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PDBsum entry 2gpw

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protein Protein-protein interface(s) links
Ligase PDB id
2gpw
Jmol
Contents
Protein chains
445 a.a. *
Waters ×1071
* Residue conservation analysis
PDB id:
2gpw
Name: Ligase
Title: Crystal structure of the biotin carboxylase subunit, f363a mutant, of acetyl-coa carboxylase from escherichia coli.
Structure: Biotin carboxylase. Chain: a, b, c, d. Synonym: a subunit of acetyl-coa carboxylase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: accc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.192     R-free:   0.250
Authors: Y.Shen,C.Y.Chou,G.G.Chang,L.Tong
Key ref:
Y.Shen et al. (2006). Is dimerization required for the catalytic activity of bacterial biotin carboxylase? Mol Cell, 22, 807-818. PubMed id: 16793549 DOI: 10.1016/j.molcel.2006.04.026
Date:
18-Apr-06     Release date:   04-Jul-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P24182  (ACCC_ECOLI) -  Biotin carboxylase
Seq:
Struc:
449 a.a.
445 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: E.C.6.3.4.14  - Biotin carboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + biotin-[carboxyl-carrier-protein] + CO2 = ADP + phosphate + carboxy-biotin-[carboxyl-carrier-protein]
ATP
+ biotin-[carboxyl-carrier-protein]
+ CO(2)
= ADP
+ phosphate
+ carboxy-biotin-[carboxyl-carrier-protein]
   Enzyme class 2: E.C.6.4.1.2  - Acetyl-CoA carboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + acetyl-CoA + HCO3- = ADP + phosphate + malonyl-CoA
ATP
+ acetyl-CoA
+ HCO(3)(-)
= ADP
+ phosphate
+ malonyl-CoA
      Cofactor: Biotin
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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.molcel.2006.04.026 Mol Cell 22:807-818 (2006)
PubMed id: 16793549  
 
 
Is dimerization required for the catalytic activity of bacterial biotin carboxylase?
Y.Shen, C.Y.Chou, G.G.Chang, L.Tong.
 
  ABSTRACT  
 
Acetyl-coenzyme A carboxylases (ACCs) have crucial roles in fatty acid metabolism. The biotin carboxylase (BC) subunit of Escherichia coli ACC is believed to be active only as a dimer, although the crystal structure shows that the active site of each monomer is 25 A from the dimer interface. We report here biochemical, biophysical, and structural characterizations of BC carrying single-site mutations in the dimer interface. Our studies demonstrate that two of the mutants, R19E and E23R, are monomeric in solution but have only a 3-fold loss in catalytic activity. The crystal structures of the E23R and F363A mutants show that they can still form the correct dimer at high concentrations. Our data suggest that dimerization is not an absolute requirement for the catalytic activity of the E. coli BC subunit, and we propose a new model for the molecular mechanism of action for BC in multisubunit and multidomain ACCs.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Sedimentation Velocity Analytical Ultracentrifugation Data for the BC Subunit
Figure 5.
Figure 5. A Model for the Mechanism of Action of BC
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 22, 807-818) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21120858 B.R.Novak, D.Moldovan, G.L.Waldrop, and M.S.de Queiroz (2011).
Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations.
  Proteins, 79, 622-632.  
21455530 E.F.Franca, F.L.Leite, R.A.Cunha, O.N.Oliveira, and L.C.Freitas (2011).
Designing an enzyme-based nanobiosensor using molecular modeling techniques.
  Phys Chem Chem Phys, 13, 8894-8899.  
20725044 C.S.Huang, K.Sadre-Bazzaz, Y.Shen, B.Deng, Z.H.Zhou, and L.Tong (2010).
Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase.
  Nature, 466, 1001-1005.
PDB code: 3n6r
20371333 S.C.Cheng, G.G.Chang, and C.Y.Chou (2010).
Mutation of Glu-166 blocks the substrate-induced dimerization of SARS coronavirus main protease.
  Biophys J, 98, 1327-1336.  
19213731 C.Y.Chou, L.P.Yu, and L.Tong (2009).
Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism.
  J Biol Chem, 284, 11690-11697.
PDB codes: 3g8c 3g8d
19523900 L.P.Yu, S.Xiang, G.Lasso, D.Gil, M.Valle, and L.Tong (2009).
A symmetrical tetramer for S. aureus pyruvate carboxylase in complex with coenzyme A.
  Structure, 17, 823-832.
PDB codes: 3hb9 3hbl 3ho8
18725455 I.Mochalkin, J.R.Miller, A.Evdokimov, S.Lightle, C.Yan, C.K.Stover, and G.L.Waldrop (2008).
Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase.
  Protein Sci, 17, 1706-1718.
PDB codes: 2c00 2j9g 2vpq 2vqd 2vr1
17659996 S.Jitrapakdee, K.H.Surinya, A.Adina-Zada, S.W.Polyak, C.Stojkoski, R.Smyth, G.W.Booker, W.W.Cleland, P.V.Attwood, and J.C.Wallace (2007).
Conserved Glu40 and Glu433 of the biotin carboxylase domain of yeast pyruvate carboxylase I isoenzyme are essential for the association of tetramers.
  Int J Biochem Cell Biol, 39, 2120-2134.  
16983687 L.Tong, and H.J.Harwood (2006).
Acetyl-coenzyme A carboxylases: versatile targets for drug discovery.
  J Cell Biochem, 99, 1476-1488.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.