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Research → β-Lactamase Enzymes.

These enzymes have been lumped and split by various authors, using either molecular or functional characteristics of the enzymes to try to make sense of more than 1,300 uniquely occurring β-lactamase variants. Functional and molecular classification schemes have been aligned as shown in Figure 1, with a clear separation of two molecular classes: the metallo-β-lactamases (MBLs), those that require zinc for β-lactam catalysis, and the serine β-lactamases, those β-lactamases that catalyze β-lactam hydrolysis via an acyl enzyme formed between substrate and an active site serine. Each molecular class has its own characteristics based on identifying features of the primary sequence of each β-lactamase. Thus, one may categorize a new β-lactamase into a distinctive molecular class as soon as the sequence has been determined, an exercise that has generally become trivial for the β-lactamase laboratory. However, the function of the enzyme is the more critical designation for the clinician who wants to know what substrates (antibiotics) may be spared from hydrolysis so that appropriate therapy can be prescribed.

As seen in Figure 1, the four major β-lactamase classes, A–D, can be separated into functional groups that have distinguishing substrate and inhibitor profiles. Molecular class C is associated with two functional subgroups, 1 and 1e, both of which hydrolyze early cephalosporins efficiently with little effect of β-lactamase inhibitors; however, enzymes in subgroup 1e, sometimes named the ESAC (extended spectrum AmpC) β-lactamases, exhibit enhanced hydrolysis of cephalosporins with aminothiazoleoxime side chains.

Molecular classes A and D, or group 2 β-lactamases, include those serine β-lactamases with the broadest, and largest, functional groups of enzymes, with multiple subgroups that overall demonstrate hydrolysis of all β-lactam antibiotics across the class. Two of the most important among the class A enzyme subgroups are the notable ESBLs (subgroup 2be) and serine carbapenemases (subgroup 2f) that are creating havoc within the global infectious disease community by hydrolyzing all classes of β-lactams. Most purified class A β-lactamases are considered to be inhibited by clavulanic acid, although their response to the common β-lactamase inhibitor combinations such as amoxicillin-clavulanic acid may be variable in whole cell testing. Class D β-lactamases are often underappreciated, but cause serious resistance in organisms like Acinetobacter baumannii and Pseudomonas aeruginosa. Another set of β-lactamases of considerable clinical concern is the molecular class B family, or functional group 3 β-lactamases, that can hydrolyze all β-lactams except for the monobactams. These enzymes are especially deleterious, as they are not inhibited by any of the current β-lactamase inhibitor combinations, including agents in late stages of clinical development. Although monobactams do not undergo hydrolysis by MBLs, it should be noted that they are hydrolyzed by the group 2f serine carbapenemases. β-Lactamase nomenclature is a bit daunting for non-β-lactamase specialists. Not only are there formal molecular and functional classification schemes as described above, but also the names ESBLs and carbapenemases are used to span different sets of enzymes in different classification schemes. Initially ESBLs were variants of the common group 2b penicillinases (TEM and SHV) that acquired the ability to hydrolyze cefotaxime or ceftazidime due to a limited number of point mutations. Today, ESBLs include not only the TEM and SHV families of group 2be ESBLs, but also the group 1e cephalosporinases with expanded substrate hydrolysis profiles, the ubiquitous CTX-Mfamily of ESBLs, and the cephalosporin-hydrolyzing group 2de OXA enzymes. Similarly, carbapenemases, as noted above, include both serine carbapenemases in functional groups 2f and 2df and the group 3 MBLs. Although carbap though carbapenemases, for the most part, also hydrolyze many expanded-spectrum cephalosporins, it is important that they retain the carbapenemase name. Infections caused by traditional ESBL-producing pathogens can often be treated successfully with a carbapenem, whereas carbapenem monotherapy to treat infections caused by carbapenemase-producing organisms is not generally recommended. Carbapenemases and ESBLs should, therefore, be viewed distinctly from a clinical perspective and should preserve their distinguishing names. Bush K. Ann N Y Acad Sci. 2013; 1277:84-90.


1.- β-lactamases classification.

Figure 1: Molecular and functional features of the major groups of β-lactamases. Bush K. Ann N Y Acad Sci. 2013; 1277:84-90.


  1. GenBank sequences for TEM phenotype 2b. FASTA for protein sequence and sequence alignment at EBI. Homology modeling at SWISS-MODEL for Q6SJ61, Q932Y6, Q2V899, B8XLJ7, Q9AFC8, Q937J3, Q00626, Q6UK85, Q6UK84, Q6ZYM6, Q56H91, E5LP65, G9FYZ8, N0D6W6.
    High resolution structures for TEM phenotype 2b β-lactamases.
  2. GenBank sequences for TEM phenotype 2be. FASTA for protein sequence and sequence alignment at EBI.
    High resolution structures for TEM phenotype 2be β-lactamases.
  3. GenBank sequences for TEM phenotype 2ber. FASTA for protein sequence and sequence alignment at EBI.
  4. GenBank sequences for TEM phenotype 2br. FASTA for protein sequence and sequence alignment at EBI.
  5. GenBank sequences for TEM unknown phenotype. FASTA for protein sequence and sequence alignment at EBI.

Representative sequences for all TEM class and their alignment.




