Three-Dimensional Structure of the Biotin Carboxylase Subunit of Acetyl-CoA Carboxylase

Waldrop, Grover L.; Rayment, Ivan; Holden, Hazel M.

doi:10.1021/bi00200a004

Cited by 198 publications

(252 citation statements)

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“…Support for this mechanism in biotin carboxylase stems from the observation that the temperature factors for atoms in the B-domain are significantly higher in the unliganded enzyme than in the ATP-bound form. 11 Analyses of the protein dynamic fluctuations have been used to help identify structural segments that undergo the conformational changes associated with ATP binding in biotin carboxylase. In the present study, two approaches are utilized.…”

Section: Resultsmentioning

confidence: 99%

“…9 ACC from the Gram-negative bacterium Escherichia coli has been used as a model system for mechanistic investigations because the purified BC and CT components retain their activities, and utilize free biotin as a substrate, thereby simplifying kinetic analysis. 10 Consequently, biotin carboxylase from E. coli has been extensively studied by X-ray crystallography 11,12 and site-directed mutagenesis. [13][14][15][16] Structural and biochemical studies have provided valuable insights into the mechanism of biotin carboxylase; however, a number of questions remain to be resolved.…”

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confidence: 99%

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Molecular Dynamics Simulations of Biotin Carboxylase

2008

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Biotin carboxylase catalyzes the ATP-dependent carboxylation of biotin and is one component of the multienzyme complex acetyl-CoA carboxylase that catalyzes the first committed step in fatty acid synthesis in all organisms. Biotin carboxylase from Escherichia coli, whose crystal structures with and without ATP bound have been determined, has served as a model system for this component of the acetyl-CoA carboxylase complex. The two crystal structures revealed a large conformational change of one domain relative to the other domains when ATP is bound. Unfortunately, the crystal structure with ATP bound was obtained with an inactive site-directed mutant of the enzyme. As a consequence the structure with ATP bound lacked key structural information such as for the Mg 2+ ions and contained altered conformations of key active-site residues. Therefore, nanosecond molecular dynamics studies of the wild-type biotin carboxylase were undertaken to supplant and amend the results of the crystal structures. Specifically, the protein-metal interactions of the two catalytically critical Mg 2+ ions bound in the active site are presented along with a reevaluation of the conformations of active-site residues bound to ATP. In addition, the regions of the polypeptide chain that serve as hinges for the large conformational change were identified. The results of the hinge analysis complemented a covariance analysis that identified the individual structural elements of biotin carboxylase that change their conformation in response to ATP binding.Acetyl-CoA carboxylase (ACC) catalyzes the first committed step in the biosynthesis of long-chain fatty acids. ACC is a biotin-dependent enzyme found in all bacteria, plants, and animals. Since fatty acids are used for membrane biogenesis and energy storage, ACC is a target for antibiotics, 1,2 herbicides, 3 and antiobesity agents. [4][5][6] ACC produces malonyl-CoA from acetyl-CoA, ATP, and bicarbonate, which serves as the source of CO 2 for all biotindependent carboxylases. 7 The reaction mechanism proceeds via two half-reactions (Scheme 1): (1) the first half-reaction is catalyzed by biotin carboxylase (BC), and (2) the second halfreaction is catalyzed by carboxyltransferase (CT). In vivo, the vitamin biotin is covalently attached to a protein called the biotin carboxyl carrier protein (designated as enzyme-biotin in Scheme 1). In mammals, these proteins comprise different domains in a single polypeptide chain. 8 In contrast, in Gramnegative and Gram-positive bacteria biotin carboxylase, carboxyltransferase, and the biotin carboxyl carrier protein are separate proteins. 9 ACC from the Gram-negative bacterium Escherichia coli has been used as a model system for mechanistic investigations because the purified BC and CT components retain their activities, and utilize free biotin as a substrate, thereby simplifying kinetic analysis. 10 Consequently, biotin carboxylase from E. coli has been extensively studied by X-ray crystallography 11,12 and site-directed mutagenesis. [13][14][15][16] Structural...

