PDBsum entry 1fj8

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Transferase PDB id
Protein chains
403 a.a. *
CER ×4
Waters ×239
* Residue conservation analysis
PDB id:
Name: Transferase
Title: The structure of beta-ketoacyl-[acyl carrier protein] synthase i in complex with cerulenin, implications for drug design
Structure: Beta-ketoacyl-[acyl carrier protein] synthase i. Chain: a, b, c, d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.27Å     R-factor:   0.230     R-free:   0.265
Authors: A.C.Price,K.Choi,R.J.Heath,Z.Li,S.W.White,C.O.Rock
Key ref:
A.C.Price et al. (2001). Inhibition of beta-ketoacyl-acyl carrier protein synthases by thiolactomycin and cerulenin. Structure and mechanism. J Biol Chem, 276, 6551-6559. PubMed id: 11050088 DOI: 10.1074/jbc.M007101200
07-Aug-00     Release date:   23-Aug-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0A953  (FABB_ECOLI) -  3-oxoacyl-[acyl-carrier-protein] synthase 1
406 a.a.
403 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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]
+ malonyl-[acyl-carrier-protein]
= 3-oxoacyl- [acyl-carrier-protein]
+ CO(2)
+ [acyl-carrier-protein]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     4 terms  


DOI no: 10.1074/jbc.M007101200 J Biol Chem 276:6551-6559 (2001)
PubMed id: 11050088  
Inhibition of beta-ketoacyl-acyl carrier protein synthases by thiolactomycin and cerulenin. Structure and mechanism.
A.C.Price, K.H.Choi, R.J.Heath, Z.Li, S.W.White, C.O.Rock.
The beta-ketoacyl-acyl carrier protein (ACP) synthases are key regulators of type II fatty acid synthesis and are the targets for two natural products, thiolactomycin (TLM) and cerulenin. The high resolution structures of the FabB-TLM and FabB-cerulenin binary complexes were determined. TLM mimics malonyl-ACP in the FabB active site. It forms strong hydrogen bond interactions with the two catalytic histidines, and the unsaturated alkyl side chain interaction with a small hydrophobic pocket is stabilized by pi stacking interactions. Cerulenin binding mimics the condensation transition state. The subtle differences between the FabB-cerulenin and FabF-cerulenin (Moche, M., Schneider, G., Edwards, P., Dehesh, K., and Lindqvist, Y. (1999) J. Biol. Chem. 244, 6031-6034) structures explain the differences in the sensitivity of the two enzymes to the antibiotic and may reflect the distinct substrate specificities protein was prepared to convert the FabB His-His-Cys active site triad into the FabH His-Asn-Cys configuration to test the importance of the two His residues in TLM and was significantly more resistant to both antibiotics than FabB and had an affinity for TLM an order of magnitude less than the wild-type enzyme, illustrating that the two-histidine active site architecture is critical to protein-antibiotic interaction. These data provide a structural framework for understanding antibiotic sensitivity within this group of enzymes.
  Selected figure(s)  
Figure 7.
Fig. 7. Overlay of TLM and cerulenin in the FabB active site. The FabB-TLM and FabB-cerulenin structures were superimposed to illustrate the differences in the binding of the antibiotics in the active site. The coloring scheme in this figure is the same as in Figs. 3 and 4. TLM binds on the malonyl-ACP side and cerulenin occupies the acyl-enzyme intermediate half. The O-1 of TLM and O-2 of cerulenin are the only portions of the antibiotics that overlap in the structure, and they form hydrogen bonds with the His-His dyad in the active site. Note that the protein structure shown is that of the FabB-TLM complex. Binding of the two antibiotics results in essentially identical changes in the conformations of the active site residues.
Figure 8.
