PDBsum entry 1dv2

Ligase

PDB id: 1dv2

Contents

Protein chains

450 a.a. *

Ligands

ATP ×2

Waters ×130

* Residue conservation analysis

PDB id:

1dv2

Name:

Ligase

Title:

The structure of biotin carboxylase, mutant e288k, complexed with atp

Structure:

Biotin carboxylase. Chain: a, b. Fragment: biotin carboxylase. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.172 R-free: 0.203

Authors:

J.B.Thoden,C.Z.Blanchard,H.M.Holden,G.L.Waldrop

Key ref:

J.B.Thoden et al. (2000). Movement of the biotin carboxylase B-domain as a result of ATP binding. J Biol Chem, 275, 16183-16190. PubMed id: 10821865 DOI: 10.1074/jbc.275.21.16183

Date:

19-Jan-00 Release date: 09-Jun-00

Protein chains

P24182  (ACCC_ECOLI) -  Biotin carboxylase from Escherichia coli (strain K12)

Seq: 449 a.a.

Struc: 450 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: 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] (Bound ligand (Het Group name = ATP) corresponds exactly) + hydrogencarbonate + ATP = N(6)- carboxybiotinyl-L-lysyl-[protein] + ADP + phosphate + H(+)

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

reference

DOI no: 10.1074/jbc.275.21.16183

J Biol Chem 275:16183-16190 (2000)

PubMed id: 10821865

Movement of the biotin carboxylase B-domain as a result of ATP binding.

J.B.Thoden, C.Z.Blanchard, H.M.Holden, G.L.Waldrop.

ABSTRACT

Acetyl-CoA carboxylase catalyzes the first committed step in fatty acid synthesis. In Escherichia coli, the enzyme is composed of three distinct protein components: biotin carboxylase, biotin carboxyl carrier protein, and carboxyltransferase. The biotin carboxylase component has served for many years as a paradigm for mechanistic studies devoted toward understanding more complicated biotin-dependent carboxylases. The three-dimensional x-ray structure of an unliganded form of E. coli biotin carboxylase was originally solved in 1994 to 2.4-A resolution. This study revealed the architecture of the enzyme and demonstrated that the protein belongs to the ATP-grasp superfamily. Here we describe the three-dimensional structure of the E. coli biotin carboxylase complexed with ATP and determined to 2.5-A resolution. The major conformational change that occurs upon nucleotide binding is a rotation of approximately 45(o) of one domain relative to the other domains thereby closing off the active site pocket. Key residues involved in binding the nucleotide to the protein include Lys-116, His-236, and Glu-201. The backbone amide groups of Gly-165 and Gly-166 participate in hydrogen bonding interactions with the phosphoryl oxygens of the nucleotide. A comparison of this closed form of biotin carboxylase with carbamoyl-phosphate synthetase is presented.

Selected figure(s)

Figure 2.
Fig. 2. Mode of binding of the inorganic phosphate ion to biotin carboxylase. Shown in a is a representative portion of the electron density map near the phosphate. The map, contoured at 1 , was calculated with coefficients of the form (2F[o] F[c]), where F[o] was the native structure factor amplitude and F[c] was the calculated structure factor amplitude. The hydrogen bonding pattern around the phosphate ion is indicated by the dashed lines in b. Water molecules are depicted as red spheres.

Figure 5.
Fig. 5. Superposition of the -carbon trace of native biotin carboxylase onto that of the E288K protein/ATP complex. The unliganded form of biotin carboxylase is shown in red bonds, while the E288K protein is displayed in black bonds. The ATP is depicted in a ball-and-stick representation.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 16183-16190) copyright 2000.

Figures were selected by an automated process.