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Hydrolase PDB id
1iys
Jmol
Contents
Protein chain
261 a.a. *
Ligands
SO4 ×8
Waters ×284
* Residue conservation analysis
PDB id:
1iys
Name: Hydrolase
Title: Crystal structure of class a beta-lactamase toho-1
Structure: Beta-lactamase toho-1. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.65Å     R-factor:   0.182     R-free:   0.197
Authors: A.S.Ibuka,Y.Ishii,K.Yamaguchi,H.Matsuzawa,H.Sakai
Key ref:
A.S.Ibuka et al. (2003). Crystal structure of extended-spectrum beta-lactamase Toho-1: insights into the molecular mechanism for catalytic reaction and substrate specificity expansion. Biochemistry, 42, 10634-10643. PubMed id: 12962487 DOI: 10.1021/bi0342822
Date:
06-Sep-02     Release date:   14-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q47066  (BLT1_ECOLX) -  Beta-lactamase Toho-1
Seq:
Struc: 		291 a.a.
261 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: Zinc
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to antibiotic   2 terms 
  Biochemical function     hydrolase activity     2 terms  

 

 
DOI no: 10.1021/bi0342822 Biochemistry 42:10634-10643 (2003)
PubMed id: 12962487  
 
 
Crystal structure of extended-spectrum beta-lactamase Toho-1: insights into the molecular mechanism for catalytic reaction and substrate specificity expansion.
A.S.Ibuka, Y.Ishii, M.Galleni, M.Ishiguro, K.Yamaguchi, J.M.Frère, H.Matsuzawa, H.Sakai.
 
