PDBsum entry 4mv6

Ligase

PDB id: 4mv6

Contents

Protein chain

412 a.a.

Ligands

EDO ×3

PCT

Waters ×175

PDB id:

4mv6

Name:

Ligase

Title:

Crystal structure of biotin carboxylase from haemophilus influenzae in complex with phosphonoacetamide

Structure:

Biotin carboxylase. Chain: a. Synonym: acetyl-coa carboxylase subunit a, acc. Engineered: yes

Source:

Haemophilus influenzae. Organism_taxid: 71421. Strain: atcc 51907 / dsm 11121 / kw20 / rd. Gene: accc, hi_0972. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.77Å R-factor: 0.176 R-free: 0.203

Authors:

T.C.Broussard,S.Pakhomova,D.B.Neau,T.S.Champion,R.J.Bonnot, G.L.Waldrop

Key ref:

T.C.Broussard et al. (2015). Structural Analysis of Substrate, Reaction Intermediate, and Product Binding in Haemophilus influenzae Biotin Carboxylase. Biochemistry, 54, 3860-3870. PubMed id: 26020841 DOI: 10.1021/acs.biochem.5b00340

Date:

23-Sep-13 Release date: 14-Jan-15

Protein chain

P43873  (ACCC_HAEIN) -  Biotin carboxylase from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

Seq: 448 a.a.

Struc: 412 a.a.

Enzyme reactions

• Enzyme class 1: E.C.6.3.4.14 - biotin carboxylase.
• Reaction: N₆-biotinyl-L-lysyl-[protein] + hydrogencarbonate + ATP = N₆- carboxybiotinyl-L-lysyl-[protein] + ADP + phosphate + H⁺

N(6)-biotinyl-L-lysyl-[protein] + hydrogencarbonate + ATP = N(6)- carboxybiotinyl-L-lysyl-[protein] + ADP + phosphate + H(+) (Bound ligand (Het Group name = PCT) matches with 44.44% similarity)

• Enzyme class 2: E.C.6.4.1.2 - acetyl-CoA carboxylase.
• Reaction: hydrogencarbonate + acetyl-CoA + ATP = malonyl-CoA + ADP + phosphate + H⁺

hydrogencarbonate + acetyl-CoA + ATP = malonyl-CoA + ADP + phosphate + H(+) (Bound ligand (Het Group name = PCT) matches with 44.44% similarity)

• Cofactor: Biotin

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/acs.biochem.5b00340

Biochemistry 54:3860-3870 (2015)

PubMed id: 26020841

Structural Analysis of Substrate, Reaction Intermediate, and Product Binding in Haemophilus influenzae Biotin Carboxylase.

T.C.Broussard, S.Pakhomova, D.B.Neau, R.Bonnot, G.L.Waldrop.

ABSTRACT

Acetyl-CoA carboxylase catalyzes the first and regulated step in fatty acid synthesis. In most Gram-negative and Gram-positive bacteria, the enzyme is composed of three proteins: biotin carboxylase, a biotin carboxyl carrier protein (BCCP), and carboxyltransferase. The reaction mechanism involves two half-reactions with biotin carboxylase catalyzing the ATP-dependent carboxylation of biotin-BCCP in the first reaction. In the second reaction, carboxyltransferase catalyzes the transfer of the carboxyl group from biotin-BCCP to acetyl-CoA to form malonyl-CoA. In this report, high-resolution crystal structures of biotin carboxylase from Haemophilus influenzae were determined with bicarbonate, the ATP analogue AMPPCP; the carboxyphosphate intermediate analogues, phosphonoacetamide and phosphonoformate; the products ADP and phosphate; and the carboxybiotin analogue N1'-methoxycarbonyl biotin methyl ester. The structures have a common theme in that bicarbonate, phosphate, and the methyl ester of the carboxyl group of N1'-methoxycarbonyl biotin methyl ester all bound in the same pocket in the active site of biotin carboxylase and as such utilize the same set of amino acids for binding. This finding suggests a catalytic mechanism for biotin carboxylase in which the binding pocket that binds tetrahedral phosphate also accommodates and stabilizes a tetrahedral dianionic transition state resulting from direct transfer of CO2 from the carboxyphosphate intermediate to biotin.