PDBsum entry 2g2y

Go to PDB code: 
protein ligands links
Transferase PDB id
Protein chain
305 a.a. *
Waters ×103
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Structure of e.Coli fabd complexed with malonate
Structure: Malonyl coa-acyl carrier protein transacylase. Chain: a. Synonym: mct, acyltransferase, malonyl-coa acp transacylase engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: fabd. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.26Å     R-factor:   0.214     R-free:   0.234
Authors: C.Oefner
Key ref:
C.Oefner et al. (2006). Mapping the active site of Escherichia coli malonyl-CoA-acyl carrier protein transacylase (FabD) by protein crystallography. Acta Crystallogr D Biol Crystallogr, 62, 613-618. PubMed id: 16699188 DOI: 10.1107/S0907444906009474
17-Feb-06     Release date:   30-May-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0AAI9  (FABD_ECOLI) -  Malonyl CoA-acyl carrier protein transacylase
309 a.a.
305 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - [Acyl-carrier-protein] S-malonyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Malonyl-CoA + an [acyl-carrier-protein] = CoA + a malonyl-[acyl-carrier- protein]
+ [acyl-carrier-protein]
= CoA
malonyl-[acyl-carrier- protein]
Bound ligand (Het Group name = MLI)
matches with 66.67% similarity
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  


DOI no: 10.1107/S0907444906009474 Acta Crystallogr D Biol Crystallogr 62:613-618 (2006)
PubMed id: 16699188  
Mapping the active site of Escherichia coli malonyl-CoA-acyl carrier protein transacylase (FabD) by protein crystallography.
C.Oefner, H.Schulz, A.D'Arcy, G.E.Dale.
Malonyl-CoA-acyl carrier protein transacylase (FabD; EC is a key enzyme in the fatty-acid biosynthesis pathway of bacteria, catalyzing the transfer of a malonyl moiety from malonyl-CoA to holo acyl carrier protein (ACP), generating malonyl-ACP and free CoASH. Malonyl-ACP, which is the product of this reaction, is the key building block for de novo fatty-acid biosynthesis. Various binary complex structures of the Escherichia coli enzyme are presented, including that of the natural substrate malonyl-CoA, indicating the functional role of the highly conserved amino acids Gln11, Ser92, Arg117 and His201 and the stabilizing function of the preformed oxyanion hole during the enzymatic reaction. Based on the presented structural data, a possible new catalytic enzyme mechanism is discussed. The data obtained could be used in aiding the process of rational inhibitor design.
  Selected figure(s)  
Figure 3.
Figure 3 Malonyl-CoA binding to FabdD. The malonyl moiety of the processed substrate is covalently bound to the catalytic serine residue 92 via an oxo-ester bond. Hydrogen bonding is indicated by dotted lines. The figure was generated with the programs MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]) and RASTER3D (Merrit & Bacon, 1997[Merritt, E. A. & Bacon, D. J. (1997). Methods Enzymol. 277, 505-524.]).
Figure 4.
Figure 4 Reaction mechanism.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 613-618) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20088879 D.Kenanov, C.Kaleta, A.Petzold, C.Hoischen, S.Diekmann, R.A.Siddiqui, and S.Schuster (2010).
Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysis.
  FEBS J, 277, 1023-1034.  
20731893 T.Maier, M.Leibundgut, D.Boehringer, and N.Ban (2010).
Structure and function of eukaryotic fatty acid synthases.
  Q Rev Biophys, 43, 373-422.  
20080587 Y.Shen, J.Liu, G.Estiu, B.Isin, Y.Y.Ahn, D.S.Lee, A.L.Barabási, V.Kapatral, O.Wiest, and Z.N.Oltvai (2010).
Blueprint for antimicrobial hit discovery targeting metabolic networks.
  Proc Natl Acad Sci U S A, 107, 1082-1087.  
19462023 A.Misra, N.Surolia, and A.Surolia (2009).
Catalysis and mechanism of malonyl transferase activity in type II fatty acid biosynthesis acyl carrier proteins.
  Mol Biosyst, 5, 651-659.  
19151726 E.J.Brignole, S.Smith, and F.J.Asturias (2009).
Conformational flexibility of metazoan fatty acid synthase enables catalysis.
  Nat Struct Mol Biol, 16, 190-197.  
18344344 L.Kizer, D.J.Pitera, B.F.Pfleger, and J.D.Keasling (2008).
Application of functional genomics to pathway optimization for increased isoprenoid production.
  Appl Environ Microbiol, 74, 3229-3241.  
18948193 M.Leibundgut, T.Maier, S.Jenni, and N.Ban (2008).
The multienzyme architecture of eukaryotic fatty acid synthases.
  Curr Opin Struct Biol, 18, 714-725.  
18772430 T.Maier, M.Leibundgut, and N.Ban (2008).
The crystal structure of a mammalian fatty acid synthase.
  Science, 321, 1315-1322.
PDB codes: 2vz8 2vz9
  17909282 H.Ghadbane, A.K.Brown, L.Kremer, G.S.Besra, and K.Fütterer (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.
PDB code: 2qj3
17448991 I.B.Lomakin, Y.Xiong, and T.A.Steitz (2007).
The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together.
  Cell, 129, 319-332.
PDB code: 2pff
17525466 L.Zhang, W.Liu, J.Xiao, T.Hu, J.Chen, K.Chen, H.Jiang, and X.Shen (2007).
Malonyl-CoA: acyl carrier protein transacylase from Helicobacter pylori: Crystal structure and its interaction with acyl carrier protein.
  Protein Sci, 16, 1184-1192.
PDB code: 2h1y
17431175 S.Jenni, M.Leibundgut, D.Boehringer, C.Frick, B.Mikolásek, and N.Ban (2007).
Structure of fungal fatty acid synthase and implications for iterative substrate shuttling.
  Science, 316, 254-261.
PDB codes: 2uv9 2uva 2uvb 2uvc
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.