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PDBsum entry 2px6

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2px6
Jmol
Contents
Protein chain
253 a.a. *
Ligands
DH9 ×2
DTT
Waters ×53
* Residue conservation analysis
PDB id:
2px6
Name: Transferase
Title: Crystal structure of the thioesterase domain of human fatty acid synthase inhibited by orlistat
Structure: Thioesterase domain. Chain: a, b. Fragment: residues 2200-2511. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: fas. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.228     R-free:   0.273
Authors: C.W.Pemble Iv,L.C.Johnson,S.J.Kridel,W.T.Lowther
Key ref:
C.W.Pemble et al. (2007). Crystal structure of the thioesterase domain of human fatty acid synthase inhibited by Orlistat. Nat Struct Biol, 14, 704-709. PubMed id: 17618296 DOI: 10.1038/nsmb1265
Date:
14-May-07     Release date:   10-Jul-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P49327  (FAS_HUMAN) -  Fatty acid synthase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2511 a.a.
253 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.1.1.1.100  - 3-oxoacyl-[acyl-carrier-protein] reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP+ = 3-oxoacyl-[acyl- carrier-protein] + NADPH
(3R)-3-hydroxyacyl-[acyl-carrier-protein]
Bound ligand (Het Group name = DTT)
matches with 45.00% similarity
+ NADP(+)
= 3-oxoacyl-[acyl- carrier-protein]
+ NADPH
   Enzyme class 2: E.C.1.3.1.39  - Enoyl-[acyl-carrier-protein] reductase (Nadph, Re-specific).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An acyl-[acyl-carrier protein] + NADP+ = a trans-2,3-dehydroacyl-[acyl- carrier protein] + NADPH
acyl-[acyl-carrier protein]
+ NADP(+)
= trans-2,3-dehydroacyl-[acyl- carrier protein]
+ NADPH
   Enzyme class 3: E.C.2.3.1.38  - [Acyl-carrier-protein] S-acetyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acetyl-CoA + [acyl-carrier-protein] = CoA + acetyl-[acyl-carrier- protein]
Acetyl-CoA
+ [acyl-carrier-protein]
= CoA
+ acetyl-[acyl-carrier- protein]
   Enzyme class 4: E.C.2.3.1.39  - [Acyl-carrier-protein] S-malonyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Malonyl-CoA + [acyl-carrier-protein] = CoA + malonyl-[acyl-carrier- protein]
Malonyl-CoA
+ [acyl-carrier-protein]
= CoA
+
malonyl-[acyl-carrier- protein]
Bound ligand (Het Group name = DTT)
matches with 45.00% similarity
   Enzyme class 5: E.C.2.3.1.41  - Beta-ketoacyl-[acyl-carrier-protein] synthase I.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl- [acyl-carrier-protein] + CO2 + [acyl-carrier-protein]
Acyl-[acyl-carrier-protein]
+
malonyl-[acyl-carrier-protein]
Bound ligand (Het Group name = DTT)
matches with 45.00% similarity
= 3-oxoacyl- [acyl-carrier-protein]
+ CO(2)
+ [acyl-carrier-protein]
   Enzyme class 6: E.C.2.3.1.85  - Fatty-acid synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acetyl-CoA + n malonyl-CoA + 2n NADPH = a long-chain fatty acid + (n+1) CoA + n CO2 + 2n NADP+
Acetyl-CoA
+ n malonyl-CoA
+ 2n NADPH
=
long-chain fatty acid
Bound ligand (Het Group name = DTT)
matches with 40.00% similarity
+ (n+1) CoA
+ n CO(2)
+ 2n NADP(+)
   Enzyme class 7: E.C.3.1.2.14  - Oleoyl-[acyl-carrier-protein] hydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Oleoyl-[acyl-carrier-protein] + H2O = [acyl-carrier-protein] + oleate
Oleoyl-[acyl-carrier-protein]
+ n H(2)O
= [acyl-carrier-protein]
+
oleate
Bound ligand (Het Group name = DH9)
matches with 48.00% similarity
   Enzyme class 8: E.C.4.2.1.59  - 3-hydroxyacyl-[acyl-carrier-protein] dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl- carrier protein] + H2O
(3R)-3-hydroxyacyl-[acyl-carrier protein]
Bound ligand (Het Group name = DH9)
matches with 48.00% similarity
= n trans-2-enoyl-[acyl- carrier protein]
+ H(2)O
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!
  Biological process     biosynthetic process   2 terms 
  Biochemical function     hydrolase activity, acting on ester bonds     12 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nsmb1265 Nat Struct Biol 14:704-709 (2007)
PubMed id: 17618296  
 
