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Hydrolase PDB id
1rgy
Jmol
Contents
Protein chain
360 a.a. *
Ligands
PTX
MPD
Waters ×412
* Residue conservation analysis
PDB id:
1rgy
Name: Hydrolase
Title: Citrobacter freundii gn346 class c beta-lactamase complexed with transition-state analog of cefotaxime
Structure: Beta-lactamase. Chain: a. Engineered: yes
Source: Citrobacter freundii. Organism_taxid: 546. Gene: bla. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.52Å     R-factor:   0.195     R-free:   0.217
Authors: M.Nukaga,S.Kumar,K.Nukaga,R.F.Pratt,J.R.Knox
Key ref:
M.Nukaga et al. (2004). Hydrolysis of third-generation cephalosporins by class C beta-lactamases. Structures of a transition state analog of cefotoxamine in wild-type and extended spectrum enzymes. J Biol Chem, 279, 9344-9352. PubMed id: 14660590 DOI: 10.1074/jbc.M312356200
Date:
13-Nov-03     Release date:   06-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05193  (AMPC_CITFR) -  Beta-lactamase
Seq:
Struc: 		381 a.a.
360 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 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!
  Cellular component     periplasmic space   2 terms 
  Biological process     response to antibiotic   2 terms 
  Biochemical function     hydrolase activity     2 terms  

 

 
DOI no: 10.1074/jbc.M312356200 J Biol Chem 279:9344-9352 (2004)
PubMed id: 14660590  
 
 
Hydrolysis of third-generation cephalosporins by class C beta-lactamases. Structures of a transition state analog of cefotoxamine in wild-type and extended spectrum enzymes.
M.Nukaga, S.Kumar, K.Nukaga, R.F.Pratt, J.R.Knox.
 
  ABSTRACT  
 
Bacterial resistance to the third-generation cephalosporins is an issue of great concern in current antibiotic therapeutics. An important source of this resistance is from production of extended-spectrum (ES) beta-lactamases by bacteria. The Enterobacter cloacae GC1 enzyme is an example of a class C ES beta-lactamase. Unlike wild-type (WT) forms, such as the E. cloacae P99 and Citrobacter freundii enzymes, the ES GC1 beta-lactamase is able to rapidly hydrolyze third-generation cephalosporins such as cefotaxime and ceftazidime. To understand the basis for this ES activity, m-nitrophenyl 2-(2-aminothiazol-4-yl)-2-[(Z)-methoxyimino]acetylaminomethyl phosphonate has been synthesized and characterized. This phosphonate was designed to generate a transition state analog for turnover of cefotaxime. The crystal structures of complexes of the phosphonate with both ES GC1 and WT C. freundii GN346 beta-lactamases have been determined to high resolution (1.4-1.5 Angstroms). The serine-bound analog of the tetrahedral transition state for deacylation exhibits a very different binding geometry in each enzyme. In the WT beta-lactamase the cefotaxime-like side chain is crowded against the Omega loop and must protrude from the binding site with its methyloxime branch exposed. In the ES enzyme, a mutated Omega loop adopts an alternate conformation allowing the side chain to be much more buried. During the binding and turnover of the cefotaxime substrate by this ES enzyme, it is proposed that ligand-protein contacts and intra-ligand contacts are considerably relieved relative to WT, facilitating positioning and activation of the hydrolytic water molecule. The ES beta-lactamase is thus able to efficiently inactivate third-generation cephalosporins.
 
  Selected figure(s)  
 
