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PDBsum entry 1pwv

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1pwv
Jmol
Contents
Protein chains
733 a.a.
Ligands
VAL-TYR-PRO-TYR-
PRO-MET-GLU-PRO-
THR
×2
PDB id:
1pwv
Name: Hydrolase
Title: Crystal structure of anthrax lethal factor wild-type protein complexed with an optimised peptide substrate.
Structure: Lethal factor. Chain: a, b. Synonym: lf, anthrax lethal toxin endopeptidase component. Engineered: yes. Lf20. Chain: c, d. Engineered: yes
Source: Bacillus anthracis. Organism_taxid: 1392. Gene: lef or pxo1-107. Expressed in: bacillus anthracis. Expression_system_taxid: 1392. Synthetic: yes. Other_details: this optimised peptide substrate was synthesised.
Biol. unit: Dimer (from PQS)
Resolution:
2.85Å     R-factor:   0.231     R-free:   0.279
Authors: T.Y.Wong,R.Schwarzenbacher,R.C.Liddington
Key ref:
B.E.Turk et al. (2004). The structural basis for substrate and inhibitor selectivity of the anthrax lethal factor. Nat Struct Mol Biol, 11, 60-66. PubMed id: 14718924 DOI: 10.1038/nsmb708
Date:
02-Jul-03     Release date:   03-Feb-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P15917  (LEF_BACAN) -  Lethal factor
Seq:
Struc:
 
Seq:
Struc:
809 a.a.
733 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.4.24.83  - Anthrax lethal factor endopeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Cofactor: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     pathogenesis   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1038/nsmb708 Nat Struct Mol Biol 11:60-66 (2004)
PubMed id: 14718924  
 
 
The structural basis for substrate and inhibitor selectivity of the anthrax lethal factor.
B.E.Turk, T.Y.Wong, R.Schwarzenbacher, E.T.Jarrell, S.H.Leppla, R.J.Collier, R.C.Liddington, L.C.Cantley.
 
  ABSTRACT  
 
Recent events have created an urgent need for new therapeutic strategies to treat anthrax. We have applied a mixture-based peptide library approach to rapidly determine the optimal peptide substrate for the anthrax lethal factor (LF), a metalloproteinase with an important role in the pathogenesis of the disease. Using this approach we have identified peptide analogs that inhibit the enzyme in vitro and that protect cultured macrophages from LF-mediated cytolysis. The crystal structures of LF bound to an optimized peptide substrate and to peptide-based inhibitors provide a rationale for the observed selectivity and may be exploited in the design of future generations of LF inhibitors.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Inhibition of LF by GM6001. (a) GM6001 inhibits cleavage of MKKs by LF in vitro. Immunoblots show LF cleavage of MKK-3 and MKK-1 in J774A.1 lysates in the presence of varying concentrations of GM6001 or 10 mM o-phenanthroline, a metal chelator. Cleavage of MKK-3 causes a mobility shift; the MKK-1 antibody is directed against the N terminus and does not react with the cleavage product, resulting in disappearance of the band upon cleavage. (b) GM6001 inhibits MKK-3 cleavage in lethal toxin -treated cells. Quantified western blot analysis of MKK-3 cleavage in J774A.1 treated with lethal toxin (0.5 g ml-1 PA with the indicated concentrations of LF) in the absence or presence of 100 M GM6001. (c) Protection of J774A.1 cells from lethal toxin -mediated cell death by GM6001. Cell viability as determined by MTT assay after lethal toxin treatment in the presence of 100 M GM6001 or 0.2% (v/v) DMSO carrier. (d) Dose-dependent neutralization of lethal toxin by GM6001. J774A.1 cell viability determined by MTT assay after treatment with lethal toxin (0.5 g ml-1 PA + 0.3 g ml-1 LF) or PA alone (0.5 g ml-1) in the presence of the indicated concentrations of GM6001. (e) GM6001 protects J774A.1 cells when added subsequent to LeTx. Cell viability is shown after treatment with PA alone (0.4 g ml-1) or PA with LF (25 ng ml-1), with GM6001 added to 100 M at the indicated time after toxin addition.
Figure 2.
