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PDBsum entry 1x8h
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Hydrolase PDB id
1x8h

 

 

 

 

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Contents
Protein chain
228 a.a. *
Ligands
_ZN-CO3
SO4 ×3
GOL ×2
Waters ×262
* Residue conservation analysis
PDB id:
1x8h
Name: Hydrolase
Title: The mono-zinc carbapenemase cpha (n220g mutant) shows a zn(ii)- nh2 arg coordination
Structure: Beta-lactamase. Chain: a. Engineered: yes. Mutation: yes
Source: Aeromonas hydrophila. Organism_taxid: 644. Gene: cpha. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.154     R-free:   0.180
Authors: G.Garau,O.Dideberg
Key ref:
G.Garau et al. (2005). A metallo-beta-lactamase enzyme in action: crystal structures of the monozinc carbapenemase CphA and its complex with biapenem. J Mol Biol, 345, 785-795. PubMed id: 15588826 DOI: 10.1016/j.jmb.2004.10.070
Date:
18-Aug-04     Release date:   28-Dec-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26918  (BLAB_AERHY) -  Metallo-beta-lactamase type 2 from Aeromonas hydrophila
Seq:
Struc: 		254 a.a.
229 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+)

 

 
DOI no: 10.1016/j.jmb.2004.10.070 J Mol Biol 345:785-795 (2005)
PubMed id: 15588826  
 
 
A metallo-beta-lactamase enzyme in action: crystal structures of the monozinc carbapenemase CphA and its complex with biapenem.
G.Garau, C.Bebrone, C.Anne, M.Galleni, J.M.Frère, O.Dideberg.
 
  ABSTRACT  
 
One strategy developed by bacteria to resist the action of beta-lactam antibiotics is the expression of metallo-beta-lactamases. CphA from Aeromonas hydrophila is a member of a clinically important subclass of metallo-beta-lactamases that have only one zinc ion in their active site and for which no structure is available. The crystal structures of wild-type CphA and its N220G mutant show the structural features of the active site of this enzyme, which is modeled specifically for carbapenem hydrolysis. The structure of CphA after reaction with a carbapenem substrate, biapenem, reveals that the enzyme traps a reaction intermediate in the active site. These three X-ray structures have allowed us to propose how the enzyme recognizes carbapenems and suggest a mechanistic pathway for hydrolysis of the beta-lactam. This will be relevant for the design of metallo-beta-lactamase inhibitors as well as of antibiotics that escape their hydrolytic activity.
 
  Selected figure(s)  
 
