DB code: D00639

RLCP classification	6.30.115000.5080 : Double-bonded atom exchange
	3.1187.65790.5550 : Transfer
	6.40.500000.5600 : Double-bonded atom exchange
CATH domain	3.40.640.10 : Aspartate Aminotransferase; domain 2	Catalytic domain
CATH 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
P0AB77	KBL_ECOLI	Acetyl-CoA + glycine = CoA + 2-amino-3-oxobutanoate.	Homodimer.		Pyridoxal phosphate.
Q83F40	Q83F40_COXBU

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 18405	15351 15351	15428 57305 15428 57305	15346 15346	40673 78948 40673 78948
PubChem	1051 1051	444493 6302 444493 6302	5257127 750 5257127 750	6816 87642 6816 87642	440033 86289686 440033 86289686

1fc4A01	Bound:PLP	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Intermediate-bound:AKB-PLP
1fc4B01	Bound:PLP	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Intermediate-bound:AKB-PLP
3tqxA02	Bound:PLP	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
3tqxB02	Bound:PLP	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1fc4A02	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1fc4B02	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
3tqxA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
3tqxB01	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	HIS 136;SER 185;ASP 210;HIS 213;LYS 244	LYS 244(PLP binding)
1fc4B01	HIS 136;SER 185;ASP 210;HIS 213;LYS 244	LYS 244(PLP binding)
3tqxA02	HIS 134;SER 183;ASP 208;HIS 211;LYS 242	LYS 242(PLP binding)
3tqxB02	HIS 134;SER 183;ASP 208;HIS 211;LYS 242	LYS 242(PLP binding)
1fc4A02
1fc4B02
3tqxA01
3tqxB01

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.

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