman J, Li Y, Larocque R, Barbosa JA, Smith C, Matte A, Schrag JD, Cygler M
TitleThree-dimensional structure of 2-amino-3-ketobutyrate CoA ligase from Escherichia coli complexed with a PLP-substrate intermediate: inferred reaction mechanism.
Related PDB1fc4
Related UniProtKBP0AB77

comments
This enzyme belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family (or Type I PLP-dependent enzyme fold). This enzyme is homologous to 8-amino-7-oxononanoate synthase (EC 2.3.1.47)(D00092 in EzCatDB).
According to the literature [6], this enzyme catalyzes the following reactions:
(A) Formation of external aldimine (with substrate glycine) (PLP-Gly; I00044)(or transaldimination)
(B) Transfer of acyl group to form an external aldimine (PLP-2-amino-3-ketobutyric acid; I00161)
(C) Reformation of internal aldimine with Lys244 (of 1fc4) (or transaldimination)
These reactions proceed in the following way:
(A) Formation of external aldimine (with substrate glycine) (PLP-Gly; I00044)(or transaldimination):
(A0) The hydrogen-bonding network, composed of His136/Ser185/Asp210, keeps the O3 atom of PLP negatively charged.
(A1) The negatively charged O3 atom of PLP acts as a general base, to deprotonate the amino group of substrate, glycine. The abstracted proton is donated to NZ nitrogen of Lys244.
(A2) The deprotonated amine group of glycine makes a nucleophilic attack on the C4A carbon of PLP, forming a transient geminal diamine intermediate.
(A3) There must be a general base, which deprotonates the amine group of the previously glycine substrate, so that the lone pair of the amine group can attack on the C4A atom to form a double-bond, and to release the amine of the catalytic residue, Lys244. His213 may play the role as the general base. (The released Lys244 must be deprotonated, so that it can act as a general base at the next stage.) By releasing Lys244, the external aldimine intermediate (PLP-Gly; I00044) is formed.
(B) Transfer of acyl group to form an external aldimine (PLP-2-amino-3-ketobutyric acid; I00161):
(B1) Lys244 acts as a general base, which abstracts a proton from alpha-carbon of glycine (covalently bound to PLP; I00044), leading to the formation of a quinonoid intermediate (I00045). Here, the intermediate is stabilized by its resonance.
(B2) The transferred group, acyl group of the second substrate, acetyl-CoA, is stabilized by Ser185.
(B3) The activated acceptor group, the alpha-carbon (sp2; double-bonde), makes a nucleophilic attack on the thioester carbon atom of acetyl-CoA, to form a tetrahedral intermediate (I00162). The tetrahedral intermediate is stabilized by Ser185.
(B4) Lys244 now acts as a general acid to protonate the sulfur atom of the leaving group, releasing the product, CoA, and forming a carbonyl group, which is stabilized by Ser185. This reaction forms an external aldimine intermediate (PLP-2-amino-3-ketobutyric acid; I00161).
(C) Reformation of internal aldimine (or transaldimination):
(C1) The deprotonated Lys244 acts as a nucleophile, which attacks on the C4A atom of PLP, forming a geminal diamine intermediate.
(C2) There must be a general acid, to protonate the amine from the external aldimine intermediate (I00161). (His213 might play the role.)
(C3) The negatively charged O3 atom of PLP abstracts a proton from the nitrogen of Lys244, and then protonates the nitrogen atom from the external aldimine intermediate, so that the lone pair of Lys244 attacks on the C4A atom again to form a double-bond, and to release the product amine group.
(C4) The hydrogen-bonding network, composed of His136/Ser185/Asp210, must keep the O3 atom of PLP negatively charged during this reaction.

createdupdated
2012-10-262015-08-06


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