Figure 2.
 Figure 7.
Figure 7. Scheme of the proposed mechanism of β-lactam hydrolysis by CphA, as deduced from the structures described here.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 345, 785-795) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21299838 L.E.Horsfall, Y.Izougarhane, P.Lassaux, N.Selevsek, B.M.Liénard, L.Poirel, M.B.Kupper, K.M.Hoffmann, J.M.Frère, M.Galleni, and C.Bebrone (2011).
Broad antibiotic resistance profile of the subclass B3 metallo-β-lactamase GOB-1, a di-zinc enzyme.
  FEBS J, 278, 1252-1263.  
21568871 L.Sun, L.Zhang, H.Zhang, and Z.G.He (2011).
Characterization of a Bifunctional β-Lactamase/Ribonuclease and Its Interaction with a Chaperone-Like Protein in the Pathogen Mycobacterium tuberculosis H37Rv.
  Biochemistry (Mosc), 76, 350-358.  
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.  
20065329 S.M.Drawz, and R.A.Bonomo (2010).
Three decades of beta-lactamase inhibitors.
  Clin Microbiol Rev, 23, 160-201.  
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
19651913 C.Bebrone, H.Delbrück, M.B.Kupper, P.Schlömer, C.Willmann, J.M.Frère, R.Fischer, M.Galleni, and K.M.Hoffmann (2009).
The structure of the dizinc subclass B2 metallo-beta-lactamase CphA reveals that the second inhibitory zinc ion binds in the histidine site.
  Antimicrob Agents Chemother, 53, 4464-4471.
PDB codes: 3f9o 3fai
19552427 D.Xu, and H.Guo (2009).
Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism.
  J Am Chem Soc, 131, 9780-9788.  
19671702 F.Simona, A.Magistrato, M.Dal Peraro, A.Cavalli, A.J.Vila, and P.Carloni (2009).
Common mechanistic features among metallo-beta-lactamases: a computational study of Aeromonas hydrophila CphA enzyme.
  J Biol Chem, 284, 28164-28171.  
19722277 M.Venkatesan, D.A.Kuntz, and D.R.Rose (2009).
Human lysosomal alpha-mannosidases exhibit different inhibition and metal binding properties.
  Protein Sci, 18, 2242-2251.  
18648687 A.I.Anzellotti, and N.P.Farrell (2008).
Zinc metalloproteins as medicinal targets.
  Chem Soc Rev, 37, 1629-1651.  
18648861 A.Tamilselvi, and G.Mugesh (2008).
Zinc and antibiotic resistance: metallo-beta-lactamases and their synthetic analogues.
  J Biol Inorg Chem, 13, 1039-1053.  
18563261 B.M.Liénard, G.Garau, L.Horsfall, A.I.Karsisiotis, C.Damblon, P.Lassaux, C.Papamicael, G.C.Roberts, M.Galleni, O.Dideberg, J.M.Frère, and C.J.Schofield (2008).
Structural basis for the broad-spectrum inhibition of metallo-beta-lactamases by thiols.
  Org Biomol Chem, 6, 2282-2294.
PDB codes: 2qds 2qdt
18627129 D.Liu, J.Momb, P.W.Thomas, A.Moulin, G.A.Petsko, W.Fast, and D.Ringe (2008).
Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures.
  Biochemistry, 47, 7706-7714.
PDB codes: 3dha 3dhb 3dhc
18652482 L.A.Abriata, L.J.González, L.I.Llarrull, P.E.Tomatis, W.K.Myers, A.L.Costello, D.L.Tierney, and A.J.Vila (2008).
Engineered mononuclear variants in Bacillus cereus metallo-beta-lactamase BcII are inactive.
  Biochemistry, 47, 8590-8599.  
18980308 M.F.Tioni, L.I.Llarrull, A.A.Poeylaut-Palena, M.A.Martí, M.Saggu, G.R.Periyannan, E.G.Mata, B.Bennett, D.H.Murgida, and A.J.Vila (2008).
Trapping and characterization of a reaction intermediate in carbapenem hydrolysis by B. cereus metallo-beta-lactamase.
  J Am Chem Soc, 130, 15852-15863.  
18551183 M.I.Page, and A.Badarau (2008).
The mechanisms of catalysis by metallo beta-lactamases.
  Bioinorg Chem Appl, (), 576297.  
18656261 M.M.Holdorf, B.Bennett, M.W.Crowder, and C.A.Makaroff (2008).
Spectroscopic studies on Arabidopsis ETHE1, a glyoxalase II-like protein.
  J Inorg Biochem, 102, 1825-1830.  
18528987 N.Sharma, Z.Hu, M.W.Crowder, and B.Bennett (2008).
Conformational changes in the metallo-beta-lactamase ImiS during the catalytic reaction: an EPR spectrokinetic study of Co(II)-spin label interactions.
  J Am Chem Soc, 130, 8215-8222.  