Figure 2. Structures of LF in complex with peptides and inhibitors. Molecular surface of LF is colored by charge (red, negative; blue, positive), with Zn2+ as a solid sphere (cyan) and the model of the peptide or inhibitor in ball-and-stick representation. The individual electron density surrounding each molecule is a 2F[o] - F[c] difference map calculated at the respective final resolution and contoured at 1.0 . (a) LF20 (yellow) in the absence of Zn2+, resolution limit 2.85 . The model of bound LF20 shows the sequence VYPYPMEPT (residues 8 -16 of the 20-residue-long LF20). This is the ordered region, and the electron density is clearly visible in difference maps (2F[o] - F[c] and F[o] - F[c]) calculated from crystal X-ray diffraction data. (b,c) SHAc-YPM (white, labeled YPM), resolution limit 3.50 , and GM6001 (green), resolution limit 2.70 , respectively. Continuous electron density extends from the zinc atom to the metal-chelating moieties of the inhibitors (hydroxamate and thioacetyl, respectively). (d) The superposed individual complex structures of all three target molecules from a -c in the substrate-binding groove of LF, using the surface calculated for LF -LF20. The targets are all bound in the same N-to-C peptide orientation. (e) An overview of LF bound to the targets LF20, GM6001 and SHAc-YPM, superposed and colored as in d. The molecular surface was calculated from the LF -LF20 complex. The domains in LF are labeled I -IV. The catalytic site is in domain IV, where the zinc atom (not shown in this figure) is bound. These figures were prepared using SPOCK (http://mackerel.tamu.edu/spock/).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 60-66) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21396916 F.Li, S.Terzyan, and J.Tang (2011).
Subsite specificity of anthrax lethal factor and its implications for inhibitor development.
  Biochem Biophys Res Commun, 407, 400-405.  
21367651 J.Fernebro (2011).
Fighting bacterial infections-Future treatment options.
  Drug Resist Updat, 14, 125-139.  
20811381 M.Drag, and G.S.Salvesen (2010).
Emerging principles in protease-based drug discovery.
  Nat Rev Drug Discov, 9, 690-701.  
19922472 S.Ngai, S.Batty, K.C.Liao, and J.Mogridge (2010).
An anthrax lethal factor mutant that is defective at causing pyroptosis retains proapoptotic activity.
  FEBS J, 277, 119-127.  
19170530 A.Agrawal, C.A.de Oliveira, Y.Cheng, J.A.Jacobsen, J.A.McCammon, and S.M.Cohen (2009).
Thioamide hydroxypyrothiones supersede amide hydroxypyrothiones in potency against anthrax lethal factor.
  J Med Chem, 52, 1063-1074.  
19520864 C.A.Blindauer, I.Harvey, K.E.Bunyan, A.J.Stewart, D.Sleep, D.J.Harrison, S.Berezenko, and P.J.Sadler (2009).
Structure, properties, and engineering of the major zinc binding site on human albumin.
  J Biol Chem, 284, 23116-23124.  
19361425 C.E.Leysath, A.F.Monzingo, J.A.Maynard, J.Barnett, G.Georgiou, B.L.Iverson, and J.D.Robertus (2009).
Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen.
  J Mol Biol, 387, 680-693.
PDB codes: 3esu 3esv 3et9 3etb
19665472 F.Tonello, and C.Montecucco (2009).
The anthrax lethal factor and its MAPK kinase-specific metalloprotease activity.
  Mol Aspects Med, 30, 431-438.  
19585464 G.A.Dalkas, A.Papakyriakou, A.Vlamis-Gardikas, and G.A.Spyroulias (2009).
Insights into the anthrax lethal factor-substrate interaction and selectivity using docking and molecular dynamics simulations.
  Protein Sci, 18, 1774-1785.  
18831046 M.Joshi, J.O.Ebalunode, and J.M.Briggs (2009).
Computational insights into the interaction of the anthrax lethal factor with the N-terminal region of its substrates.
  Proteins, 75, 323-335.  
19860382 M.X.Macrae, S.Blake, X.Jiang, R.Capone, D.J.Estes, M.Mayer, and J.Yang (2009).
A semi-synthetic ion channel platform for detection of phosphatase and protease activity.
