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PDBsum entry 1blc

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Hydrolase(acting in cyclic amides) PDB id
1blc
Jmol
Contents
Protein chain
257 a.a. *
Ligands
SO4
CEM
TEM
Waters ×324
* Residue conservation analysis
PDB id:
1blc
Name: Hydrolase(acting in cyclic amides)
Title: Inhibition of beta-lactamase by clavulanate: trapped intermediates in cryocrystallographic studies
Structure: Beta-lactamase. Chain: a. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.179    
Authors: C.C.H.Chen,O.Herzberg
Key ref: C.C.Chen and O.Herzberg (1992). Inhibition of beta-lactamase by clavulanate. Trapped intermediates in cryocrystallographic studies. J Mol Biol, 224, 1103-1113. PubMed id: 1569569
Date:
27-Sep-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00807  (BLAC_STAAU) -  Beta-lactamase
Seq:
Struc:
281 a.a.
257 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.2.6  - Beta-lactamase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Penicillin Biosynthesis and Metabolism
      Reaction: A beta-lactam + H2O = a substituted beta-amino acid
      Cofactor: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to antibiotic   2 terms 
  Biochemical function     hydrolase activity     2 terms  

 

 
J Mol Biol 224:1103-1113 (1992)
PubMed id: 1569569  
 
 
Inhibition of beta-lactamase by clavulanate. Trapped intermediates in cryocrystallographic studies.
C.C.Chen, O.Herzberg.
 
