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PDBsum entry 1qg6

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1qg6
Jmol
Contents
Protein chains
257 a.a. *
Ligands
NAD ×4
TCL ×4
Waters ×352
* Residue conservation analysis
PDB id:
1qg6
Name: Oxidoreductase
Title: Crystal structure of e. Coli enoyl acyl carrier protein reductase in complex with NAD and triclosan
Structure: Protein (enoyl-[acyl-carrier protein] reductase). Chain: a, b, c, d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: fabi. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
1.90Å     R-factor:   0.202     R-free:   0.207
Authors: S.Rowsell,R.A.Pauptit
Key ref:
W.H.Ward et al. (1999). Kinetic and structural characteristics of the inhibition of enoyl (acyl carrier protein) reductase by triclosan. Biochemistry, 38, 12514-12525. PubMed id: 10493822 DOI: 10.1021/bi9907779
Date:
20-Apr-99     Release date:   21-Sep-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AEK4  (FABI_ECOLI) -  Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Seq:
Struc:
262 a.a.
257 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.3.1.9  - Enoyl-[acyl-carrier-protein] reductase (NADH).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An acyl-[acyl-carrier protein] + NAD+ = a trans-2,3-dehydroacyl-[acyl- carrier protein] + NADH
acyl-[acyl-carrier protein]
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
= trans-2,3-dehydroacyl-[acyl- carrier protein]
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     metabolic process   10 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi9907779 Biochemistry 38:12514-12525 (1999)
PubMed id: 10493822  
 
 
Kinetic and structural characteristics of the inhibition of enoyl (acyl carrier protein) reductase by triclosan.
W.H.Ward, G.A.Holdgate, S.Rowsell, E.G.McLean, R.A.Pauptit, E.Clayton, W.W.Nichols, J.G.Colls, C.A.Minshull, D.A.Jude, A.Mistry, D.Timms, R.Camble, N.J.Hales, C.J.Britton, I.W.Taylor.
 
  ABSTRACT  
 
Triclosan is used widely as an antibacterial agent in dermatological products, mouthwashes, and toothpastes. Recent studies imply that antibacterial activity results from binding to enoyl (acyl carrier protein) reductase (EACPR, EC 1.3.1.9). We first recognized the ability of triclosan to inhibit EACPR from Escherichia coli in a high throughput screen where the enzyme and test compound were preincubated with NAD(+), which is a product of the reaction. The concentration of triclosan required for 50% inhibition approximates to 50% of the enzyme concentration, indicating that the free compound is depleted by binding to EACPR. With no preincubation or added NAD(+), the degree of inhibition by 150 nM triclosan increases gradually over several minutes. The onset of inhibition is more rapid when NAD(+) is added. Gel filtration and mass spectrometry show that inhibition by triclosan is reversible. Steady-state assays were designed to avoid depletion of free inhibitor and changes in the degree of inhibition. The results suggest that triclosan binds to E-NAD(+) complex, with a dissociation constant around 20-40 pM. Triclosan follows competitive kinetics with respect to NADH, giving an inhibition constant of 38 pM at zero NADH and saturating NAD(+). Uncompetitive kinetics are observed when NAD(+) is varied, giving an inhibition constant of 22 pM at saturating NAD(+). By following regain of catalytic activity after dilution of EACPR that had been preincubated with triclosan and NAD(+), the rate constant for dissociation of the inhibitor (k(off)) is measured as 1.9 x 10(-4) s(-1). The association rate constant (k(on)) is estimated as 2.6 x 10(7) s(-1) M(-1) by monitoring the onset of inhibition during assays started by addition of EACPR. As expected, the ratio k(off)/k(on) = 7.1 pM is similar to the inhibition constants from the steady-state studies. The crystal structure of E. coli EACPR in a complex with coenzyme and triclosan has been determined at 1.9 A resolution, showing that this compound binds in a similar site to the diazaborine inhibitors. The high affinity of triclosan appears to be due to structural similarity to a tightly bound intermediate in catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21280175 K.Maity, T.Banerjee, N.Prabakaran, N.Surolia, A.Surolia, and K.Suguna (2011).