Figure 5.
FIG. 5. Overlay of phosphonate (blue) and boronic acid (yellow) analogs in WT GN346 and WT AmpC complexes, respectively (a), and phosphonate (blue) and acylceftazidime (yellow) complexes (b). 		Figure 6.
FIG. 6. a, schematic of potential close contacts in a class C -lactamase complex with an acylated cephalosporin having a branched side chain; b, overlay of ES GC1 phosphonate complex (red) and WT AmpC acylceftazidime complex (blue).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 9344-9352) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21443768 W.T.Wong, H.W.Au, H.K.Yap, Y.C.Leung, K.Y.Wong, and Y.Zhao (2011).
Structural studies of the mechanism for biosensing antibiotics in a fluorescein-labeled β-lactamase.
  BMC Struct Biol, 11, 15.  
19889645 K.Yasuhira, N.Shibata, G.Mongami, Y.Uedo, Y.Atsumi, Y.Kawashima, A.Hibino, Y.Tanaka, Y.H.Lee, D.Kato, M.Takeo, Y.Higuchi, and S.Negoro (2010).
X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation.
  J Biol Chem, 285, 1239-1248.
PDB codes: 3a2p 3a2q
20065329 S.M.Drawz, and R.A.Bonomo (2010).
Three decades of beta-lactamase inhibitors.
  Clin Microbiol Rev, 23, 160-201.  
19913034 V.L.Thomas, A.C.McReynolds, and B.K.Shoichet (2010).
Structural bases for stability-function tradeoffs in antibiotic resistance.
  J Mol Biol, 396, 47-59.
PDB codes: 3iwi 3iwo 3iwq 3ixb 3ixd 3ixg 3ixh
19104021 A.Zioga, J.M.Whichard, S.D.Kotsakis, L.S.Tzouvelekis, E.Tzelepi, and V.Miriagou (2009).
CMY-31 and CMY-36 cephalosporinases encoded by ColE1-like plasmids.
  Antimicrob Agents Chemother, 53, 1256-1259.  
19470510 S.D.Kotsakis, C.C.Papagiannitsis, E.Tzelepi, L.S.Tzouvelekis, and V.Miriagou (2009).
Extended-spectrum properties of CMY-30, a Val211Gly mutant of CMY-2 cephalosporinase.
  Antimicrob Agents Chemother, 53, 3520-3523.  
19521995 T.Ohki, N.Shibata, Y.Higuchi, Y.Kawashima, M.Takeo, D.Kato, and S.Negoro (2009).
Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase.
  Protein Sci, 18, 1662-1673.
PDB codes: 2zly 2zm2 2zm8 2zm9
18323628 S.Okazaki, A.Suzuki, T.Mizushima, H.Komeda, Y.Asano, and T.Yamane (2008).
Structures of D-amino-acid amidase complexed with L-phenylalanine and with L-phenylalanine amide: insight into the D-stereospecificity of D-amino-acid amidase from Ochrobactrum anthropi SV3.
  Acta Crystallogr D Biol Crystallogr, 64, 331-334.
PDB codes: 2efu 2efx
16677302 J.Y.Kim, H.I.Jung, Y.J.An, J.H.Lee, S.J.Kim, S.H.Jeong, K.J.Lee, P.G.Suh, H.S.Lee, S.H.Lee, and S.S.Cha (2006).
Structural basis for the extended substrate spectrum of CMY-10, a plasmid-encoded class C beta-lactamase.
  Mol Microbiol, 60, 907-916.
PDB code: 1zkj
17077507 M.Hata, Y.Fujii, Y.Tanaka, H.Ishikawa, M.Ishii, S.Neya, M.Tsuda, and T.Hoshino (2006).
Substrate deacylation mechanisms of serine-beta-lactamases.
  Biol Pharm Bull, 29, 2151-2159.  
16250067 B.T.Carter, H.Lin, S.D.Goldberg, E.A.Althoff, J.Raushel, and V.W.Cornish (2005).
Investigation of the mechanism of resistance to third-generation cephalosporins by class C beta-lactamases by using chemical complementation.
  Chembiochem, 6, 2055-2067.  
16189104 C.Bauvois, A.S.Ibuka, A.Celso, J.Alba, Y.Ishii, J.M.Frère, and M.Galleni (2005).
Kinetic properties of four plasmid-mediated AmpC beta-lactamases.
  Antimicrob Agents Chemother, 49, 4240-4246.  
17192008 C.Fenollar-Ferrer, J.Donoso, J.Frau, and F.Muñoz (2005).
Molecular modeling of Henry-Michaelis and acyl-enzyme complexes between imipenem and Enterobacter cloacae P99 beta-lactamase.
  Chem Biodivers, 2, 645-656.  
16253882 S.H.Lee, S.H.Jeong, and S.S.Cha (2005).
Minimising antibiotic resistance.
  Lancet Infect Dis, 5, 668-670.  
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.