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PDBsum entry 1djb

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protein links
Hydrolase PDB id
1djb
Jmol
Contents
Protein chain
257 a.a. *
Waters ×161
* Residue conservation analysis
PDB id:
1djb
Name: Hydrolase
Title: Structure of beta-lactamase precursor, s70a mutant, at 298k
Structure: Beta-lactamase. Chain: a. Synonym: penicillinase. Engineered: yes. Mutation: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Strain: pc1. Gene: blaz. Expressed in: shuttle plasmid from escherichia coli mc staphylococcus aureus rn4220.
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.170    
Authors: C.C.H.Chen,O.Herzberg
Key ref:
C.C.Chen et al. (1996). Structure and kinetics of the beta-lactamase mutants S70A and K73H from Staphylococcus aureus PC1. Biochemistry, 35, 12251-12258. PubMed id: 8823158 DOI: 10.1021/bi961153v
Date:
13-Aug-96     Release date:   12-Mar-97    
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
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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  

 

 
DOI no: 10.1021/bi961153v Biochemistry 35:12251-12258 (1996)
PubMed id: 8823158  
 
 
Structure and kinetics of the beta-lactamase mutants S70A and K73H from Staphylococcus aureus PC1.
C.C.Chen, T.J.Smith, G.Kapadia, S.Wäsch, L.E.Zawadzke, A.Coulson, O.Herzberg.
 
  ABSTRACT  
 
Two mutant beta-lactamases from Staphylococcus aureus PC1 which probe key catalytic residues have been produced by site-directed mutagenesis. In the S70A enzyme, the nucleophilic group that attacks the beta-lactam carbonyl carbon atom was eliminated. Consequently, the kcat values for hydrolysis of benzylpenicillin and nitrocefin have been reduced by 10(4)-10(5) compared with the wild-type enzyme. The crystal structure of S70A beta-lactamase has been determined at 2.1 A resolution. With the exception of the mutation site, the structure is identical to that of the native enzyme. The residual activity is attributed either to mistranslation that leads to production of wild-type enzyme and/or to remaining features of the active site that stabilize the tetrahedral transition state. Soaking of the crystals with ampicillin or clavulanate, followed by flash-freezing, has been carried out and the structures examined at 2.0 A resolution. For both experiments, the difference electron density maps revealed buildup of density in the active site that presumably corresponds to beta-lactam binding. However, neither electron density is sufficiently clear for defining the atomic details of the bound compounds. The K73H beta-lactamase has been prepared to test the possible role of Lys73 in proton transfer. It exhibits no detectable activity toward benzylpenicillin, and 10(5)-fold reduction of kcat for nitrocefin hydrolysis compared with the wild-type enzyme. No significant recovery of activity has been measured when the pH was varied between 5.0 and 8.0. The crystal structure of K73H beta-lactamase has been determined at 1.9 A resolution. While the overall structure is similar to that of the native enzyme, the electrostatic interactions between His73 and neighboring residues indicate that the imidazole ring is positively charged. In addition, the hydroxyl group of Ser70 adopts a position that is incompatible with nucleophilic attack on substrates. A crystal soaked with ampicillin was flash-frozen, and diffraction data were collected at 2.1 A resolution. The electron density map showed no indication of substrate binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19485421 K.D.Schneider, C.R.Bethel, A.M.Distler, A.M.Hujer, R.A.Bonomo, and D.A.Leonard (2009).
Mutation of the active site carboxy-lysine (K70) of OXA-1 beta-lactamase results in a deacylation-deficient enzyme.
  Biochemistry, 48, 6136-6145.  
19812041 N.G.Brown, S.Shanker, B.V.Prasad, and T.Palzkill (2009).
Structural and biochemical evidence that a TEM-1 beta-lactamase N170G active site mutant acts via substrate-assisted catalysis.
  J Biol Chem, 284, 33703-33712.
PDB code: 3jyi
16041072 B.Stec, K.M.Holtz, C.L.Wojciechowski, and E.R.Kantrowitz (2005).
Structure of the wild-type TEM-1 beta-lactamase at 1.55 A and the mutant enzyme Ser70Ala at 2.1 A suggest the mode of noncovalent catalysis for the mutant enzyme.
  Acta Crystallogr D Biol Crystallogr, 61, 1072-1079.
PDB codes: 1zg4 1zg6
15152012 D.Golemi-Kotra, S.O.Meroueh, C.Kim, S.B.Vakulenko, A.Bulychev, A.J.Stemmler, T.L.Stemmler, and S.Mobashery (2004).
The importance of a critical protonation state and the fate of the catalytic steps in class A beta-lactamases and penicillin-binding proteins.
  J Biol Chem, 279, 34665-34673.  
15267723 L.Xie, H.Liu, and W.Yang (2004).
Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes.
  J Chem Phys, 120, 8039-8052.  
12627955 N.Rhazi, P.Charlier, D.Dehareng, D.Engher, M.Vermeire, J.M.Frère, M.Nguyen-Distèche, and E.Fonzé (2003).
Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis.
  Biochemistry, 42, 2895-2906.
PDB codes: 1es2 1es3 1es4 1j9m
12395425 I.Massova, and P.A.Kollman (2002).
pKa, MM, and QM studies of mechanisms of beta-lactamases and penicillin-binding proteins: acylation step.
  J Comput Chem, 23, 1559-1576.  
11504626 A.Peracchi (2001).
Enzyme catalysis: removing chemically 'essential' residues by site-directed mutagenesis.
  Trends Biochem Sci, 26, 497-503.  
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
9283075 S.Banerjee, N.Shigematsu, L.K.Pannell, S.Ruvinov, J.Orban, F.Schwarz, and O.Herzberg (1997).
Probing the non-proline cis peptide bond in beta-lactamase from Staphylococcus aureus PC1 by the replacement Asn136 --> Ala.
  Biochemistry, 36, 10857-10866.  
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
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.