 
Crystal structure of the thioesterase domain of human fatty acid synthase inhibited by Orlistat.
C.W.Pemble, L.C.Johnson, S.J.Kridel, W.T.Lowther.
 
  ABSTRACT  
 
Human fatty acid synthase (FAS) is uniquely expressed at high levels in many tumor types. Pharmacological inhibition of FAS therefore represents an important therapeutic opportunity. The drug Orlistat, which has been approved by the US Food and Drug Administration, inhibits FAS, induces tumor cell-specific apoptosis and inhibits the growth of prostate tumor xenografts. We determined the 2.3-A-resolution crystal structure of the thioesterase domain of FAS inhibited by Orlistat. Orlistat was captured in the active sites of two thioesterase molecules as a stable acyl-enzyme intermediate and as the hydrolyzed product. The details of these interactions reveal the molecular basis for inhibition and suggest a mechanism for acyl-chain length discrimination during the FAS catalytic cycle. Our findings provide a foundation for the development of new cancer drugs that target FAS.
 
  Selected figure(s)  
 
Figure 1.
(a) Domain organization of FAS and its seven catalytic activities: -ketoacyl synthase (KS), acetyl/malonyl-CoA transferase (MAT), -hydroxyacyl dehydratase (DH), enoyl reductase (ER), -ketoacyl reductase (KR), acyl-carrier protein (ACP) and thioesterase (TE). (b) Structural comparison between FAS substrates and Orlistat. R-S represents the thioester-linked 4'-phosphopantetheine moiety attached to either the ACP domain or CoA. (c) Overall fold of the thioesterase domain with Orlistat bound. The topology of the thioesterase within the Orlistat complex shares similarities with the apoenzyme structure^19; superposition of the C carbon atoms results in an r.m.s. deviation of 3.5 Å. (d) Orlistat bound in the active site of chain A. The Orlistat scaffold is divided into three fragments: peptidyl moiety (N-formyl-L-leucine substituent extending off the C5 carbon atom), palmitic core and hexanoyl tail (C2 substituent). Shown covering Orlistat and Ser2308 is the F[o] – F[c] simulated-annealing omit electron density contoured at 3 . (e,f) Molecular (e) and electrostatic (f) surface representations colored to reflect the subdomain division (as in c) and electrostatic potential, respectively. The potential contours in f are shown on a scale from +130 (blue) to -40 k[b]T e^-1 (red); white indicates no charge.
Figure 4.
(a) Proposed interactions with the intact -lactone form of Orlistat. (b) The Orlistat acyl-enzyme intermediate. Semicircles with tick marks indicate van der Waals interactions. (c) Hydrolyzed Orlistat and its movements. (d) Hypothetical mechanism for chain-length sampling. Red spheres represent four water molecules involved in an intricate hydrogen-bonding network within the interface cavity (Fig. 2a); for simplicity, waters are omitted in a–c. The 4'-phosphopantetheine arm (gray stick model) of ACP is shown bound to the putative pantetheine channel. Representative growing acyl chains measuring 8 and 12 carbons in length (extrapolated from the Orlistat covalent complex) are shown binding transiently to the short-chain pocket and interface cavity, respectively. (e) Selection of C[16] and C[18] substrates and formation of the Michaelis complex. (f) Hydrolysis of the acyl-enzyme intermediate.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2007, 14, 704-709) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20457000 A.F.Kluge, and R.C.Petter (2010).