Fig. 8. Schematic diagrams illustrating how cerulenin and TLM mimic substrates in the active site of FabB. Upper panel, the thiolactone ring of TLM mimics the bent conformation of the thiomalonate, and this is emphasized by the shaded atoms. The O-1s form hydrogen bonds with His-298 and His-333, and the C-1, C-2, and C-3s of malonate are mimicked by the C-1, C-2, and C-9s of TLM. The O-2 of TLM points out the active site tunnel that would be occupied by the pantetheine arm of the malonyl-ACP substrate. Lower panel, cerulenin mimics the condensation transition state and spans the two halves of the active site. The O-3 of cerulenin lies in the oxyanion hole formed by the amides of Cys-163 and Phe-392 enclosed by the phenyl side chain of Phe-392. This structure mimics the postulated location of the oxyanion of the tetrahedral transition state. The side chain of Cys-163 rotates in the cerulenin structure to form a covalent bond with C-2, but in the transition state, it is postulated to reside in the location observed in the native enzyme. The acyl chain of cerulenin feeds into the hydrophobic groove that accommodates the long chain acyl-enzyme intermediate.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 6551-6559) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20018879 C.A.Machutta, G.R.Bommineni, S.R.Luckner, K.Kapilashrami, B.Ruzsicska, C.Simmerling, C.Kisker, and P.J.Tonge (2010).
Slow onset inhibition of bacterial beta-ketoacyl-acyl carrier protein synthases by thiolactomycin.
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20662770 D.I.Chan, and H.J.Vogel (2010).
Current understanding of fatty acid biosynthesis and the acyl carrier protein.
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20547796 H.H.Xu, J.D.Trawick, R.J.Haselbeck, R.A.Forsyth, R.T.Yamamoto, R.Archer, J.Patterson, M.Allen, J.M.Froelich, I.Taylor, D.Nakaji, R.Maile, G.C.Kedar, M.Pilcher, V.Brown-Driver, M.McCarthy, A.Files, D.Robbins, P.King, S.Sillaots, C.Malone, C.S.Zamudio, T.Roemer, L.Wang, P.J.Youngman, and D.Wall (2010).
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Discovery and syntheses of "superbug challengers"-platensimycin and platencin.
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20477946 M.Hughes, V.Snetkov, R.S.Rose, S.Trousil, J.E.Mermoud, and C.Dingwall (2010).
Neurite-like structures induced by mevalonate pathway blockade are due to the stability of cell adhesion foci and are enhanced by the presence of APP.
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20936198 R.Orth, T.Böttcher, and S.A.Sieber (2010).
The biological targets of acivicin inspired 3-chloro- and 3-bromodihydroisoxazole scaffolds.
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19152182 J.M.Draper, and C.D.Smith (2009).
Palmitoyl acyltransferase assays and inhibitors (Review).
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Recent advances in the chemistry and biology of naturally occurring antibiotics.
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Synthesis and biological activity of enantiomeric pairs of 5-(Alk-2-enyl)thiolactomycin and 5-[(E)-Cycloalk-2-enylidenemethyl]thiolactomycin congeners.
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19191586 P.J.Lee, J.B.Bhonsle, H.W.Gaona, D.P.Huddler, T.N.Heady, M.Kreishman-Deitrick, A.Bhattacharjee, W.F.McCalmont, L.Gerena, M.Lopez-Sanchez, N.E.Roncal, T.H.Hudson, J.D.Johnson, S.T.Prigge, and N.C.Waters (2009).
Targeting the fatty acid biosynthesis enzyme, beta-ketoacyl-acyl carrier protein synthase III (PfKASIII), in the identification of novel antimalarial agents.
  J Med Chem, 52, 952-963.  
19223628 P.J.McNamara, R.E.Syverson, K.Milligan-Myhre, O.Frolova, S.Schroeder, J.Kidder, T.Hoang, and R.A.Proctor (2009).
Surfactants, aromatic and isoprenoid compounds, and fatty acid biosynthesis inhibitors suppress Staphylococcus aureus production of toxic shock syndrome toxin 1.
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19440303 Q.Al-Balas, N.G.Anthony, B.Al-Jaidi, A.Alnimr, G.Abbott, A.K.Brown, R.C.Taylor, G.S.Besra, T.D.McHugh, S.H.Gillespie, B.F.Johnston, S.P.Mackay, and G.D.Coxon (2009).
Identification of 2-Aminothiazole-4-Carboxylate Derivatives Active against Mycobacterium tuberculosis H(37)R(v) and the beta-Ketoacyl-ACP Synthase mtFabH.
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19262672 S.Brinster, G.Lamberet, B.Staels, P.Trieu-Cuot, A.Gruss, and C.Poyart (2009).
Type II fatty acid synthesis is not a suitable antibiotic target for Gram-positive pathogens.
  Nature, 458, 83-86.  
19604480 S.R.Luckner, C.A.Machutta, P.J.Tonge, and C.Kisker (2009).
Crystal structures of Mycobacterium tuberculosis KasA show mode of action within cell wall biosynthesis and its inhibition by thiolactomycin.
