EzCatDB D00639

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

Synonyms

AKB ligase
EC 2.3.1.29
Glycine acetyltransferase

2-amino-3-ketobutyrate coenzyme A ligase
EC 2.3.1.29

RefSeq

NP_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)

Pfam

PF00155 (Aminotran_1_2)
[Graphical view]

KEGG pathways

MAP code

Pathways

MAP00260

Glycine, serine and threonine metabolism

UniProtKB:Accession Number

P0AB77

Q83F40

Entry name

KBL_ECOLI

Q83F40_COXBU

Activity

Acetyl-CoA + glycine = CoA + 2-amino-3-oxobutanoate.

Subunit

Homodimer.

Subcellular location

Cofactor

Pyridoxal phosphate.

Compound table: links to PDB-related databases & PoSSuM

Cofactors

Substrates

Products

intermediates

KEGG-id

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

PubChem

Bound:PLP

Unbound

Intermediate-bound:AKB-PLP

1fc4B01

Bound:PLP

Unbound

Intermediate-bound:AKB-PLP

3tqxA02

Bound:PLP

Unbound

3tqxB02

Bound:PLP

Unbound

Unbound

Unbound

Unbound

Unbound

Active-site residues

resource

literature[6]

pdb

Catalytic residues

Cofactor-binding residues

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)

References for Catalytic Mechanism

References

Sections

No. of steps in catalysis

[6]

Fig.8, p.5158-5159

references

[1]

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.

[2]

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.

[3]

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.

[4]

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.

[5]

PubMed ID

7880831

Journal

Biochemistry

Year

1995

Volume

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.

[6]

Comments

X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND PYRIDOXAL PHOSPHATE, REACTION MECHANISM, SUBUNIT.

PubMed ID

11318637

Journal

Biochemistry

Year

2001

Volume

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

Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
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)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )