DB code: D00639

RLCP classification 6.40.500000.5600 : Double-bonded atom exchange
3.1187.65790.5550 : Transfer
6.30.115000.5080 : Double-bonded atom exchange
CATH domain 3.40.640.10 : Aspartate Aminotransferase; domain 2 Catalytic domain
3.90.1150.10 : Aspartate Aminotransferase, domain 1
E.C. 2.3.1.29
CSA 1fc4
M-CSA 1fc4
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0AB77 2-amino-3-ketobutyrate coenzyme A ligase
AKB ligase
EC 2.3.1.29
Glycine acetyltransferase
NP_418074.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491816.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00155 (Aminotran_1_2)
[Graphical View]
Q83F40
2-amino-3-ketobutyrate coenzyme A ligase
EC 2.3.1.29
NP_819161.1 (Protein)
NC_002971.3 (DNA/RNA sequence)
PF00155 (Aminotran_1_2)
[Graphical View]

KEGG enzyme name
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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q83F40 Q83F40_COXBU
P0AB77 KBL_ECOLI Acetyl-CoA + glycine = CoA + 2-amino-3-oxobutanoate. Homodimer. Pyridoxal phosphate.

KEGG Pathways
Map code Pathways E.C.
MAP00260 Glycine, serine and threonine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00018 C00024 C00037 C00010 C03508 I00044 I00045 I00162 I00161
E.C.
Compound Pyridoxal phosphate acetyl-CoA glycine CoA L-2-amino-3-oxobutanoate External 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)
Type aromatic ring (with nitrogen atoms),phosphate group/phosphate ion amine group,carbohydrate,nucleotide ,peptide/protein,sulfide group amino acids amine group,carbohydrate,nucleotide ,peptide/protein,sulfhydryl group amino acids,carbohydrate
ChEBI 18405
15351
15428
57305
15346
40673
78948
PubChem 1051
444493
6302
5257127
750
6816
87642
440033
86289686
1fc4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:AKB-PLP
1fc4B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:AKB-PLP
3tqxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3tqxB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fc4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fc4B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3tqxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3tqxB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature[6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1fc4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 136;SER 185;ASP 210;HIS 213;LYS 244 LYS 244(PLP binding)
1fc4B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 136;SER 185;ASP 210;HIS 213;LYS 244 LYS 244(PLP binding)
3tqxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 134;SER 183;ASP 208;HIS 211;LYS 242 LYS 242(PLP binding)
3tqxB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 134;SER 183;ASP 208;HIS 211;LYS 242 LYS 242(PLP binding)
1fc4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1fc4B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3tqxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3tqxB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[6]
Fig.8, p.5158-5159

References
[1]
Resource
Comments
Medline ID
PubMed ID 3117785
Journal J Biol Chem
Year 1987
Volume 262
Pages 14441-7
Authors Mukherjee JJ, Dekker EE
Title Purification, properties, and N-terminal amino acid sequence of homogeneous Escherichia coli 2-amino-3-ketobutyrate CoA ligase, a pyridoxal phosphate-dependent enzyme.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2104756
Journal Biochim Biophys Acta
Year 1990
Volume 1037
Pages 24-9
Authors Mukherjee JJ, Dekker EE
Title 2-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.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1903922
Journal Biochem J
Year 1991
Volume 275
Pages 575-9
Authors Ray S, Sarkar D, Ray M
Title Aminoacetone synthase from goat liver. Involvement of arginine residue at the active site and on the stability of the enzyme.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1444446
Journal Arch Biochem Biophys
Year 1992
Volume 299
Pages 147-53
Authors Mukherjee JJ, Dekker EE
Title Inactivation of Escherichia coli 2-amino-3-ketobutyrate CoA ligase by phenylglyoxal and identification of an active-site arginine peptide.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7880831
Journal Biochemistry
Year 1995
Volume 34
Pages 3362-7
Authors Tong H, Davis L
Title 2-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.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND PYRIDOXAL PHOSPHATE, REACTION MECHANISM, SUBUNIT.
Medline ID
PubMed ID 11318637
Journal Biochemistry
Year 2001
Volume 40
Pages 5151-60
Authors Schmidt A, Sivaraman J, Li Y, Larocque R, Barbosa JA, Smith C, Matte A, Schrag JD, Cygler M
Title Three-dimensional structure of 2-amino-3-ketobutyrate CoA ligase from Escherichia coli complexed with a PLP-substrate intermediate: inferred reaction mechanism.
Related PDB 1fc4
Related UniProtKB P0AB77

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.

Created Updated
2012-10-26 2015-08-06