  Structure, 17, 1004-1013.
PDB codes: 2wgd 2wge 2wgf 2wgg
  18453702 B.Bagautdinov, Y.Ukita, M.Miyano, and N.Kunishima (2008).
Structure of 3-oxoacyl-(acyl-carrier protein) synthase II from Thermus thermophilus HB8.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 358-366.
PDB code: 1j3n
18219113 G.Parthasarathy, R.Cummings, J.W.Becker, and S.M.Soisson (2008).
Surface-entropy reduction approaches to manipulate crystal forms of beta-ketoacyl acyl carrier protein synthase II from Streptococcus pneumoniae.
  Acta Crystallogr D Biol Crystallogr, 64, 141-148.
PDB code: 2rjt
18725634 P.Johansson, B.Wiltschi, P.Kumari, B.Kessler, C.Vonrhein, J.Vonck, D.Oesterhelt, and M.Grininger (2008).
Inhibition of the fungal fatty acid synthase type I multienzyme complex.
  Proc Natl Acad Sci U S A, 105, 12803-12808.
PDB code: 2vkz
18835990 R.N.Brown, and P.A.Gulig (2008).
Regulation of fatty acid metabolism by FadR is essential for Vibrio vulnificus to cause infection of mice.
  J Bacteriol, 190, 7633-7644.  
17555433 A.Bhatt, V.Molle, G.S.Besra, W.R.Jacobs, and L.Kremer (2007).
The Mycobacterium tuberculosis FAS-II condensing enzymes: their role in mycolic acid biosynthesis, acid-fastness, pathogenesis and in future drug development.
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17242430 C.E.Christensen, B.B.Kragelund, P.von Wettstein-Knowles, and A.Henriksen (2007).
Structure of the human beta-ketoacyl [ACP] synthase from the mitochondrial type II fatty acid synthase.
  Protein Sci, 16, 261-272.
PDB codes: 2iwy 2iwz 2ix4
17112527 D.J.Ferguson, S.A.Campbell, F.L.Henriquez, L.Phan, E.Mui, T.A.Richards, S.P.Muench, M.Allary, J.Z.Lu, S.T.Prigge, F.Tomley, M.W.Shirley, D.W.Rice, R.McLeod, and C.W.Roberts (2007).
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17827660 F.Kudo, Y.Kasama, T.Hirayama, and T.Eguchi (2007).
Cloning of the pactamycin biosynthetic gene cluster and characterization of a crucial glycosyltransferase prior to a unique cyclopentane ring formation.
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18084068 G.Pappenberger, T.Schulz-Gasch, E.Kusznir, F.Müller, and M.Hennig (2007).
Structure-assisted discovery of an aminothiazole derivative as a lead molecule for inhibition of bacterial fatty-acid synthesis.
  Acta Crystallogr D Biol Crystallogr, 63, 1208-1216.
PDB codes: 2vb7 2vb8 2vb9 2vba
17707686 H.T.Wright, and K.A.Reynolds (2007).
Antibacterial targets in fatty acid biosynthesis.
  Curr Opin Microbiol, 10, 447-453.  
17456595 J.Wang, S.Kodali, S.H.Lee, A.Galgoci, R.Painter, K.Dorso, F.Racine, M.Motyl, L.Hernandez, E.Tinney, S.L.Colletti, K.Herath, R.Cummings, O.Salazar, I.González, A.Basilio, F.Vicente, O.Genilloud, F.Pelaez, H.Jayasuriya, K.Young, D.F.Cully, and S.B.Singh (2007).
Discovery of platencin, a dual FabF and FabH inhibitor with in vivo antibiotic properties.
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  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
17183501 K.L.Dormann, and R.Brückner (2007).
Variable synthesis of the optically active thiotetronic acid antibiotics thiolactomycin, thiotetromycin, and 834-B1.
  Angew Chem Int Ed Engl, 46, 1160-1163.  
17524982 M.M.Alhamadsheh, F.Musayev, A.A.Komissarov, S.Sachdeva, H.T.Wright, N.Scarsdale, G.Florova, and K.A.Reynolds (2007).
Alkyl-CoA disulfides as inhibitors and mechanistic probes for FabH enzymes.
  Chem Biol, 14, 513-524.
PDB codes: 2eft 2gyo
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.  
