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Hydrolase PDB id
1dxk
Jmol
Contents
Protein chain
221 a.a. *
Ligands
BCT
Metals
_ZN
Waters ×232
* Residue conservation analysis
PDB id:
1dxk
Name: Hydrolase
Title: Metallo-beta-lactamase from bacillus cereus 569/h/9 c168s mutant
Structure: Class b beta-lactamase. Chain: a. Synonym: penicillinase, cephalosporinase. Engineered: yes. Mutation: yes. Other_details: 1mm zn in the buffer
Source: Bacillus cereus. Organism_taxid: 1396. Strain: dh1. Plasmid: prtwho12. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.85Å     R-factor:   0.205     R-free:   0.261
Authors: L.Chantalat,E.Duee,O.Dideberg
Key ref: L.Chantalat et al. (2000). Structural effects of the active site mutation cysteine to serine in Bacillus cereus zinc-beta-lactamase. Protein Sci, 9, 1402-1406. PubMed id: 10933508 Ref: Full text
Date:
10-Jan-00     Release date:   25-Aug-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04190  (BLA2_BACCE) -  Beta-lactamase 2
Seq:
Struc:
257 a.a.
221 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: Zinc
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to antibiotic   2 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
Full text Protein Sci 9:1402-1406 (2000)
PubMed id: 10933508  
 
 
Structural effects of the active site mutation cysteine to serine in Bacillus cereus zinc-beta-lactamase.
L.Chantalat, E.Duée, M.Galleni, J.M.Frère, O.Dideberg.
 
  ABSTRACT  
 
Beta-lactamases are involved in bacterial resistance. Members of the metallo-enzyme class are now found in many pathogenic bacteria and are becoming thus of major clinical importance. Despite the availability of Zn-beta-lactamase X-ray structures their mechanism of action is still unclear. One puzzling observation is the presence of one or two zincs in the active site. To aid in assessing the role of zinc content in beta-lactam hydrolysis, the replacement by Ser of the zinc-liganding residue Cys168 in the Zn-beta-lactamase from Bacillus cereus strain 569/H/9 was carried out: the mutant enzyme (C168S) is inactive in the mono-Zn form, but active in the di-Zn form. The structure of the mono-Zn form of the C168S mutant has been determined at 1.85 A resolution. Ser168 occupies the same position as Cys168 in the wild-type enzyme. The protein residues mostly affected by the mutation are Asp90-Arg91 and His210. A critical factor for the activity of the mono-Zn species is the distance between Asp90 and the Zn ion, which is controlled by Arg91: a slight movement of Asp90 impairs catalysis. The evolution of a large superfamily including Zn-beta-lactamases suggests that they may not all share the same mechanism.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20305272 Y.Yamaguchi, N.Takashio, J.Wachino, Y.Yamagata, Y.Arakawa, K.Matsuda, and H.Kurosaki (2010).
Structure of metallo-beta-lactamase IND-7 from a Chryseobacterium indologenes clinical isolate at 1.65-A resolution.
  J Biochem, 147, 905-915.
PDB code: 3l6n
12210153 J.Antony, N.Gresh, L.Olsen, L.Hemmingsen, C.J.Schofield, and R.Bauer (2002).
Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics.
  J Comput Chem, 23, 1281-1296.  
11714924 I.C.Materon, and T.Palzkill (2001).
Identification of residues critical for metallo-beta-lactamase function by codon randomization and selection.
  Protein Sci, 10, 2556-2565.  
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.