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PDBsum entry 2blt

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protein links
Hydrolase(acting in cyclic amides) PDB id
2blt
Jmol
Contents
Protein chains
359 a.a.
Superseded by: 1xx2 1xx2
PDB id:
2blt
Name: Hydrolase(acting in cyclic amides)
Structure: Beta-lactamase (cephalosporinase)
Source: (Enterobacter cloacae) strain: p99
Authors: J.R.Knox,P.C.Moews,E.Lobkovsky
Key ref: E.Lobkovsky et al. (1993). Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase. Proc Natl Acad Sci U S A, 90, 11257-11261. PubMed id: 8248237 DOI: 10.1073/pnas.90.23.11257
Date:
19-Jul-94     Release date:   26-Jan-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05364  (AMPC_ENTCL) -  Beta-lactamase
Seq:
Struc:
381 a.a.
359 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: Zn(2+)

 

 
DOI no: 10.1073/pnas.90.23.11257 Proc Natl Acad Sci U S A 90:11257-11261 (1993)
PubMed id: 8248237  
 
 
Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase.
E.Lobkovsky, P.C.Moews, H.Liu, H.Zhao, J.M.Frere, J.R.Knox.
 
  ABSTRACT  
 
The structure of the class C ampC beta-lactamase (cephalosporinase) from Enterobacter cloacae strain P99 has been established by x-ray crystallography to 2-A resolution and compared to a class A beta-lactamase (penicillinase) structure. The binding site for beta-lactam (penicillinase) structure. The binding site for beta-lactam antibiotics is generally more open than that in penicillinases, in agreement with the ability of the class C beta-lactamases to better bind third-generation cephalosporins. Four corresponding catalytic residues (Ser-64/70, Lys-67/73, Lys-315/234, and Tyr-150/Ser-130 in class C/A) lie in equivalent positions within 0.4 A. Significant differences in positions and accessibilities of Arg-349/244 may explain the inability of clavulanate-type inhibitors to effectively inactivate the class C beta-lactamases. Glu-166, required for deacylation of the beta-lactamoyl intermediate in class A penicillinases, has no counterpart in this cephalosporinase; the nearest candidate, Asp-217, is 10 A from the reactive Ser-64. A comparison of overall tertiary folding shows that the cephalosporinase, more than the penicillinase, is broadly similar to the ancestral beta-lactam-inhibited enzymes of bacterial cell wall synthesis. On this basis, it is proposed that the cephalosporinase is the older of the two beta-lactamases, and, therefore, that a local refolding in the active site, rather than a simple point mutation, was required for the primordial class C beta-lactamase to evolve to the class A beta-lactamase having an improved ability to catalyze the deacylation step of beta-lactam hydrolysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21266781 M.Nishizawa, Y.Yabusaki, and M.Kanaoka (2011).
Identification of the catalytic residues of carboxylesterase from Arthrobacter globiformis by diisopropyl fluorophosphate-labeling and site-directed mutagenesis.
  Biosci Biotechnol Biochem, 75, 89-94.  
20206184 A.Fedarovich, R.A.Nicholas, and C.Davies (2010).
Unusual conformation of the SxN motif in the crystal structure of penicillin-binding protein A from Mycobacterium tuberculosis.
  J Mol Biol, 398, 54-65.
PDB code: 3lo7
20562876 M.Funabashi, Z.Yang, K.Nonaka, M.Hosobuchi, Y.Fujita, T.Shibata, X.Chi, and S.G.Van Lanen (2010).
An ATP-independent strategy for amide bond formation in antibiotic biosynthesis.
  Nat Chem Biol, 6, 581-586.  
19136439 G.A.Jacoby (2009).
AmpC beta-lactamases.
  Clin Microbiol Rev, 22, 161.  
19437416 G.S.Shukla, and D.N.Krag (2009).
Developing bifunctional beta-lactamase molecules with built-in target-recognizing module for prodrug therapy: identification of Enterobacter Cloacae P99 cephalosporinase loops suitable for randomization and phage-display selection.