Acylating drugs: redesigning natural covalent inhibitors.
  Curr Opin Chem Biol, 14, 421-427.  
19603203 C.E.Cassidy, and W.N.Setzer (2010).
Cancer-relevant biochemical targets of cytotoxic Lonchocarpus flavonoids: a molecular docking analysis.
  J Mol Model, 16, 311-326.  
19669620 D.H.Jones, S.E.Cellitti, X.Hao, Q.Zhang, M.Jahnz, D.Summerer, P.G.Schultz, T.Uno, and B.H.Geierstanger (2010).
Site-specific labeling of proteins with NMR-active unnatural amino acids.
  J Biomol NMR, 46, 89.  
20662770 D.I.Chan, and H.J.Vogel (2010).
Current understanding of fatty acid biosynthesis and the acyl carrier protein.
  Biochem J, 430, 1.  
  20706604 H.Liu, J.Y.Liu, X.Wu, and J.T.Zhang (2010).
Biochemistry, molecular biology, and pharmacology of fatty acid synthase, an emerging therapeutic target and diagnosis/prognosis marker.
  Int J Biochem Mol Biol, 1, 69-89.  
20577697 M.H.Ngai, P.Y.Yang, K.Liu, Y.Shen, M.R.Wenk, S.Q.Yao, and M.J.Lear (2010).
Click-based synthesis and proteomic profiling of lipstatin analogues.
  Chem Commun (Camb), 46, 8335-8337.  
21145456 M.R.Wenk (2010).
Lipidomics: new tools and applications.
  Cell, 143, 888-895.  
20373869 R.Flavin, S.Peluso, P.L.Nguyen, and M.Loda (2010).
Fatty acid synthase as a potential therapeutic target in cancer.
  Future Oncol, 6, 551-562.  
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.  
20332208 T.P.Korman, J.M.Crawford, J.W.Labonte, A.G.Newman, J.Wong, C.A.Townsend, and S.C.Tsai (2010).
Structure and function of an iterative polyketide synthase thioesterase domain catalyzing Claisen cyclization in aflatoxin biosynthesis.
  Proc Natl Acad Sci U S A, 107, 6246-6251.
PDB code: 3ils
19169353 S.K.Parker, R.M.Barkley, J.G.Rino, and M.L.Vasil (2009).
Mycobacterium tuberculosis Rv3802c encodes a phospholipase/thioesterase and is inhibited by the antimycobacterial agent tetrahydrolipstatin.
  PLoS ONE, 4, e4281.  
18287618 C.A.Haynes, J.C.Allegood, K.Sims, E.W.Wang, M.C.Sullards, and A.H.Merrill (2008).
Quantitation of fatty acyl-coenzyme As in mammalian cells by liquid chromatography-electrospray ionization tandem mass spectrometry.
  J Lipid Res, 49, 1113-1125.  
18312417 M.J.Vázquez, W.Leavens, R.Liu, B.Rodríguez, M.Read, S.Richards, D.Winegar, and J.M.Domínguez (2008).
Discovery of GSK837149A, an inhibitor of human fatty acid synthase targeting the beta-ketoacyl reductase reaction.
  FEBS J, 275, 1556-1567.  
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.  
18576636 S.E.Cellitti, D.H.Jones, L.Lagpacan, X.Hao, Q.Zhang, H.Hu, S.M.Brittain, A.Brinker, J.Caldwell, B.Bursulaya, G.Spraggon, A.Brock, Y.Ryu, T.Uno, P.G.Schultz, and B.H.Geierstanger (2008).
In vivo incorporation of unnatural amino acids to probe structure, dynamics, and ligand binding in a large protein by nuclear magnetic resonance spectroscopy.
  J Am Chem Soc, 130, 9268-9281.  
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
17882277 J.A.Menendez, and R.Lupu (2007).
Fatty acid synthase and the lipogenic phenotype in cancer pathogenesis.
  Nat Rev Cancer, 7, 763-777.  
17970640 S.J.Kridel, W.T.Lowther, and C.W.Pemble (2007).
Fatty acid synthase inhibitors: new directions for oncology.
  Expert Opin Investig Drugs, 16, 1817-1829.  
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.