  ACS Nano, 3, 3567-3580.  
19359249 M.Y.Zakharova, N.A.Kuznetsov, S.A.Dubiley, A.V.Kozyr, O.S.Fedorova, D.M.Chudakov, D.G.Knorre, I.G.Shemyakin, A.G.Gabibov, and A.V.Kolesnikov (2009).
Substrate Recognition of Anthrax Lethal Factor Examined by Combinatorial and Pre-steady-state Kinetic Approaches.
  J Biol Chem, 284, 17902-17913.  
19359184 S.L.Johnson, L.H.Chen, E.Barile, A.Emdadi, M.Sabet, H.Yuan, J.Wei, D.Guiney, and M.Pellecchia (2009).
Structure-activity relationship studies of a novel series of anthrax lethal factor inhibitors.
  Bioorg Med Chem, 17, 3352-3368.  
19928768 T.L.Chiu, J.Solberg, S.Patil, T.W.Geders, X.Zhang, S.Rangarajan, R.Francis, B.C.Finzel, M.A.Walters, D.J.Hook, and E.A.Amin (2009).
Identification of novel non-hydroxamate anthrax toxin lethal factor inhibitors by topomeric searching, docking and scoring, and in vitro screening.
  J Chem Inf Model, 49, 2726-2734.  
19389405 Z.Kang, J.I.Webster Marketon, A.Johnson, and E.M.Sternberg (2009).
Bacillus anthracis lethal toxin represses MMTV promoter activity through transcription factors.
  J Mol Biol, 389, 595-605.  
18079741 L.Cegelski, G.R.Marshall, G.R.Eldridge, and S.J.Hultgren (2008).
The biology and future prospects of antivirulence therapies.
  Nat Rev Microbiol, 6, 17-27.  
18649128 M.Vuyisich, S.Gnanakaran, J.A.Lovchik, C.R.Lyons, and G.Gupta (2008).
A dual-purpose protein ligand for effective therapy and sensitive diagnosis of anthrax.
  Protein J, 27, 292-302.  
18429598 M.Y.Zakharova, S.A.Dubiley, D.M.Chudakov, A.G.Gabibov, I.G.Shemyakin, and A.V.Kolesnikov (2008).
Substrate specificity of the anthrax lethal factor.
  Dokl Biochem Biophys, 418, 14-17.  
18787455 S.V.Lynch, and J.P.Wiener-Kronish (2008).
Novel strategies to combat bacterial virulence.
  Curr Opin Crit Care, 14, 593-599.  
17710100 A.E.Clatworthy, E.Pierson, and D.T.Hung (2007).
Targeting virulence: a new paradigm for antimicrobial therapy.
  Nat Chem Biol, 3, 541-548.  
17637984 D.P.Giedroc, and A.I.Arunkumar (2007).
Metal sensor proteins: nature's metalloregulated allosteric switches.
  Dalton Trans, (), 3107-3120.  
17163561 F.E.Jacobsen, J.A.Lewis, and S.M.Cohen (2007).
The Design of Inhibitors for Medicinally Relevant Metalloproteins.
  ChemMedChem, 2, 152-171.  
  19081825 J.Mogridge (2007).
Defensive strategies of Bacillus anthracis that promote a fatal disease.
  Drug Discov Today Dis Mech, 4, 253-258.  
17095744 K.Sherer, Y.Li, X.Cui, and P.Q.Eichacker (2007).
Lethal and edema toxins in the pathogenesis of Bacillus anthracis septic shock: implications for therapy.
  Am J Respir Crit Care Med, 175, 211-221.  
17474906 M.Benghezal, E.Adam, A.Lucas, C.Burn, M.G.Orchard, C.Deuschel, E.Valentino, S.Braillard, J.P.Paccaud, and P.Cosson (2007).
Inhibitors of bacterial virulence identified in a surrogate host model.
  Cell Microbiol, 9, 1336-1342.  
16710861 M.Matziari, V.Dive, and A.Yiotakis (2007).
Matrix metalloproteinase 11 (MMP-11; stromelysin-3) and synthetic inhibitors.