  J Mol Recognit, 22, 425-436.  
19678665 S.Majumdar, and R.F.Pratt (2009).
Inhibition of class A and C beta-lactamases by diaroyl phosphates.
  Biochemistry, 48, 8285-8292.  
  18453698 A.Shimizu-Ibuka, C.Bauvois, H.Sakai, and M.Galleni (2008).
Structure of the plasmid-mediated class C beta-lactamase ACT-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 334-337.
PDB code: 2zc7
18312599 C.Michaux, J.Massant, F.Kerff, J.M.Frère, J.D.Docquier, I.Vandenberghe, B.Samyn, A.Pierrard, G.Feller, P.Charlier, J.Van Beeumen, and J.Wouters (2008).
Crystal structure of a cold-adapted class C beta-lactamase.
  FEBS J, 275, 1687-1697.
PDB code: 2qz6
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
17294326 M.Schütte, and S.Fetzner (2007).
EstA from Arthrobacter nitroguajacolicus Rü61a, a thermo- and solvent-tolerant carboxylesterase related to class C beta-lactamases.
  Curr Microbiol, 54, 230-236.  
18029418 S.T.Lefurgy, R.M.de Jong, and V.W.Cornish (2007).
Saturation mutagenesis of Asn152 reveals a substrate selectivity switch in P99 cephalosporinase.
  Protein Sci, 16, 2636-2646.  
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.  
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.  
16506777 Y.Chen, G.Minasov, T.A.Roth, F.Prati, and B.K.Shoichet (2006).
The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution.
  J Am Chem Soc, 128, 2970-2976.
PDB code: 2ffy
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.  
16132461 M.de P M A Ribeiro, M.de T F Dellias, S.M.Tsai, A.Bolmströn, L.W.Meinhardt, and C.de M Bellato (2005).
Utilization of the Etest assay for comparative antibiotic susceptibility profiles of citrus variegated Chlorosis and Pierce's disease strains of Xylella fastidiosa.
  Curr Microbiol, 51, 262-266.  
15637155 P.Macheboeuf, A.M.Di Guilmi, V.Job, T.Vernet, O.Dideberg, and A.Dessen (2005).
Active site restructuring regulates ligand recognition in class A penicillin-binding proteins.
  Proc Natl Acad Sci U S A, 102, 577-582.
PDB codes: 2bg1 2bg3 2bg4 2uwx 2uwy 2xd1
15388462 A.M.Hujer, C.R.Bethel, and R.A.Bonomo (2004).
Antibody mapping of the linear epitopes of CMY-2 and SHV-1 beta-lactamases.
  Antimicrob Agents Chemother, 48, 3980-3988.  
15388478 H.Mammeri, H.Nazic, T.Naas, L.Poirel, S.Léotard, and P.Nordmann (2004).
AmpC beta-lactamase in an Escherichia coli clinical isolate confers resistance to expanded-spectrum cephalosporins.
  Antimicrob Agents Chemother, 48, 4050-4053.  
14982755 H.Mammeri, L.Poirel, P.Bemer, H.Drugeon, and P.Nordmann (2004).
Resistance to cefepime and cefpirome due to a 4-amino-acid deletion in the chromosome-encoded AmpC beta-lactamase of a Serratia marcescens clinical isolate.
  Antimicrob Agents Chemother, 48, 716-720.  
15461559 N.H.Georgopapadakou (2004).
Beta-lactamase inhibitors: evolving compounds for evolving resistance targets.
  Expert Opin Investig Drugs, 13, 1307-1318.  
14747733 S.J.Lee, J.Y.Kim, H.I.Jung, P.G.Suh, H.S.Lee, S.H.Lee, and S.S.Cha (2004).
Crystallization and preliminary X-ray crystallographic analyses of CMY-1 and CMY-10, plasmidic class C beta-lactamases with extended substrate spectrum.
