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PDBsum entry 2qj3

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protein metals Protein-protein interface(s) links
Transferase PDB id
2qj3
Jmol
Contents
Protein chains
314 a.a. *
Metals
_NI ×5
Waters ×43
* Residue conservation analysis
PDB id:
2qj3
Name: Transferase
Title: Mycobacterium tuberculosis fabd
Structure: Malonyl coa-acyl carrier protein transacylase. Chain: a, b. Synonym: mct. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. Gene: fabd. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.00Å     R-factor:   0.226     R-free:   0.267
Authors: H.Ghadbane,A.K.Brown,L.Kremer,G.S.Besra,K.Futterer
Key ref:
H.Ghadbane et al. (2007). Structure of Mycobacterium tuberculosis mtFabD, a malonyl-CoA:acyl carrier protein transacylase (MCAT). Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 831-835. PubMed id: 17909282 DOI: 10.1107/S1744309107042455
Date:
06-Jul-07     Release date:   04-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P9WNG5  (FABD_MYCTU) -  Malonyl CoA-acyl carrier protein transacylase
Seq:
Struc:
302 a.a.
314 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.39  - [Acyl-carrier-protein] S-malonyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Malonyl-CoA + an [acyl-carrier-protein] = CoA + a malonyl-[acyl-carrier- protein]
Malonyl-CoA
+ [acyl-carrier-protein]
= CoA
+ malonyl-[acyl-carrier- protein]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S1744309107042455 Acta Crystallogr Sect F Struct Biol Cryst Commun 63:831-835 (2007)
PubMed id: 17909282  
 
 
Structure of Mycobacterium tuberculosis mtFabD, a malonyl-CoA:acyl carrier protein transacylase (MCAT).
H.Ghadbane, A.K.Brown, L.Kremer, G.S.Besra, K.Fütterer.
 
  ABSTRACT  
 
Mycobacteria display a unique and unusual cell-wall architecture, central to which is the membrane-proximal mycolyl-arabinogalactan-peptidoglycan core (mAGP). The biosynthesis of mycolic acids, which form the outermost layer of the mAGP core, involves malonyl-CoA:acyl carrier protein transacylase (MCAT). This essential enzyme catalyses the transfer of malonyl from coenzyme A to acyl carrier protein AcpM, thus feeding these two-carbon units into the chain-elongation cycle of the type II fatty-acid synthase. The crystal structure of M. tuberculosis mtFabD, the mycobacterial MCAT, has been determined to 3.0 A resolution by multi-wavelength anomalous dispersion. Phasing was facilitated by Ni2+ ions bound to the 20-residue N-terminal affinity tag, which packed between the two independent copies of mtFabD.
 
  Selected figure(s)  
 
Figure 1.
Ribbon diagram of M. tuberculosis mtFabD and experimental density. (a) The large and small subdomains are highlighted in green and magenta, respectively. The N--terminal affinity tag is shown as a stick model, with Ni^2+ ions appearing as blue spheres. The location of the active site is indicated by a stick model of CoA, based on the superposition with the structure of E. coli FabD in complex with CoA and malonate (PDB code 2g2z; Oefner et al., 2006[triangle]). (b) Close-up view of the affinity tag in the superposition of the two independent copies of mtFabD with respect to the C^[alpha] atoms of residues 1 --302, i.e. excluding the affinity tag. Molecules A and B are shown in pale red and cyan, respectively. Experimental density corresponding to molecule B contoured at 1.2[sigma] is shown, but is restricted to the vicinity of the affinity tag for clarity. All figures were generated using PyMOL v.0.97 (DeLano Scientific LLC). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 October 1; 63(Pt 10): 831–835. Published online 2007 September 19. doi: 10.1107/S1744309107042455. Copyright [copyright] International Union of Crystallography 2007
Figure 4.
Affinity-tag-mediated interface between molecules A (pale red) and B (cyan) of the asymmetric unit, with tag residues in stick representation and Ni^2+ ions as blue spheres. (a) Close-up view, with the ribbon in yellow and magenta representing residues 210 --218, which make contacts with the tag of the opposite monomer. Yellow dashed lines indicate the main-chain hydrogen bonds between the NCS-related copies of His[minus sign]15. The NCS twofold axis is approximately parallel to the viewing direction and runs through nickel site 4 (labels in magenta). (b) View perpendicular to (a), demonstrating that the (pseudo)-dimer interface is located distal to the active site (indicated for molecule B by the sphere model of CoA). Selected residues are labelled with subscripts denoting the polypeptide chain. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 October 1; 63(Pt 10): 831–835. Published online 2007 September 19. doi: 10.1107/S1744309107042455. Copyright [copyright] International Union of Crystallography 2007
 
  The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr Sect F Struct Biol Cryst Commun (2007, 63, 831-835) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19099550 K.Raman, Y.Kalidas, and N.Chandra (2008).
targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.
  BMC Syst Biol, 2, 109.  
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