Effect of substrate binding loop mutations on the structure, kinetics, and inhibition of enoyl acyl carrier protein reductase from plasmodium falciparum.
  IUBMB Life, 63, 30-41.
PDB codes: 3am3 3am4 3am5
21393229 N.Liu, J.E.Cummings, K.England, R.A.Slayden, and P.J.Tonge (2011).
Mechanism and inhibition of the FabI enoyl-ACP reductase from Burkholderia pseudomallei.
  J Antimicrob Chemother, 66, 564-573.  
20055482 H.Lu, and P.J.Tonge (2010).
Mechanism and inhibition of the FabV enoyl-ACP reductase from Burkholderia mallei.
  Biochemistry, 49, 1281-1289.  
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.  
19282328 C.J.Zheng, M.J.Sohn, and W.G.Kim (2009).
Vinaxanthone, a new FabI inhibitor from Penicillium sp.
  J Antimicrob Chemother, 63, 949-953.  
  19206187 H.Lu, K.England, C.am Ende, J.J.Truglio, S.Luckner, B.G.Reddy, N.L.Marlenee, S.E.Knudson, D.L.Knudson, R.A.Bowen, C.Kisker, R.A.Slayden, and P.J.Tonge (2009).
Slow-onset inhibition of the FabI enoyl reductase from francisella tularensis: residence time and in vivo activity.
  ACS Chem Biol, 4, 221-231.
PDB code: 2jjy
19734171 K.England, C.am Ende, H.Lu, T.J.Sullivan, N.L.Marlenee, R.A.Bowen, S.E.Knudson, D.L.Knudson, P.J.Tonge, and R.A.Slayden (2009).
Substituted diphenyl ethers as a broad-spectrum platform for the development of chemotherapeutics for the treatment of tularaemia.
  J Antimicrob Chemother, 64, 1052-1061.  
18703160 E.Freire (2008).
Do enthalpy and entropy distinguish first in class from best in class?
  Drug Discov Today, 13, 869-874.  
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.  
18032386 R.P.Massengo-Tiassé, and J.E.Cronan (2008).
Vibrio cholerae FabV defines a new class of enoyl-acyl carrier protein reductase.
  J Biol Chem, 283, 1308-1316.  
18694482 S.Goh, and L.Good (2008).
Plasmid selection in Escherichia coli using an endogenous essential gene marker.
  BMC Biotechnol, 8, 61.  
  17697396 J.Z.Lu, S.P.Muench, M.Allary, S.Campbell, C.W.Roberts, E.Mui, R.L.McLeod, D.W.Rice, and S.T.Prigge (2007).
Type I and type II fatty acid biosynthesis in Eimeria tenella: enoyl reductase activity and structure.
  Parasitology, 134, 1949-1962.
PDB code: 2ptg
17723305 X.He, A.Alian, and P.R.Ortiz de Montellano (2007).
Inhibition of the Mycobacterium tuberculosis enoyl acyl carrier protein reductase InhA by arylamides.
  Bioorg Med Chem, 15, 6649-6658.
PDB code: 2nsd
17012233 S.Rafi, P.Novichenok, S.Kolappan, X.Zhang, C.F.Stratton, R.Rawat, C.Kisker, C.Simmerling, and P.J.Tonge (2006).
Structure of acyl carrier protein bound to FabI, the FASII enoyl reductase from Escherichia coli.
  J Biol Chem, 281, 39285-39293.
PDB code: 2fhs
17034137 X.He, A.Alian, R.Stroud, and P.R.Ortiz de Montellano (2006).
Pyrrolidine carboxamides as a novel class of inhibitors of enoyl acyl carrier protein reductase from Mycobacterium tuberculosis.
  J Med Chem, 49, 6308-6323.
PDB codes: 2h7i 2h7l 2h7m 2h7n 2h7p
16257377 G.A.Holdgate, and W.H.Ward (2005).
Measurements of binding thermodynamics in drug discovery.
  Drug Discov Today, 10, 1543-1550.  
15516341 S.Kodali, A.Galgoci, K.Young, R.Painter, L.L.Silver, K.B.Herath, S.B.Singh, D.Cully, J.F.Barrett, D.Schmatz, and J.Wang (2005).