17485508 S.Sharma, S.K.Sharma, R.Modak, K.Karmodiya, N.Surolia, and A.Surolia (2007).
Mass spectrometry-based systems approach for identification of inhibitors of Plasmodium falciparum fatty acid synthase.
  Antimicrob Agents Chemother, 51, 2552-2558.  
17174327 S.Sridharan, L.Wang, A.K.Brown, L.G.Dover, L.Kremer, G.S.Besra, and J.C.Sacchettini (2007).
X-ray crystal structure of Mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase II (mtKasB).
  J Mol Biol, 366, 469-480.
PDB code: 2gp6
17719492 Y.Tang, A.Y.Chen, C.Y.Kim, D.E.Cane, and C.Khosla (2007).
Structural and mechanistic analysis of protein interactions in module 3 of the 6-deoxyerythronolide B synthase.
  Chem Biol, 14, 931-943.
PDB code: 2qo3
16356722 A.M.Haapalainen, G.Meriläinen, and R.K.Wierenga (2006).
The thiolase superfamily: condensing enzymes with diverse reaction specificities.
  Trends Biochem Sci, 31, 64-71.  
16699188 C.Oefner, H.Schulz, A.D'Arcy, and G.E.Dale (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.
PDB codes: 2g1h 2g2o 2g2y 2g2z
16952137 D.Häbich, and F.von Nussbaum (2006).
Platensimycin, a new antibiotic and "superbug challenger" from nature.
  ChemMedChem, 1, 951-954.  
16710421 J.Wang, S.M.Soisson, K.Young, W.Shoop, S.Kodali, A.Galgoci, R.Painter, G.Parthasarathy, Y.S.Tang, R.Cummings, S.Ha, K.Dorso, M.Motyl, H.Jayasuriya, J.Ondeyka, K.Herath, C.Zhang, L.Hernandez, J.Allocco, A.Basilio, J.R.Tormo, O.Genilloud, F.Vicente, F.Pelaez, L.Colwell, S.H.Lee, B.Michael, T.Felcetto, C.Gill, L.L.Silver, J.D.Hermes, K.Bartizal, J.Barrett, D.Schmatz, J.W.Becker, D.Cully, and S.B.Singh (2006).
Platensimycin is a selective FabF inhibitor with potent antibiotic properties.
  Nature, 441, 358-361.
PDB codes: 2gfv 2gfw 2gfx 2gfy
16436705 K.Young, H.Jayasuriya, J.G.Ondeyka, K.Herath, C.Zhang, S.Kodali, A.Galgoci, R.Painter, V.Brown-Driver, R.Yamamoto, L.L.Silver, Y.Zheng, J.I.Ventura, J.Sigmund, S.Ha, A.Basilio, F.Vicente, J.R.Tormo, F.Pelaez, P.Youngman, D.Cully, J.F.Barrett, D.Schmatz, S.B.Singh, and J.Wang (2006).
Discovery of FabH/FabF inhibitors from natural products.
  Antimicrob Agents Chemother, 50, 519-526.  
16699591 P.Kim, C.E.Barry, and C.S.Dowd (2006).
Novel route to 5-position vinyl derivatives of thiolactomycin: Olefination vs. deformylation.
  Tetrahedron Lett, 47, 3447-3451.  
16392800 P.Kim, Y.M.Zhang, G.Shenoy, Q.A.Nguyen, H.I.Boshoff, U.H.Manjunatha, M.B.Goodwin, J.Lonsdale, A.C.Price, D.J.Miller, K.Duncan, S.W.White, C.O.Rock, C.E.Barry, and C.S.Dowd (2006).
Structure-activity relationships at the 5-position of thiolactomycin: an intact (5R)-isoprene unit is required for activity against the condensing enzymes from Mycobacterium tuberculosis and Escherichia coli.
  J Med Chem, 49, 159-171.
PDB codes: 2aq7 2aqb
16441657 P.von Wettstein-Knowles, J.G.Olsen, K.A.McGuire, and A.Henriksen (2006).
Fatty acid synthesis. Role of active site histidines and lysine in Cys-His-His-type beta-ketoacyl-acyl carrier protein synthases.
  FEBS J, 273, 695-710.
PDB codes: 1h4f 2buh 2bui 2byw 2byx 2byy 2byz 2bz3 2bz4
15681420 A.Punjabi, and P.Traktman (2005).
Cell biological and functional characterization of the vaccinia virus F10 kinase: implications for the mechanism of virion morphogenesis.