  ABSTRACT  
 
The crystallographic structure of the class A beta-lactamase Toho-1, an extended-spectrum beta-lactamase with potent activity against expanded-spectrum cephems, has been determined at 1.65 A resolution. The result reveals that the Lys73 side chain can adopt two alternative conformations. The predominant conformation of Lys73 is different from that observed in the E166A mutant, indicating that removal of the Glu166 side chain changes the conformation of the Lys73 side chain and thus the interaction between Lys73 and Glu166. The Lys73 side chain would play an important role in proton relay, switching its conformation from one to the other depending on the circumstances. The electron density map also implies possible rotation of Ser237. Comparison of the Toho-1 structure with the structure of other class A beta-lactamases shows that the hydroxyl group of Ser237 is likely to rotate through interaction with the carboxyl group of the substrate. Another peculiarity is the existence of three sulfate ions positioned in or near the substrate-binding cavity. One of these sulfate ions is tightly bound to the active center, while the other two are held by a region of positive charge formed by two arginine residues, Arg274 and Arg276. This positively charged region is speculated to represent a pseudo-binding site of the beta-lactam antibiotics, presumably catching the methoxyimino group of the third-generation cephems prior to proper binding in the substrate-binding cleft for hydrolysis. This high-resolution structure, together with detailed kinetic analysis of Toho-1, provides a new hypothesis for the catalytic mechanism and substrate specificity of Toho-1.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20394454 C.Bebrone, P.Lassaux, L.Vercheval, J.S.Sohier, A.Jehaes, E.Sauvage, and M.Galleni (2010).
Current challenges in antimicrobial chemotherapy: focus on ß-lactamase inhibition.
  Drugs, 70, 651-679.  
20421396 K.M.Papp-Wallace, M.Taracila, J.M.Hornick, A.M.Hujer, K.M.Hujer, A.M.Distler, A.Endimiani, and R.A.Bonomo (2010).
Substrate selectivity and a novel role in inhibitor discrimination by residue 237 in the KPC-2 beta-lactamase.
  Antimicrob Agents Chemother, 54, 2867-2877.  
20065329 S.M.Drawz, and R.A.Bonomo (2010).
Three decades of beta-lactamase inhibitors.
  Clin Microbiol Rev, 23, 160-201.  
19342785 T.Shimamura, Y.Nitanai, T.Uchiyama, and H.Matsuzawa (2009).
Improvement of crystal quality by surface mutations of beta-lactamase Toho-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 379-382.
PDB code: 2zq8
19305397 Y.Chen, and B.K.Shoichet (2009).
Molecular docking and ligand specificity in fragment-based inhibitor discovery.
  Nat Chem Biol, 5, 358-364.
PDB codes: 3g2y 3g2z 3g30 3g31 3g32 3g34 3g35
18822298 D.C.Marciano, J.M.Pennington, X.Wang, J.Wang, Y.Chen, V.L.Thomas, B.K.Shoichet, and T.Palzkill (2008).
Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase.
  J Mol Biol, 384, 151-164.
PDB code: 3cmz
18459799 G.Brown, A.Singer, M.Proudfoot, T.Skarina, Y.Kim, C.Chang, I.Dementieva, E.Kuznetsova, C.F.Gonzalez, A.Joachimiak, A.Savchenko, and A.F.Yakunin (2008).
Functional and structural characterization of four glutaminases from Escherichia coli and Bacillus subtilis.
  Biochemistry, 47, 5724-5735.
PDB codes: 1mki 1u60 3brm
18755695 G.Celenza, C.Luzi, M.Aschi, B.Segatore, D.Setacci, C.Pellegrini, C.Forcella, G.Amicosante, and M.Perilli (2008).
Natural D240G Toho-1 mutant conferring resistance to ceftazidime: biochemical characterization of CTX-M-43.
  J Antimicrob Chemother, 62, 991-997.  
18154526 G.M.Rossolini, M.M.D'Andrea, and C.Mugnaioli (2008).
The spread of CTX-M-type extended-spectrum beta-lactamases.
  Clin Microbiol Infect, 14, 33-41.  
17875405 F.Perez, A.Endimiani, K.M.Hujer, and R.A.Bonomo (2007).
The continuing challenge of ESBLs.
  Curr Opin Pharmacol, 7, 459-469.  
17207608 Y.Ishii, M.Galleni, L.Ma, J.M.Frère, and K.Yamaguchi (2007).
Biochemical characterisation of the CTX-M-14 beta-lactamase.
  Int J Antimicrob Agents, 29, 159-164.  
16801434 E.Sauvage, E.Fonzé, B.Quinting, M.Galleni, J.M.Frère, and P.Charlier (2006).
Crystal structure of the Mycobacterium fortuitum class A beta-lactamase: structural basis for broad substrate specificity.
  Antimicrob Agents Chemother, 50, 2516-2521.
PDB code: 2cc1
16870770 F.Wang, C.Cassidy, and J.C.Sacchettini (2006).
Crystal structure and activity studies of the Mycobacterium tuberculosis beta-lactamase reveal its critical role in resistance to beta-lactam antibiotics.
  Antimicrob Agents Chemother, 50, 2762-2771.
PDB code: 2gdn
17661642 G.M.Rossolini, and J.D.Docquier (2006).
New beta-lactamases: a paradigm for the rapid response of bacterial evolution in the clinical setting.
  Future Microbiol, 1, 295-308.  
16436733 J.Delmas, F.Robin, F.Carvalho, C.Mongaret, and R.Bonnet (2006).
Prediction of the evolution of ceftazidime resistance in extended-spectrum beta-lactamase CTX-M-9.
  Antimicrob Agents Chemother, 50, 731-738.  
16048956 F.K.Majiduddin, and T.Palzkill (2005).
Amino acid residues that contribute to substrate specificity of class A beta-lactamase SME-1.
  Antimicrob Agents Chemother, 49, 3421-3427.  
15826180 Y.Chen, B.Shoichet, and R.Bonnet (2005).
Structure, function, and inhibition along the reaction coordinate of CTX-M beta-lactamases.
  J Am Chem Soc, 127, 5423-5434.
PDB codes: 1yly 1ylz 1ym1 1yms 1ymx
15105092 S.Kimura, M.Ishiguro, Y.Ishii, J.Alba, and K.Yamaguchi (2004).
Role of a mutation at position 167 of CTX-M-19 in ceftazidime hydrolysis.
  Antimicrob Agents Chemother, 48, 1454-1460.  
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.