  Acta Crystallogr D Biol Crystallogr, 60, 382-384.  
15215122 Y.Doi, J.Wachino, M.Ishiguro, H.Kurokawa, K.Yamane, N.Shibata, K.Shibayama, K.Yokoyama, H.Kato, T.Yagi, and Y.Arakawa (2004).
Inhibitor-sensitive AmpC beta-lactamase variant produced by an Escherichia coli clinical isolate resistant to oxyiminocephalosporins and cephamycins.
  Antimicrob Agents Chemother, 48, 2652-2658.  
12957918 H.Hoffmann, and A.Roggenkamp (2003).
Population genetics of the nomenspecies Enterobacter cloacae.
  Appl Environ Microbiol, 69, 5306-5318.  
14579323 L.N.Kinch, Y.Qi, T.J.Hubbard, and N.V.Grishin (2003).
CASP5 target classification.
  Proteins, 53, 340-351.  
12876313 S.D.Goldberg, W.Iannuccilli, T.Nguyen, J.Ju, and V.W.Cornish (2003).
Identification of residues critical for catalysis in a class C beta-lactamase by combinatorial scanning mutagenesis.
  Protein Sci, 12, 1633-1645.  
12005439 B.M.Beadle, I.Trehan, P.J.Focia, and B.K.Shoichet (2002).
Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase.
  Structure, 10, 413-424.
PDB codes: 1kvl 1kvm
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.  
12482929 K.Baker, C.Bleczinski, H.Lin, G.Salazar-Jimenez, D.Sengupta, S.Krane, and V.W.Cornish (2002).
Chemical complementation: a reaction-independent genetic assay for enzyme catalysis.
  Proc Natl Acad Sci U S A, 99, 16537-16542.  
12019116 S.B.Vakulenko, D.Golemi, B.Geryk, M.Suvorov, J.R.Knox, S.Mobashery, and S.A.Lerner (2002).
Mutational replacement of Leu-293 in the class C Enterobacter cloacae P99 beta-lactamase confers increased MIC of cefepime.
  Antimicrob Agents Chemother, 46, 1966-1970.  
11847270 U.G.Wagner, E.I.Petersen, H.Schwab, and C.Kratky (2002).
EstB from Burkholderia gladioli: a novel esterase with a beta-lactamase fold reveals steric factors to discriminate between esterolytic and beta-lactam cleaving activity.
  Protein Sci, 11, 467-478.
PDB codes: 1ci8 1ci9
11451693 A.Raimondi, F.Sisto, and H.Nikaido (2001).
Mutation in Serratia marcescens AmpC beta-lactamase producing high-level resistance to ceftazidime and cefpirome.
  Antimicrob Agents Chemother, 45, 2331-2339.  
11179650 G.Barnaud, R.Labia, L.Raskine, M.J.Sanson-Le Pors, A.Philippon, and G.Arlet (2001).
Extension of resistance to cefepime and cefpirome associated to a six amino acid deletion in the H-10 helix of the cephalosporinase of an Enterobacter cloacae clinical isolate.
  FEMS Microbiol Lett, 195, 185-190.  
11371184 G.V.Crichlow, M.Nukaga, V.R.Doppalapudi, J.D.Buynak, and J.R.Knox (2001).
Inhibition of class C beta-lactamases: structure of a reaction intermediate with a cephem sulfone.
  Biochemistry, 40, 6233-6239.
PDB code: 1ga0
11709298 G.W.Rudgers, W.Huang, and T.Palzkill (2001).
Binding properties of a peptide derived from beta-lactamase inhibitory protein.
  Antimicrob Agents Chemother, 45, 3279-3286.  
11434768 I.Trehan, B.M.Beadle, and B.K.Shoichet (2001).
Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site.
  Biochemistry, 40, 7992-7999.