  J Virol, 79, 2171-2190.  
15744497 N.Sirinupong, P.Suwanmanee, R.F.Doolittle, and W.Suvachitanont (2005).
Molecular cloning of a new cDNA and expression of 3-hydroxy-3-methylglutaryl-CoA synthase gene from Hevea brasiliensis.
  Planta, 221, 502-512.  
15727041 R.J.Wilson (2005).
Parasite plastids: approaching the endgame.
  Biol Rev Camb Philos Soc, 80, 129-153.  
15952903 S.W.White, J.Zheng, Y.M.Zhang, and Rock (2005).
The structural biology of type II fatty acid biosynthesis.
  Annu Rev Biochem, 74, 791-831.  
15987898 X.Qiu, A.E.Choudhry, C.A.Janson, M.Grooms, R.A.Daines, J.T.Lonsdale, and S.S.Khandekar (2005).
Crystal structure and substrate specificity of the beta-ketoacyl-acyl carrier protein synthase III (FabH) from Staphylococcus aureus.
  Protein Sci, 14, 2087-2094.
PDB code: 1zow
16240117 Z.J.Witczak, and J.M.Culhane (2005).
Thiosugars: new perspectives regarding availability and potential biochemical and medicinal applications.
  Appl Microbiol Biotechnol, 69, 237-244.  
  16733529 G.Shenoy, P.Kim, M.Goodwin, Q.A.Nguyen, C.E.Barry, and C.S.Dowd (2004).
  Heterocycles, 63, 519-527.  
  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.  
15273125 X.He, A.M.Reeve, U.R.Desai, G.E.Kellogg, and K.A.Reynolds (2004).
1,2-dithiole-3-ones as potent inhibitors of the bacterial 3-ketoacyl acyl carrier protein synthase III (FabH).
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15052334 Y.J.Lu, Y.M.Zhang, and C.O.Rock (2004).
Product diversity and regulation of type II fatty acid synthases.
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12837788 A.C.Price, C.O.Rock, and S.W.White (2003).
The 1.3-Angstrom-resolution crystal structure of beta-ketoacyl-acyl carrier protein synthase II from Streptococcus pneumoniae.
  J Bacteriol, 185, 4136-4143.
PDB codes: 1ox0 1oxh
12163601 C.Ritzenthaler, C.Laporte, F.Gaire, P.Dunoyer, C.Schmitt, S.Duval, A.Piéquet, A.M.Loudes, O.Rohfritsch, C.Stussi-Garaud, and P.Pfeiffer (2002).
Grapevine fanleaf virus replication occurs on endoplasmic reticulum-derived membranes.
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12429097 H.Pan, S.Tsai, E.S.Meadows, L.J.Miercke, A.T.Keatinge-Clay, J.O'Connell, C.Khosla, and R.M.Stroud (2002).
Crystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway.
  Structure, 10, 1559-1568.
PDB code: 1mzj
11959552 S.Jackowski, Y.M.Zhang, A.C.Price, S.W.White, and C.O.Rock (2002).
A missense mutation in the fabB (beta-ketoacyl-acyl carrier protein synthase I) gene confers tiolactomycin resistance to Escherichia coli.
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12164806 T.K.Zank, U.Zähringer, C.Beckmann, G.Pohnert, W.Boland, H.Holtorf, R.Reski, J.Lerchl, and E.Heinz (2002).
Cloning and functional characterisation of an enzyme involved in the elongation of Delta6-polyunsaturated fatty acids from the moss Physcomitrella patens.
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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.
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11679314 H.J.Lee, M.H.Choi, T.U.Kim, and S.C.Yoon (2001).
Accumulation of polyhydroxyalkanoic acid containing large amounts of unsaturated monomers in Pseudomonas fluorescens BM07 utilizing saccharides and its inhibition by 2-bromooctanoic acid.
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11566998 J.W.Campbell, and J.E.Cronan (2001).
Escherichia coli FadR positively regulates transcription of the fabB fatty acid biosynthetic gene.
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11544358 J.W.Campbell, and J.E.Cronan (2001).
Bacterial fatty acid biosynthesis: targets for antibacterial drug discovery.
  Annu Rev Microbiol, 55, 305-332.  
11445460 R.J.Heath (2001).
Bacterial fatty-acid biosynthesis: an antibacterial drug target waiting to be exploited.
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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.  
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.