Determination of selectivity and efficacy of fatty acid synthesis inhibitors.
  J Biol Chem, 280, 1669-1677.  
  15043388 R.J.Heath, and C.O.Rock (2004).
Fatty acid biosynthesis as a target for novel antibacterials.
  Curr Opin Investig Drugs, 5, 146-153.  
12606558 M.R.Kuo, H.R.Morbidoni, D.Alland, S.F.Sneddon, B.B.Gourlie, M.M.Staveski, M.Leonard, J.S.Gregory, A.D.Janjigian, C.Yee, J.M.Musser, B.Kreiswirth, H.Iwamoto, R.Perozzo, W.R.Jacobs, J.C.Sacchettini, and D.A.Fidock (2003).
Targeting tuberculosis and malaria through inhibition of Enoyl reductase: compound activity and structural data.
  J Biol Chem, 278, 20851-20859.
PDB codes: 1p44 1p45
12692093 P.Gilbert, and A.J.McBain (2003).
Potential impact of increased use of biocides in consumer products on prevalence of antibiotic resistance.
  Clin Microbiol Rev, 16, 189-208.  
12930838 S.K.Sharma, M.Kapoor, T.N.Ramya, S.Kumar, G.Kumar, R.Modak, S.Sharma, N.Surolia, and A.Surolia (2003).
Identification, characterization, and inhibition of Plasmodium falciparum beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ).
  J Biol Chem, 278, 45661-45671.  
12192068 C.A.Bottoms, P.E.Smith, and J.J.Tanner (2002).
A structurally conserved water molecule in Rossmann dinucleotide-binding domains.
  Protein Sci, 11, 2125-2137.  
12384334 F.Fan, K.Yan, N.G.Wallis, S.Reed, T.D.Moore, S.F.Rittenhouse, W.E.DeWolf, J.Huang, D.McDevitt, W.H.Miller, M.A.Seefeld, K.A.Newlander, D.R.Jakas, M.S.Head, and D.J.Payne (2002).
Defining and combating the mechanisms of triclosan resistance in clinical isolates of Staphylococcus aureus.
  Antimicrob Agents Chemother, 46, 3343-3347.  
11792710 R.Perozzo, M.Kuo, A.S.Sidhu, J.T.Valiyaveettil, R.Bittman, W.R.Jacobs, D.A.Fidock, and J.C.Sacchettini (2002).
Structural elucidation of the specificity of the antibacterial agent triclosan for malarial enoyl acyl carrier protein reductase.
  J Biol Chem, 277, 13106-13114.
PDB codes: 1nhd 1nhg 1nhw 1nnu 1vrw
11959561 X.He, and K.A.Reynolds (2002).
Purification, characterization, and identification of novel inhibitors of the beta-ketoacyl-acyl carrier protein synthase III (FabH) from Staphylococcus aureus.
  Antimicrob Agents Chemother, 46, 1310-1318.  
11369293 D.J.Payne, P.V.Warren, D.J.Holmes, Y.Ji, and J.T.Lonsdale (2001).
Bacterial fatty-acid biosynthesis: a genomics-driven target for antibacterial drug discovery.
  Drug Discov Today, 6, 537-544.  
11544358 J.W.Campbell, and J.E.Cronan (2001).
Bacterial fatty acid biosynthesis: targets for antibacterial drug discovery.
  Annu Rev Microbiol, 55, 305-332.  
11591436 R.J.Heath, S.W.White, and C.O.Rock (2001).
Lipid biosynthesis as a target for antibacterial agents.
  Prog Lipid Res, 40, 467-497.  
11069675 R.A.Slayden, R.E.Lee, and C.E.Barry (2000).
Isoniazid affects multiple components of the type II fatty acid synthase system of Mycobacterium tuberculosis.
  Mol Microbiol, 38, 514-525.  
10869170 S.L.Parikh, G.Xiao, and P.J.Tonge (2000).
Inhibition of InhA, the enoyl reductase from Mycobacterium tuberculosis, by triclosan and isoniazid.
  Biochemistry, 39, 7645-7650.  
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.