PDB code: 1i5q
11134945 J.Wouters, P.Charlier, D.Monnaie, J.M.Frère, and E.Fonzé (2001).
Expression, purification, crystallization and preliminary X-ray analysis of the native class C beta-lactamase from Enterobacter cloacae 908R and two mutants.
  Acta Crystallogr D Biol Crystallogr, 57, 162-164.  
11717515 T.Sun, M.Nukaga, K.Mayama, G.V.Crichlow, A.P.Kuzin, and J.R.Knox (2001).
Crystallization and preliminary X-ray study of OXA-1, a class D beta-lactamase.
  Acta Crystallogr D Biol Crystallogr, 57, 1912-1914.  
11354367 Y.Kato-Toma, and M.Ishiguro (2001).
Reaction of Lys-Tyr-Lys triad mimics with benzylpenicillin: insight into the role of Tyr150 in class C beta-lactamase.
  Bioorg Med Chem Lett, 11, 1161-1164.  
10986464 C.Bompard-Gilles, H.Remaut, V.Villeret, T.Prangé, L.Fanuel, M.Delmarcelle, B.Joris, J.Frère, and J.Van Beeumen (2000).
Crystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family.
  Structure, 8, 971-980.
PDB code: 1ei5
11036059 D.Girlich, T.Naas, S.Bellais, L.Poirel, A.Karim, and P.Nordmann (2000).
Heterogeneity of AmpC cephalosporinases of Hafnia alvei clinical isolates expressing inducible or constitutive ceftazidime resistance phenotypes.
  Antimicrob Agents Chemother, 44, 3220-3223.  
10813827 J.Lamotte-Brasseur, A.Dubus, and R.C.Wade (2000).
pK(a) calculations for class C beta-lactamases: the role of Tyr-150.
  Proteins, 40, 23-28.  
11498383 L.B.Rice, and R.A.Bonomo (2000).
beta -Lactamases: which ones are clinically important?
  Drug Resist Updat, 3, 178-189.  
11498375 M.G.Page (2000).
b-Lactamase inhibitors.
  Drug Resist Updat, 3, 109-125.  
10231522 A.P.Kuzin, M.Nukaga, Y.Nukaga, A.M.Hujer, R.A.Bonomo, and J.R.Knox (1999).
Structure of the SHV-1 beta-lactamase.
  Biochemistry, 38, 5720-5727.
PDB code: 1shv
  10493583 B.M.Beadle, S.L.McGovern, A.Patera, and B.K.Shoichet (1999).
Functional analyses of AmpC beta-lactamase through differential stability.
  Protein Sci, 8, 1816-1824.  
  10048333 J.Lamotte-Brasseur, V.Lounnas, X.Raquet, and R.C.Wade (1999).
pKa calculations for class A beta-lactamases: influence of substrate binding.
  Protein Sci, 8, 404-409.  
10406957 J.Walther-Rasmussen, A.H.Johnsen, and N.Høiby (1999).
Terminal truncations in amp C beta-lactamase from a clinical isolate of Pseudomonas aeruginosa.
  Eur J Biochem, 263, 478-485.  
  10103179 L.Poirel, M.Guibert, D.Girlich, T.Naas, and P.Nordmann (1999).
Cloning, sequence analyses, expression, and distribution of ampC-ampR from Morganella morganii clinical isolates.
  Antimicrob Agents Chemother, 43, 769-776.  
  10595535 R.A.Powers, J.Blázquez, G.S.Weston, M.I.Morosini, F.Baquero, and B.K.Shoichet (1999).
The complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase.
  Protein Sci, 8, 2330-2337.
PDB code: 1c3b
9931012 S.A.Adediran, and R.F.Pratt (1999).
Beta-secondary and solvent deuterium kinetic isotope effects on catalysis by the Streptomyces R61 DD-peptidase: comparisons with a structurally similar class C beta-lactamase.
  Biochemistry, 38, 1469-1477.  