  ABSTRACT  
 
Crystallographic studies of the complex between beta-lactamase and clavulanate reveal a structure of two acyl-enzymes with covalent bonds at the active site Ser70, representing two different stages of inhibitor degradation alternately occupying the active site. Models that are consistent with biochemical data are derived from the electron density map and refined at 2.2 A resolution: cis enamine, in which the carboxylate group of the clavulanate molecule makes a salt bridge with Lys234 of beta-lactamase; decarboxylated trans enamine, which is oriented away from Lys234. For both acyl-enzymes, the carbonyl oxygen atom of the ester group occupies the oxyanion hole in a manner similar to that found in inhibitor binding to serine proteases. Whereas the oxygen atom in the trans product is optimally positioned in the oxyanion hole, that of the cis product clashes with the main-chain nitrogen atom of Ser70 and the beta-carbon atom of the adjacent Ala69. In contrast to cis to trans isomerization in solution that relieves the steric strain inherent in a cis double bond, at the enzyme-inhibitor interface two additional factors play an important role. The salt bridge enhances the stability of the cis product, while the steric strain introduced by the short contacts with the protein reduces its stability.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20065329 S.M.Drawz, and R.A.Bonomo (2010).
Three decades of beta-lactamase inhibitors.
  Clin Microbiol Rev, 23, 160-201.  
17704567 C.A.Smith, M.Caccamo, K.A.Kantardjieff, and S.Vakulenko (2007).
Structure of GES-1 at atomic resolution: insights into the evolution of carbapenamase activity in the class A extended-spectrum beta-lactamases.
  Acta Crystallogr D Biol Crystallogr, 63, 982-992.
PDB code: 2qpn
17915954 J.E.Hugonnet, and J.S.Blanchard (2007).
Irreversible inhibition of the Mycobacterium tuberculosis beta-lactamase by clavulanate.
  Biochemistry, 46, 11998-12004.  
17630699 M.A.Totir, M.S.Helfand, M.P.Carey, A.Sheri, J.D.Buynak, R.A.Bonomo, and P.R.Carey (2007).
Sulbactam forms only minimal amounts of irreversible acrylate-enzyme with SHV-1 beta-lactamase.
  Biochemistry, 46, 8980-8987.  
17311346 S.Sacquin-Mora, E.Laforet, and R.Lavery (2007).
Locating the active sites of enzymes using mechanical properties.
  Proteins, 67, 350-359.  
16280623 C.Chennubhotla, A.J.Rader, L.W.Yang, and I.Bahar (2005).
Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies.
  Phys Biol, 2, S173-S180.  
15987690 D.Sulton, D.Pagan-Rodriguez, X.Zhou, Y.Liu, A.M.Hujer, C.R.Bethel, M.S.Helfand, J.M.Thomson, V.E.Anderson, J.D.Buynak, L.M.Ng, and R.A.Bonomo (2005).
Clavulanic acid inactivation of SHV-1 and the inhibitor-resistant S130G SHV-1 beta-lactamase. Insights into the mechanism of inhibition.
  J Biol Chem, 280, 35528-35536.  
15939021 L.W.Yang, and I.Bahar (2005).
Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes.
  Structure, 13, 893-904.  
16055923 P.S.Padayatti, M.S.Helfand, M.A.Totir, M.P.Carey, P.R.Carey, R.A.Bonomo, and F.van den Akker (2005).
High resolution crystal structures of the trans-enamine intermediates formed by sulbactam and clavulanic acid and E166A SHV-1 {beta}-lactamase.
  J Biol Chem, 280, 34900-34907.
PDB codes: 2a3u 2a49
15461559 N.H.Georgopapadakou (2004).
Beta-lactamase inhibitors: evolving compounds for evolving resistance targets.
  Expert Opin Investig Drugs, 13, 1307-1318.  
14621983 M.S.Helfand, M.A.Totir, M.P.Carey, A.M.Hujer, R.A.Bonomo, and P.R.Carey (2003).
Following the reactions of mechanism-based inhibitors with beta-lactamase by Raman crystallography.
  Biochemistry, 42, 13386-13392.  
12121656 R.A.Powers, F.Morandi, and B.K.Shoichet (2002).
Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase.
  Structure, 10, 1013-1023.
PDB code: 1l2s
12058046 X.Wang, G.Minasov, and B.K.Shoichet (2002).
The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34.
  J Biol Chem, 277, 32149-32156.
PDB codes: 1lhy 1li0 1li9
11870868 X.Wang, G.Minasov, and B.K.Shoichet (2002).
Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams.
  Proteins, 47, 86-96.
PDB code: 1jvj
11327849 A.P.Kuzin, M.Nukaga, Y.Nukaga, A.Hujer, R.A.Bonomo, and J.R.Knox (2001).
Inhibition of the SHV-1 beta-lactamase by sulfones: crystallographic observation of two reaction intermediates with tazobactam.
  Biochemistry, 40, 1861-1866.
PDB codes: 1g56 1vm1
11327855 C.C.Chen, and O.Herzberg (2001).
Structures of the acyl-enzyme complexes of the Staphylococcus aureus beta-lactamase mutant Glu166Asp:Asn170Gln with benzylpenicillin and cephaloridine.
  Biochemistry, 40, 2351-2358.
PDB codes: 1ghi 1ghm 1ghp
10841972 C.Therrien, and R.C.Levesque (2000).
Molecular basis of antibiotic resistance and beta-lactamase inhibition by mechanism-based inactivators: perspectives and future directions.
  FEMS Microbiol Rev, 24, 251-262.  
11498375 M.G.Page (2000).
b-Lactamase inhibitors.
  Drug Resist Updat, 3, 109-125.  
10455164 P.Taylor, V.Anderson, J.Dowden, S.L.Flitsch, N.J.Turner, K.Loughran, and M.D.Walkinshaw (1999).
