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PDBsum entry 1blh

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Hydrolase(beta-lactamase) PDB id
1blh
Jmol
Contents
Protein chain
257 a.a. *
Ligands
FOS
Waters ×195
* Residue conservation analysis
PDB id:
1blh
Name: Hydrolase(beta-lactamase)
Title: Structure of a phosphonate-inhibited beta-lactamase. An analog of the tetrahedral transition state(slash) intermediate of beta-lactam hydrolysis
Structure: Beta-lactamase. Chain: a. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.166    
Authors: C.C.H.Chen,O.Herzberg
Key ref: C.C.Chen et al. (1993). Structure of a phosphonate-inhibited beta-lactamase. An analog of the tetrahedral transition state/intermediate of beta-lactam hydrolysis. J Mol Biol, 234, 165-178. PubMed id: 8230196
Date:
30-Sep-93     Release date:   31-Aug-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 234:165-178 (1993)
PubMed id: 8230196  
 
 
Structure of a phosphonate-inhibited beta-lactamase. An analog of the tetrahedral transition state/intermediate of beta-lactam hydrolysis.
C.C.Chen, J.Rahil, R.F.Pratt, O.Herzberg.
 
  ABSTRACT  
 
The crystal structure of beta-lactamase from Staphylococcus aureus inactivated by p-nitrophenyl[[N-(benzyloxycarbonyl)amino]methyl]phosphonate, a methylphosphonate monoester monoanion inhibitor, has been determined and refined at 2.3 A resolution. The structure reveals a tetrahedral phosphorus covalently bonded to the O gamma atom of the active site serine, Ser70. One of the oxygen atoms bonded to phosphorus is located in the oxyanion hole formed by the two main-chain nitrogen atoms of Ser70 and Gln237, and the second bonded oxygen is solvated. The (benzyloxycarbonyl)aminomethyl group is oriented towards the active site gully such that the peptide group forms compensating electrostatic interactions with polar groups on the enzyme. The benzyl group forms a hydrophobic interaction with Ile239 and an aromatic-aromatic edge-to-face interaction with Tyr105, which has undergone a conformational transition relative to the native structure. The mode of binding supports the proposal that on reaction with the enzyme, the phosphonate generates a structure analogous to the tetrahedral transition state/intermediate associated with the acylation step of a normal substrate. The disposition of the phosphonyl group in this complex is the same as that of the corresponding phosphoryl group in the complex resulting from the inhibition of trypsin by diisopropylphosphofluoridate. The structure is consistent with a mechanism of inactivation that follows an associative pathway, proceeding via a transition state/intermediate in which phosphorus is penta-co-ordinated, forming a trigonal bipyramidal geometry with the phosphonyl donor (p-nitrophenol) and acceptor (Ser70 O gamma atom) in apical positions. A model of this transition state can be accommodated in the active site of beta-lactamase without any steric hindrance. A model of the tetrahedral transition state associated with the acylation step by benzyl penicillin has been derived. Because of the conformational rigidity of the fused rings of penicillin molecules, the orientation of the substrate is fixed once the tetrahedral carbonyl carbon and its ligands are superimposed on the phosphonate group. The outcome is that the carboxylate substituent on the thiazolidine ring forms a salt bridge with Lys234, and the preferred puckering of the ring is that observed in the crystal structure of ampicillin, the so-called "open" conformer.
 

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.  
  19241376 Y.Chen, A.McReynolds, and B.K.Shoichet (2009).
Re-examining the role of Lys67 in class C beta-lactamase catalysis.
  Protein Sci, 18, 662-669.
PDB codes: 3fkv 3fkw
17048043 P.de Figueiredo, B.Terra, J.K.Anand, T.Hikita, M.Sadilek, D.E.Monks, A.Lenskiy, S.Hakomori, and E.W.Nester (2007).
A catalytic carbohydrate contributes to bacterial antibiotic resistance.
  Extremophiles, 11, 133-143.  
16506777 Y.Chen, G.Minasov, T.A.Roth, F.Prati, and B.K.Shoichet (2006).
The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution.
  J Am Chem Soc, 128, 2970-2976.
PDB code: 2ffy
16061816 G.Guntas, T.J.Mansell, J.R.Kim, and M.Ostermeier (2005).
Directed evolution of protein switches and their application to the creation of ligand-binding proteins.
  Proc Natl Acad Sci U S A, 102, 11224-11229.  
15326193 N.Doucet, P.Y.De Wals, and J.N.Pelletier (2004).
Site-saturation mutagenesis of Tyr-105 reveals its importance in substrate stabilization and discrimination in TEM-1 beta-lactamase.
  J Biol Chem, 279, 46295-46303.  
15461559 N.H.Georgopapadakou (2004).
Beta-lactamase inhibitors: evolving compounds for evolving resistance targets.
  Expert Opin Investig Drugs, 13, 1307-1318.  
14572533 L.L.Silver (2003).
Novel inhibitors of bacterial cell wall synthesis.
  Curr Opin Microbiol, 6, 431-438.  
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
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
11410378 D.Tondi, R.A.Powers, E.Caselli, M.C.Negri, J.Blázquez, M.P.Costi, and B.K.Shoichet (2001).
Structure-based design and in-parallel synthesis of inhibitors of AmpC beta-lactamase.
  Chem Biol, 8, 593-611.
PDB code: 1ga9
11182316 E.Caselli, R.A.Powers, L.C.Blasczcak, C.Y.Wu, F.Prati, and B.K.Shoichet (2001).
Energetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases.
  Chem Biol, 8, 17-31.
PDB codes: 1fsw 1fsy
10716727 B.P.Atanasov, D.Mustafi, and M.W.Makinen (2000).
Protonation of the beta-lactam nitrogen is the trigger event in the catalytic action of class A beta-lactamases.
  Proc Natl Acad Sci U S A, 97, 3160-3165.  
11498375 M.G.Page (2000).
b-Lactamase inhibitors.
  Drug Resist Updat, 3, 109-125.  
10820001 S.Ness, R.Martin, A.M.Kindler, M.Paetzel, M.Gold, S.E.Jensen, J.B.Jones, and N.C.Strynadka (2000).
Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 beta-Lactamase(,).
  Biochemistry, 39, 5312-5321.
PDB codes: 1erm 1ero 1erq
  10595535 R.A.Powers, J.Blázquez, G.S.Weston, M.I.Morosini, F.Baquero, and B.K.Shoichet (1999).
The complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase.
  Protein Sci, 8, 2330-2337.
PDB code: 1c3b
9449253 I.Massova, and S.Mobashery (1998).
Kinship and diversification of bacterial penicillin-binding proteins and beta-lactamases.
  Antimicrob Agents Chemother, 42, 1.  
9485412 L.Maveyraud, R.F.Pratt, and J.P.Samama (1998).
Crystal structure of an acylation transition-state analog of the TEM-1 beta-lactamase. Mechanistic implications for class A beta-lactamases.
  Biochemistry, 37, 2622-2628.
PDB code: 1axb
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
9354233 N.Li, J.Rahil, M.E.Wright, and R.F.Pratt (1997).
Structure-activity studies of the inhibition of serine beta-lactamases by phosphonate monoesters.
  Bioorg Med Chem, 5, 1783-1788.  
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.  
8639512 S.A.Adediran, S.A.Deraniyagala, Y.Xu, and R.F.Pratt (1996).
Beta-secondary and solvent deuterium kinetic isotope effects on beta-lactamase catalysis.
  Biochemistry, 35, 3604-3613.  
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.  
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.  
7712290 P.M.Colman (1994).
Structure-based drug design.
  Curr Opin Struct Biol, 4, 868-874.  
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.