  10049265 S.Trépanier, J.R.Knox, N.Clairoux, F.Sanschagrin, R.C.Levesque, and A.Huletsky (1999).
Structure-function studies of Ser-289 in the class C beta-lactamase from Enterobacter cloacae P99.
  Antimicrob Agents Chemother, 43, 543-548.  
9761898 A.Carfi, E.Duée, M.Galleni, J.M.Frère, and O.Dideberg (1998).
1.85 A resolution structure of the zinc (II) beta-lactamase from Bacillus cereus.
  Acta Crystallogr D Biol Crystallogr, 54, 313-323.
PDB code: 1bvt
9588800 C.Spangenberg, T.C.Montie, and B.Tümmler (1998).
Structural and functional implications of sequence diversity of Pseudomonas aeruginosa genes oriC, ampC and fliC.
  Electrophoresis, 19, 545-550.  
9449253 I.Massova, and S.Mobashery (1998).
Kinship and diversification of bacterial penicillin-binding proteins and beta-lactamases.
  Antimicrob Agents Chemother, 42, 1.  
  9593136 L.Bret, C.Chanal-Claris, D.Sirot, E.B.Chaibi, R.Labia, and J.Sirot (1998).
Chromosomally encoded ampC-type beta-lactamase in a clinical isolate of Proteus mirabilis.
  Antimicrob Agents Chemother, 42, 1110-1114.  
9671516 M.Nukaga, K.Taniguchi, Y.Washio, and T.Sawai (1998).
Effect of an amino acid insertion into the omega loop region of a class C beta-lactamase on its substrate specificity.
  Biochemistry, 37, 10461-10468.  
9521648 S.Banerjee, U.Pieper, G.Kapadia, L.K.Pannell, and O.Herzberg (1998).
Role of the omega-loop in the activity, substrate specificity, and structure of class A beta-lactamase.
  Biochemistry, 37, 3286-3296.
PDB code: 1ome
9063463 G.Feller, Z.Zekhnini, J.Lamotte-Brasseur, and C.Gerday (1997).
Enzymes from cold-adapted microorganisms. The class C beta-lactamase from the antarctic psychrophile Psychrobacter immobilis A5.
  Eur J Biochem, 244, 186-191.  
  9158770 F.Guo, G.I.Dmitrienko, A.J.Clarke, and T.Viswanatha (1996).
The role of the nonconserved residues at position 167 of class A beta-lactamases in susceptibility to mechanism-based inhibitors.
  Microb Drug Resist, 2, 261-268.  
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
8756327 N.C.Strynadka, R.Martin, S.E.Jensen, M.Gold, and J.B.Jones (1996).
Structure-based design of a potent transition state analogue for TEM-1 beta-lactamase.
  Nat Struct Biol, 3, 688-695.  
8652552 N.O.Siemers, D.E.Yelton, J.Bajorath, and P.D.Senter (1996).
Modifying the specificity and activity of the Enterobacter cloacae P99 beta-lactamase by mutagenesis within an M13 phage vector.
  Biochemistry, 35, 2104-2111.  
8605631 S.Pares, N.Mouz, Y.Pétillot, R.Hakenbeck, and O.Dideberg (1996).
X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme.
  Nat Struct Biol, 3, 284-289.
PDB code: 1pmd
8639511 Y.Xu, G.Soto, K.R.Hirsch, and R.F.Pratt (1996).
Kinetics and mechanism of the hydrolysis of depsipeptides catalyzed by the beta-lactamase of Enterobacter cloacae P99.
  Biochemistry, 35, 3595-3603.  
7565100 J.M.Frère (1995).
Beta-lactamases and bacterial resistance to antibiotics.
  Mol Microbiol, 16, 385-395.  
  8592985 J.R.Knox (1995).
Extended-spectrum and inhibitor-resistant TEM-type beta-lactamases: mutations, specificity, and three-dimensional structure.
  Antimicrob Agents Chemother, 39, 2593-2601.  
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.