PDBsum entry: 3g8c

Ligase

PDB-id: 3g8c

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

444 a.a. *

Ligands

ADP ×2

BTN ×2

BCT ×2

Metal ions

_MG ×2

Waters ×856

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

3g8c

Name:

Ligase

Title:

Crystal stucture of biotin carboxylase in complex with biotin, bicarbonate, adp and mg ion

Structure:

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

Source:

Escherichia coli. Organism_taxid: 83333. Gene: accc, b3256, fabg, jw3224. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Chains A, B: P24182 (ACCC_ECOLI)

Seq:

Struc:

Seq:

449 a.a.

Struc:

444 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class 1:

E.C.6.3.4.14   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP + biotin-carboxyl-carrier protein + CO₂ = ADP + phosphate + carboxybiotin-carboxyl-carrier protein (see diagram below)

Enzyme class 2:

E.C.6.4.1.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP + acetyl-CoA + HCO₃^- = ADP + phosphate + malonyl-CoA (see diagram below)

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.

Resolution:

2.00Å

R-factor:

0.184

R-free:

0.216

Authors:

C.Y.Chou,L.P.Yu,L.Tong

Key ref:

C.Y.Chou et al. (2009). Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism.. J Biol Chem, 284, 11690-11697. [PubMed id: 19213731] [DOI: 10.1074/jbc.M805783200]

Date:

12-Feb-09

Release date:

03-Mar-09

Related entries:

3g8d

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M805783200

J Biol Chem 284:11690-11697 (2009)

PubMed id: 19213731

Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism.

C.Y.Chou, L.P.Yu, L.Tong.

ABSTRACT

Biotin-dependent carboxylases are widely distributed in nature and have important functions in many cellular processes. These enzymes share a conserved biotin carboxylase (BC) component, which catalyzes the ATP-dependent carboxylation of biotin using bicarbonate as the donor. Despite the availability of a large amount of biochemical and structural information on BC, the molecular basis for its catalysis is currently still poorly understood. We report here the crystal structure at 2.0 A resolution of wild-type Escherichia coli BC in complex with its substrates biotin, bicarbonate, and Mg-ADP. The structure suggests that Glu(296) is the general base that extracts the proton from bicarbonate, and Arg(338) is the residue that stabilizes the enolate biotin intermediate in the carboxylation reaction. The B domain of BC is positioned closer to the active site, leading to a 2-A shift in the bound position of the adenine nucleotide and bringing it near the bicarbonate for catalysis. One of the oxygen atoms of bicarbonate is located in the correct position to initiate the nucleophilic attack on ATP to form the carboxyphosphate intermediate. This oxygen is also located close to the N1' atom of biotin, providing strong evidence that the phosphate group, derived from decomposition of carboxyphosphate, is the general base that extracts the proton on this N1' atom. The structural observations are supported by mutagenesis and kinetic studies. Overall, this first structure of BC in complex with substrates offers unprecedented insights into the molecular mechanism for the catalysis by this family of enzymes.

Selected figure(s)

Figure 1.
Structure of wild-type E. coli BC in complex with biotin, bicarbonate, and Mg-ADP. A, overall structure of the E. coli BC dimer in complex with the substrates. Biotin, bicarbonate, and ADP are shown in pink, black, and green for carbon atoms, respectively. The modeled binding mode of ATP (in gray) is shown for the monomer in yellow (PDB 3G8C). B, final 2F[o] - F[c] electron density for biotin at 2.0 Å resolution, contoured at 1σ. The omit F[o] - F[c] density looks essentially the same. C, electron density for bicarbonate. D, electron density for Mg-ADP. E, schematic drawing showing detailed interactions in the active site of BC. Hydrogen bonding and ion pair interactions are indicated with the dashed lines in red. All structure figures in this paper are produced with PyMOL (44).

Figure 3.
Molecular mechanism for the catalysis by BC. A, modeled binding mode of ATP (in gray) in the active site of BC. The bicarbonate is in the appropriate location to initiate the reaction. B, schematic drawing of the catalytic mechanism of BC. Glu^296 and Arg^338 have crucial roles in this reaction.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 11690-11697) copyright 2009.

Figures were selected by an automated process.