  Med Res Rev, 27, 528-552.  
17537721 S.A.Shiryaev, A.G.Remacle, B.I.Ratnikov, N.A.Nelson, A.Y.Savinov, G.Wei, M.Bottini, M.F.Rega, A.Parent, R.Desjardins, M.Fugere, R.Day, M.Sabet, M.Pellecchia, R.C.Liddington, J.W.Smith, T.Mustelin, D.G.Guiney, M.Lebl, and A.Y.Strongin (2007).
Targeting host cell furin proprotein convertases as a therapeutic strategy against bacterial toxins and viral pathogens.
  J Biol Chem, 282, 20847-20853.  
17555370 Y.Li, K.Sherer, X.Cui, and P.Q.Eichacker (2007).
New insights into the pathogenesis and treatment of anthrax toxin-induced shock.
  Expert Opin Biol Ther, 7, 843-854.  
16537471 C.Guarise, L.Pasquato, V.De Filippis, and P.Scrimin (2006).
Gold nanoparticles-based protease assay.
  Proc Natl Acad Sci U S A, 103, 3978-3982.  
16814591 D.T.Hung, and E.J.Rubin (2006).
Chemical biology and bacteria: not simply a matter of life or death.
  Curr Opin Chem Biol, 10, 321-326.  
16902919 J.A.Lewis, J.Mongan, J.A.McCammon, and S.M.Cohen (2006).
Evaluation and binding-mode prediction of thiopyrone-based inhibitors of anthrax lethal factor.
  ChemMedChem, 1, 694-697.  
16926147 M.C.Chung, T.G.Popova, B.A.Millis, D.V.Mukherjee, W.Zhou, L.A.Liotta, E.F.Petricoin, V.Chandhoke, C.Bailey, and S.G.Popov (2006).
Secreted neutral metalloproteases of Bacillus anthracis as candidate pathogenic factors.
  J Biol Chem, 281, 31408-31418.  
16762077 M.E.Goldman, L.Cregar, D.Nguyen, O.Simo, S.O'Malley, and T.Humphreys (2006).
Cationic polyamines inhibit anthrax lethal factor protease.
  BMC Pharmacol, 6, 8.  
16475828 M.L.Peterson, and P.M.Schlievert (2006).
Glycerol monolaurate inhibits the effects of Gram-positive select agents on eukaryotic cells.
  Biochemistry, 45, 2387-2397.  
16817854 P.Kuzmic, L.Cregar, S.Z.Millis, and M.Goldman (2006).
Mixed-type noncompetitive inhibition of anthrax lethal factor protease by aminoglycosides.
  FEBS J, 273, 3054-3062.  
16790431 W.Wang, C.Mulakala, S.C.Ward, G.Jung, H.Luong, D.Pham, A.J.Waring, Y.Kaznessis, W.Lu, K.A.Bradley, and R.I.Lehrer (2006).
Retrocyclins kill bacilli and germinating spores of Bacillus anthracis and inactivate anthrax lethal toxin.
  J Biol Chem, 281, 32755-32764.  
15772169 C.Kim, N.Gajendran, H.W.Mittrücker, M.Weiwad, Y.H.Song, R.Hurwitz, M.Wilmanns, G.Fischer, and S.H.Kaufmann (2005).
Human alpha-defensins neutralize anthrax lethal toxin and protect against its fatal consequences.
  Proc Natl Acad Sci U S A, 102, 4830-4835.  
16223984 D.T.Hung, E.A.Shakhnovich, E.Pierson, and J.J.Mekalanos (2005).
Small-molecule inhibitor of Vibrio cholerae virulence and intestinal colonization.
  Science, 310, 670-674.  
15803193 J.C.Burnett, E.A.Henchal, A.L.Schmaljohn, and S.Bavari (2005).
The evolving field of biodefence: therapeutic developments and diagnostics.
  Nat Rev Drug Discov, 4, 281-297.  
15983377 M.Forino, S.Johnson, T.Y.Wong, D.V.Rozanov, A.Y.Savinov, W.Li, R.Fattorusso, B.Becattini, A.J.Orry, D.Jung, R.A.Abagyan, J.W.Smith, K.Alibek, R.C.Liddington, A.Y.Strongin, and M.Pellecchia (2005).