18230049 V.Gupta (2008).
Metallo beta lactamases in Pseudomonas aeruginosa and Acinetobacter species.
  Expert Opin Investig Drugs, 17, 131-143.  
18445468 Z.Hu, G.R.Periyannan, and M.W.Crowder (2008).
Folding strategy to prepare Co(II)-substituted metallo-beta-lactamase L1.
  Anal Biochem, 378, 177-183.  
17623844 F.Simona, A.Magistrato, D.M.Vera, G.Garau, A.J.Vila, and P.Carloni (2007).
Protonation state and substrate binding to B2 metallo-beta-lactamase CphA from Aeromonas hydrofila.
  Proteins, 69, 595-605.  
17403673 J.Morán-Barrio, J.M.González, M.N.Lisa, A.L.Costello, M.D.Peraro, P.Carloni, B.Bennett, D.L.Tierney, A.S.Limansky, A.M.Viale, and A.J.Vila (2007).
The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site.
  J Biol Chem, 282, 18286-18293.  
17307979 L.E.Horsfall, G.Garau, B.M.Liénard, O.Dideberg, C.J.Schofield, J.M.Frère, and M.Galleni (2007).
Competitive inhibitors of the CphA metallo-beta-lactamase from Aeromonas hydrophila.
  Antimicrob Agents Chemother, 51, 2136-2142.
PDB code: 2gkl
17426028 L.I.Llarrull, S.M.Fabiane, J.M.Kowalski, B.Bennett, B.J.Sutton, and A.J.Vila (2007).
Asp-120 locates Zn2 for optimal metallo-beta-lactamase activity.
  J Biol Chem, 282, 18276-18285.
PDB code: 2uyx
17305336 M.Dal Peraro, A.J.Vila, P.Carloni, and M.L.Klein (2007).
Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases.
  J Am Chem Soc, 129, 2808-2816.  
16423823 D.Xu, D.Xie, and H.Guo (2006).
Catalytic mechanism of class B2 metallo-beta-lactamase.
  J Biol Chem, 281, 8740-8747.  
16773613 G.Estiu, D.Suárez, and K.M.Merz (2006).
Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases.
  J Comput Chem, 27, 1240-1262.  
16404761 J.Spencer, and T.R.Walsh (2006).
A new approach to the inhibition of metallo-beta-lactamases.
  Angew Chem Int Ed Engl, 45, 1022-1026.  
16406807 K.De Vriendt, G.Van Driessche, B.Devreese, C.Bebrone, C.Anne, J.M.Frère, M.Galleni, and J.Van Beeumen (2006).
Monitoring the zinc affinity of the metallo-beta-lactamase CphA by automated nanoESI-MS.
  J Am Soc Mass Spectrom, 17, 180-188.  
16939225 N.P.Sharma, C.Hajdin, S.Chandrasekar, B.Bennett, K.W.Yang, and M.W.Crowder (2006).
Mechanistic studies on the mononuclear ZnII-containing metallo-beta-lactamase ImiS from Aeromonas sobria.
  Biochemistry, 45, 10729-10738.  
16911039 P.Macheboeuf, C.Contreras-Martel, V.Job, O.Dideberg, and A.Dessen (2006).
Penicillin binding proteins: key players in bacterial cell cycle and drug resistance processes.
  FEMS Microbiol Rev, 30, 673-691.  
15863831 C.Bebrone, C.Anne, K.De Vriendt, B.Devreese, G.M.Rossolini, J.Van Beeumen, J.M.Frère, and M.Galleni (2005).
Dramatic broadening of the substrate profile of the Aeromonas hydrophila CphA metallo-beta-lactamase by site-directed mutagenesis.
  J Biol Chem, 280, 28195-28202.  
15980349 G.Garau, A.M.Di Guilmi, and B.G.Hall (2005).
Structure-based phylogeny of the metallo-beta-lactamases.
  Antimicrob Agents Chemother, 49, 2778-2784.  
16129657 M.S.Wilke, A.L.Lovering, and N.C.Strynadka (2005).
Beta-lactam antibiotic resistance: a current structural perspective.
  Curr Opin Microbiol, 8, 525-533.  
  16510987 N.Sharma, J.H.Toney, and P.M.Fitzgerald (2005).
Expression, purification, crystallization and preliminary X-ray analysis of Aeromonas hydrophilia metallo-beta-lactamase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 180-182.  
16172409 P.E.Tomatis, R.M.Rasia, L.Segovia, and A.J.Vila (2005).
Mimicking natural evolution in metallo-beta-lactamases through second-shell ligand mutations.
  Proc Natl Acad Sci U S A, 102, 13761-13766.  
15831827 T.R.Walsh, M.A.Toleman, L.Poirel, and P.Nordmann (2005).
Metallo-beta-lactamases: the quiet before the storm?
  Clin Microbiol Rev, 18, 306-325.  
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.

 

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