Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.96 kDa 
• Atom Count: 7197 
• Modelled Residue Count: 862 
• Deposited Residue Count: 898 
• Unique protein chains: 1

1DV1

STRUCTURE OF BIOTIN CARBOXYLASE (APO)

• PDB DOI: 10.2210/pdb1DV1/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-01-19 Released: 2000-06-09 
• Deposition Author(s): Thoden, J.B., Blanchard, C.Z., Holden, H.M., Waldrop, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.238 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

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

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

(2000) J Biol Chem 275: 16183-16190

• PubMed: 10821865 
• DOI: 10.1074/jbc.275.21.16183
• Primary Citation of Related Structures:  
  1DV1, 1DV2


• PubMed 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.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53705, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BIOTIN CARBOXYLASE	A, B	449	Escherichia coli	Mutation(s): 0  EC: 6.3.4.14 (PDB Primary Data), 6.4.1.2 (UniProt)
UniProt
Find proteins for P24182 (Escherichia coli (strain K12)) Explore P24182  Go to UniProtKB:  P24182

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.238 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.7	α = 90
b = 95.8	β = 90
c = 180.7	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
TNT	refinement
FRAMBO	data collection
SAINT	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-01-19 
• Released Date: 2000-06-09 
Deposition Author(s): Thoden, J.B., Blanchard, C.Z., Holden, H.M., Waldrop, G.L.

Revision History  

• Version 1.0: 2000-06-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-01
  Changes: Structure summary
• Version 1.4: 2017-10-04
  Changes: Refinement description