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Section: Resultsmentioning

confidence: 99%

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Molecular Dynamics Simulations of Biotin Carboxylase

2008

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“…In accordance with the site mutagenesis data , Tyr-216 can be substituted by other hydrophobic residues. On the other hand, most of the amino acid residues forming the active center of BCase (Waldrop et al, 1994), such as Tyr-82, His-236, Lys-238, Glu-241, Gln-294, and Glu-296, are conserved only among BCases. These residues are not conserved even in phosphoribosylaminoimidazole carboxylase (Fig.…”

Section: R-co-0-rh-r-co-op03'-/'v R-co-s-coamentioning

confidence: 99%

A diverse superfamily of enzymes with ATP‐dependent carboxylate—amine/thiol ligase activity

1997

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Abstract:The recently developed PSI-BLAST method for sequence database search and methods for motif analysis were used to define and expand a superfamily of enzymes with an unusual nucleotide-binding fold, referred to as palmate, or ATP-grasp fold. In addition to D-alanine-D-alanine ligase, glutathione synthetase, biotin carboxylase, and carbamoyl phosphate synthetase, enzymes with known three-dimensional structures, the ATP-grasp domain is predicted in the ribosomal protein S6 modification enzyme (RimK), urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis. All these enzymes possess ATP-dependent carboxylate-amine ligase activity, and their catalytic mechanisms are likely to include acylphosphate intermediates. The ATP-grasp superfamily also includes succinate-CoA ligase (both ADP-forming and GDP-forming variants), malate-CoA ligase, and ATP-citrate lyase, enzymes with a carboxylate-thiol ligase activity, and several uncharacterized proteins. These findings significantly extend the variety of the substrates of ATP-grasp enzymes and the range of biochemical pathways in which they are involved, and demonstrate the complementarity between structural comparison and powerful methods for sequence analysis.

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“…Superposition of MTb AccA3, subunit A (blue) and subunit B (yellow) with the defined ‘open’ state conformation observed in nucleotide unbound BDC from Escherichia coli (gray) (PDB:1BNC) 43. Positive difference density [F obs − F calc contoured at 2.0 σ (0.21 e − ·Å −3 )] associated with subunit B of MTb AccA3 is displayed in green.…”

Section: Resultsmentioning

confidence: 99%

“…2) 40, 43. In addition, the biotin carboxylase domain of pyruvate carboxylase from Bacillus thermodenitrificans displays what appears to be an intermediate, but defined, conformation 44.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of the essential biotin‐dependent carboxylase AccA3 from Mycobacterium tuberculosis

Bennett

Högbom

2017

FEBS Open Bio

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Biotin‐dependent acetyl‐CoA carboxylases catalyze the committed step in type II fatty acid biosynthesis, the main route for production of membrane phospholipids in bacteria, and are considered a key target for antibacterial drug discovery. Here we describe the first structure of AccA3, an essential component of the acetyl‐CoA carboxylase system in Mycobacterium tuberculosis (MTb). The structure, sequence comparisons, and modeling of ligand‐bound states reveal that the ATP cosubstrate‐binding site shows distinct differences compared to other bacterial and eukaryotic biotin carboxylases, including all human homologs. This suggests the possibility to design MTb AccA3 subtype‐specific inhibitors. Database Coordinates and structure factors have been deposited in the Protein Data Bank with the accession number http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5MLK.

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Three-Dimensional Structure of the Biotin Carboxylase Subunit of Acetyl-CoA Carboxylase

Cited by 198 publications

References 36 publications

Molecular Dynamics Simulations of Biotin Carboxylase

Molecular Dynamics Simulations of Biotin Carboxylase

A diverse superfamily of enzymes with ATP‐dependent carboxylate—amine/thiol ligase activity

Crystal structure of the essential biotin‐dependent carboxylase AccA3 from Mycobacterium tuberculosis

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