Efficient synthetic inhibitors of anthrax lethal factor.
  Proc Natl Acad Sci U S A, 102, 9499-9504.
PDB code: 1zxv
15624157 M.Fridman, V.Belakhov, L.V.Lee, F.S.Liang, C.H.Wong, and T.Baasov (2005).
Dual effect of synthetic aminoglycosides: antibacterial activity against Bacillus anthracis and inhibition of anthrax lethal factor.
  Angew Chem Int Ed Engl, 44, 447-452.  
16118206 M.L.Geddie, T.L.O'Loughlin, K.K.Woods, and I.Matsumura (2005).
Rational design of p53, an intrinsically unstructured protein, for the fabrication of novel molecular sensors.
  J Biol Chem, 280, 35641-35646.  
15880659 M.M.Numa, L.V.Lee, C.C.Hsu, K.E.Bower, and C.H.Wong (2005).
Identification of novel anthrax lethal factor inhibitors generated by combinatorial Pictet-Spengler reaction followed by screening in situ.
  Chembiochem, 6, 1002-1006.  
15644338 R.G.Panchal, K.M.Halverson, W.Ribot, D.Lane, T.Kenny, T.G.Abshire, J.W.Ezzell, T.A.Hoover, B.Powell, S.Little, J.J.Kasianowicz, and S.Bavari (2005).
Purified Bacillus anthracis lethal toxin complex formed in vitro and during infection exhibits functional and biological activity.
  J Biol Chem, 280, 10834-10839.  
15819985 S.G.Popov, T.G.Popova, S.Hopkins, R.S.Weinstein, R.MacAfee, K.J.Fryxell, V.Chandhoke, C.Bailey, and K.Alibek (2005).
Effective antiprotease-antibiotic treatment of experimental anthrax.
  BMC Infect Dis, 5, 25.  
16316448 S.Gazal, L.R.Masterson, and G.Barany (2005).
Facile solid-phase synthesis of C-terminal peptide aldehydes and hydroxamates from a common Backbone Amide-Linked (BAL) intermediate.
  J Pept Res, 66, 324-332.  
16239558 S.S.Kocer, S.G.Walker, B.Zerler, L.M.Golub, and S.R.Simon (2005).
Metalloproteinase inhibitors, nonantimicrobial chemically modified tetracyclines, and ilomastat block Bacillus anthracis lethal factor activity in viable cells.
  Infect Immun, 73, 7548-7557.  
16153847 S.Sikora, A.Strongin, and A.Godzik (2005).
Convergent evolution as a mechanism for pathogenic adaptation.
  Trends Microbiol, 13, 522-527.  
16127065 T.Komiyama, J.A.Swanson, and R.S.Fuller (2005).
Protection from anthrax toxin-mediated killing of macrophages by the combined effects of furin inhibitors and chloroquine.
  Antimicrob Agents Chemother, 49, 3875-3882.  
15911756 W.L.Shoop, Y.Xiong, J.Wiltsie, A.Woods, J.Guo, J.V.Pivnichny, T.Felcetto, B.F.Michael, A.Bansal, R.T.Cummings, B.R.Cunningham, A.M.Friedlander, C.M.Douglas, S.B.Patel, D.Wisniewski, G.Scapin, S.P.Salowe, D.M.Zaller, K.T.Chapman, E.M.Scolnick, D.M.Schmatz, K.Bartizal, M.MacCoss, and J.D.Hermes (2005).
Anthrax lethal factor inhibition.
  Proc Natl Acad Sci U S A, 102, 7958-7963.
PDB code: 1yqy
15372082 G.J.Rainey, and J.A.Young (2004).
Antitoxins: novel strategies to target agents of bioterrorism.
  Nat Rev Microbiol, 2, 721-726.  
15465830 X.Liang, J.J.Young, S.A.Boone, D.S.Waugh, and N.S.Duesbery (2004).
Involvement of domain II in toxicity of anthrax lethal factor.
  J Biol Chem, 279, 52473-52478.  
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.