Novel mechanism of inhibition of elastase by beta-lactams is defined by two inhibitor crystal complexes.
  J Biol Chem, 274, 24901-24905.  
10511459 Y.Yang, B.A.Rasmussen, and D.M.Shlaes (1999).
Class A beta-lactamases--enzyme-inhibitor interactions and resistance.
  Pharmacol Ther, 83, 141-151.  
  9736532 D.Sirot, R.Labia, P.Pouedras, C.Chanal-Claris, C.Cerceau, and J.Sirot (1998).
Inhibitor-resistant OXY-2-derived beta-lactamase produced by Klebsiella oxytoca.
  Antimicrob Agents Chemother, 42, 2184-2187.  
  9624468 M.M.Caniça, N.Caroff, M.Barthélémy, R.Labia, R.Krishnamoorthy, G.Paul, and J.M.Dupret (1998).
Phenotypic study of resistance of beta-lactamase-inhibitor-resistant TEM enzymes which differ by naturally occurring variations and by site-directed substitution at Asp276.
  Antimicrob Agents Chemother, 42, 1323-1328.  
9521648 S.Banerjee, U.Pieper, G.Kapadia, L.K.Pannell, and O.Herzberg (1998).
Role of the omega-loop in the activity, substrate specificity, and structure of class A beta-lactamase.
  Biochemistry, 37, 3286-3296.
PDB code: 1ome
9730812 S.M.Fabiane, M.K.Sohi, T.Wan, D.J.Payne, J.H.Bateson, T.Mitchell, and B.J.Sutton (1998).
Crystal structure of the zinc-dependent beta-lactamase from Bacillus cereus at 1.9 A resolution: binuclear active site with features of a mononuclear enzyme.
  Biochemistry, 37, 12404-12411.
PDB code: 1bc2
9281835 K.H.Baggaley, A.G.Brown, and C.J.Schofield (1997).
Chemistry and biosynthesis of clavulanic acid and other clavams.
  Nat Prod Rep, 14, 309-333.  
8673602 B.L.Stoddard, A.Dean, and P.A.Bash (1996).
Combining Laue diffraction and molecular dynamics to study enzyme intermediates.
  Nat Struct Biol, 3, 590-595.  
8888067 B.L.Stoddard (1996).
Intermediate trapping and laue X-ray diffraction: potential for enzyme mechanism, dynamics, and inhibitor screening.
  Pharmacol Ther, 70, 215-256.  
8823158 C.C.Chen, T.J.Smith, G.Kapadia, S.Wäsch, L.E.Zawadzke, A.Coulson, and O.Herzberg (1996).
Structure and kinetics of the beta-lactamase mutants S70A and K73H from Staphylococcus aureus PC1.
  Biochemistry, 35, 12251-12258.
PDB codes: 1dja 1djb 1djc
  9158770 F.Guo, G.I.Dmitrienko, A.J.Clarke, and T.Viswanatha (1996).
The role of the nonconserved residues at position 167 of class A beta-lactamases in susceptibility to mechanism-based inhibitors.
  Microb Drug Resist, 2, 261-268.  
8987980 L.E.Zawadzke, C.C.Chen, S.Banerjee, Z.Li, S.Wäsch, G.Kapadia, J.Moult, and O.Herzberg (1996).
Elimination of the hydrolytic water molecule in a class A beta-lactamase mutant: crystal structure and kinetics.
  Biochemistry, 35, 16475-16482.
PDB codes: 1kge 1kgf
8756327 N.C.Strynadka, R.Martin, S.E.Jensen, M.Gold, and J.B.Jones (1996).
Structure-based design of a potent transition state analogue for TEM-1 beta-lactamase.
  Nat Struct Biol, 3, 688-695.  
8823177 R.P.Brown, R.T.Aplin, and C.J.Schofield (1996).
Inhibition of TEM-2 beta-lactamase from Escherichia coli by clavulanic acid: observation of intermediates by electrospray ionization mass spectrometry.
  Biochemistry, 35, 12421-12432.  
8590009 B.L.Stoddard, and G.K.Farber (1995).
Direct measurement of reactivity in the protein crystal by steady-state kinetic studies.
  Structure, 3, 991-996.  
7822311 H.Viadiu, J.Osuna, A.L.Fink, and X.Soberón (1995).
A new TEM beta-lactamase double mutant with broadened specificity reveals substrate-dependent functional interactions.
  J Biol Chem, 270, 781-787.  
7629142 I.Saves, O.Burlet-Schiltz, P.Swarén, F.Lefèvre, J.M.Masson, J.C.Promé, and J.P.Samama (1995).
The asparagine to aspartic acid substitution at position 276 of TEM-35 and TEM-36 is involved in the beta-lactamase resistance to clavulanic acid.
  J Biol Chem, 270, 18240-18245.  
7822310 J.Osuna, H.Viadiu, A.L.Fink, and X.Soberón (1995).
Substitution of Asp for Asn at position 132 in the active site of TEM beta-lactamase. Activity toward different substrates and effects of neighboring residues.
  J Biol Chem, 270, 775-780.  
  8592985 J.R.Knox (1995).
Extended-spectrum and inhibitor-resistant TEM-type beta-lactamases: mutations, specificity, and three-dimensional structure.
  Antimicrob Agents Chemother, 39, 2593-2601.  
8574702 K.Moffat, and R.Henderson (1995).
Freeze trapping of reaction intermediates.
  Curr Opin Struct Biol, 5, 656-663.  
7704524 D.W.Rodgers (1994).
Cryocrystallography.
  Structure, 2, 1135-1140.  
8248236 E.L.Bearer, J.A.DeGiorgis, R.A.Bodner, A.W.Kao, and T.S.Reese (1993).
Evidence for myosin motors on organelles in squid axoplasm.
  Proc Natl Acad Sci U S A, 90, 11252-11256.  
8248237 E.Lobkovsky, P.C.Moews, H.Liu, H.Zhao, J.M.Frere, and J.R.Knox (1993).
Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase.
  Proc Natl Acad Sci U S A, 90, 11257-11261.
PDB code: 2blt
  8388201 K.Bush, C.Macalintal, B.A.Rasmussen, V.J.Lee, and Y.Yang (1993).
Kinetic interactions of tazobactam with beta-lactamases from all major structural classes.
  Antimicrob Agents Chemother, 37, 851-858.  
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.