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PDBsum entry 2vpq

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
2vpq
Jmol
Contents
Protein chains
447 a.a. *
Ligands
ANP ×2
Metals
_CL ×2
_MG ×4
Waters ×817
* Residue conservation analysis
PDB id:
2vpq
Name: Ligase
Title: Crystal structure of biotin carboxylase from s. Aureus complexed with amppnp
Structure: Acetyl-coa carboxylase. Chain: a, b. Synonym: biotin carboxylase. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.10Å     R-factor:   0.219     R-free:   0.284
Authors: I.Mochalkin
Key ref:
I.Mochalkin et al. (2008). Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase. Protein Sci, 17, 1706-1718. PubMed id: 18725455 DOI: 10.1110/ps.035584.108
Date:
03-Mar-08     Release date:   09-Sep-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q99TW7  (Q99TW7_STAAM) -  Acetyl-CoA carboxylase
Seq:
Struc:
451 a.a.
447 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1110/ps.035584.108 Protein Sci 17:1706-1718 (2008)
PubMed id: 18725455  
 
 
Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase.
I.Mochalkin, J.R.Miller, A.Evdokimov, S.Lightle, C.Yan, C.K.Stover, G.L.Waldrop.
 
  ABSTRACT  
 
Bacterial acetyl-CoA carboxylase is a multifunctional biotin-dependent enzyme that consists of three separate proteins: biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), and carboxyltransferase (CT). Acetyl-CoA carboxylase is a potentially attractive target for novel antibiotics because it catalyzes the first committed step in fatty acid biosynthesis. In the first half-reaction, BC catalyzes the ATP-dependent carboxylation of BCCP. In the second half-reaction, the carboxyl group is transferred from carboxybiotinylated BCCP to acetyl-CoA to produce malonyl-CoA. A series of structures of BC from several bacteria crystallized in the presence of various ATP analogs is described that addresses three major questions concerning the catalytic mechanism. The structure of BC bound to AMPPNP and the two catalytically essential magnesium ions resolves inconsistencies between the kinetics of active-site BC mutants and previously reported BC structures. Another structure of AMPPNP bound to BC shows the polyphosphate chain folded back on itself, and not in the correct (i.e., extended) conformation for catalysis. This provides the first structural evidence for the hypothesis of substrate-induced synergism, which posits that ATP binds nonproductively to BC in the absence of biotin. The BC homodimer has been proposed to exhibit half-sites reactivity where the active sites alternate or "flip-flop" their catalytic cycles. A crystal structure of BC showed the ATP analog AMPPCF(2)P bound to one subunit while the other subunit was unliganded. The liganded subunit was in the closed or catalytic conformation while the unliganded subunit was in the open conformation. This provides the first structural evidence for half-sites reactivity in BC.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Stereoview of superimposed AMPPNP in SaBC and EcBC crystal structures. SaBC/AMPPNP structure is colored in red. EcBC/AMPPNP structure is colored in blue. SaBC residues involved in interactions with the ligand are shown in sticks with the following atom colors: carbon, yellow; nitrogen, blue; oxygen, red. Images were prepared using PyMOL molecular graphics systems (DeLano Scientific).
Figure 5.
Figure 5. View of octahedrally coordinated magnesium ions in BC crystal structures. Nucleotide molecules and protein residues are shown in sticks with the following atom colors: carbon, green; nitrogen, blue; oxygen, red; phosphorus, orange. Magnesium ions and water molecules are shown as green and red spheres. (A) View of two magnesium-binding sites in the SaBC/AMPPNP structure. (B) View of one magnesium-binding site in the PaBC/AMPCP structure.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2008, 17, 1706-1718) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21426897 A.Adina-Zada, R.Hazra, C.Sereeruk, S.Jitrapakdee, T.N.Zeczycki, M.S.Maurice, W.W.Cleland, J.C.Wallace, and P.V.Attwood (2011).
Probing the allosteric activation of pyruvate carboxylase using 2',3'-O-(2,4,6-trinitrophenyl) adenosine 5'-triphosphate as a fluorescent mimic of the allosteric activator acetyl CoA.
  Arch Biochem Biophys, 509, 117-126.  
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.  
21097780 U.Pieper, B.M.Webb, D.T.Barkan, D.Schneidman-Duhovny, A.Schlessinger, H.Braberg, Z.Yang, E.C.Meng, E.F.Pettersen, C.C.Huang, R.S.Datta, P.Sampathkumar, M.S.Madhusudhan, K.Sjölander, T.E.Ferrin, S.K.Burley, and A.Sali (2011).
ModBase, a database of annotated comparative protein structure models, and associated resources.
  Nucleic Acids Res, 39, D465-D474.  
19193851 C.T.Walsh, and M.A.Fischbach (2009).
Repurposing libraries of eukaryotic protein kinase inhibitors for antibiotic discovery.
  Proc Natl Acad Sci U S A, 106, 1689-1690.  
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
19164768 J.R.Miller, S.Dunham, I.Mochalkin, C.Banotai, M.Bowman, S.Buist, B.Dunkle, D.Hanna, H.J.Harwood, M.D.Huband, A.Karnovsky, M.Kuhn, C.Limberakis, J.Y.Liu, S.Mehrens, W.T.Mueller, L.Narasimhan, A.Ogden, J.Ohren, J.V.Prasad, J.A.Shelly, L.Skerlos, M.Sulavik, V.H.Thomas, S.VanderRoest, L.Wang, Z.Wang, A.Whitton, T.Zhu, and C.K.Stover (2009).
A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore.
  Proc Natl Acad Sci U S A, 106, 1737-1742.
PDB codes: 2v58 2v59 2v5a
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 codes are shown on the right.