  1. GenBank sequences for SHV phenotype 2br. FASTA for protein sequence and sequence alignment at EBI.
    High resolution structures for SHV phenotype 2br β-lactamases.
  2. GenBank sequences for SHV phenotype 2be. FASTA for protein sequence and sequence alignment at EBI.
    High resolution structures for SHV phenotype 2be β-lactamases.
  3. GenBank sequences for SHV phenotype 2b. FASTA for protein sequence and sequence alignment at EBI.
    High resolution structures for SHV phenotype 2b β-lactamases.
  4. GenBank sequences for SHV unknown phenotype. FASTA for protein sequence and sequence alignment at EBI.
    High resolution structures for SHV unknown phenotype β-lactamases.

Representative sequences for all SHV class and their alignment.

TEM versus SHV sequences alignment.




  1. GenBank sequences for OXA phenotype 2d. FASTA for protein sequence and sequence alignment at EBI.
  2. GenBank sequences for OXA phenotype 2de. FASTA for protein sequence and sequence alignment at EBI.
  3. GenBank sequences for OXA phenotype 2df. FASTA for protein sequence and sequence alignment at EBI.
  4. GenBank sequences for OXA unknown phenotype. FASTA for protein sequence and sequence alignment at EBI.
  5. GenBank sequences for CTX-M. FASTA for protein sequence and sequence alignment at EBI.
  6. GenBank sequences for CMY. FASTA for protein sequence and sequence alignment at EBI.
  7. GenBank sequences for ACT. FASTA for protein sequence and sequence alignment at EBI.
  8. GenBank sequences for ACC. FASTA for protein sequence and sequence alignment at EBI.
  9. GenBank sequences for CFE. FASTA for protein sequence.
  10. GenBank sequences for DHA. FASTA for protein sequence and sequence alignment at EBI.
  11. GenBank sequences for FOX. FASTA for protein sequence and sequence alignment at EBI.
    High resolution structures for FOX β-lactamases.
  12. GenBank sequences for LAT. FASTA for protein sequence.
  13. GenBank sequences for MIR. FASTA for protein sequence and sequence alignment at EBI.
  14. GenBank sequences for MOX. FASTA for protein sequence and sequence alignment at EBI.
    High resolution structures for MOX β-lactamases.
  15. GenBank sequences for IMP. FASTA for protein sequence and sequence alignment at EBI.
    High resolution structures for IMP β-lactamases.
  16. GenBank sequences for CARB. FASTA for protein sequence and sequence alignment at EBI.

2.- Structure alignment for Pfam PF00144 proteins.






5F1G.pdb E.coli | Secondary structure, S-x-x-K motif on pink color at catalitic binding site.



5F1G.pdb E.coli | molecular surface with inhibitor.
   



3PTE.pdb Streptomyces sp. R61 | Secondary structure, S-x-x-K motif on pink color at catalitic binding site.



3PTE.pdb Streptomyces sp. R61 | molecular surface with inhibitor.
   



5HAI.pdb Enterobacter cloacae | Secondary structure, S-x-x-K motif on pink color at catalitic binding site.



5HAI.pdb Enterobacter cloacae | molecular surface with inhibitor.
   



1WYB.pdb Flavobacterium sp. | Secondary structure, S-x-x-K motif on pink color at catalitic binding site.



1WYB.pdb Flavobacterium sp. | molecular surface with inhibitor.
   



2EFX.pdb Ochrobactrum anthropi | Secondary structure, S-x-x-K motif on pink color at catalitic binding site.



2EFX.pdb Ochrobactrum anthropi | molecular surface with inhibitor.
   



4LCL.pdb Aspergillus terreus | Secondary structure, S-x-x-K motif on pink color at catalitic binding site.



4LCL.pdb Aspergillus terreus | molecular surface with inhibitor.
   



2E8I.pdb Flavobacterium sp. K172 | Secondary structure, S-x-x-K motif on pink color at catalitic binding site.



2E8I.pdb Flavobacterium sp. K172 | molecular surface with inhibitor.
   



4U0X.pdb Acinetobacter baumannii | Secondary structure, S-x-x-K motif on pink color at catalitic binding site.



4U0X.pdb Acinetobacter baumannii | molecular surface with inhibitor.
   



4X68.pdb Pseudomonas aeruginosa | Secondary structure, S-x-x-K motif on pink color at catalitic binding site.



4X68.pdb Pseudomonas aeruginosa | molecular surface with inhibitor.
   

3.- β-lactamase inhibitors.

Figure 2: Compounds 1 to 7, a representative penicillin (compound 1), an extended spectrum cephalosporin (compound 2), a monobactam (compound 3), and carbapenems (compounds 4 to 7). The numbering scheme for penicillins, cephalosporins, and monobactams is shown. Compounds 8 to 10, β-lactamase inhibitors in clinical practice. Compounds 11 to 38, investigational β-lactamase inhibitors: monobactam derivatives (compounds 11 to 14), a penicillin derivative (compound 15), penems (compounds 16 to 20), penam sulfones (compounds 21 to 24), a boronic acid transition state analog (compound 25), non-β-lactams (compounds 26 to 28), and metallo-β-lactamase inhibitors (compounds 29 to 38).


4.- PDB resources.

Beta-lactamase structures.



5.- General references.

  1. Bush, K. and G. Jacoby. Nomenclature of TEM β-lactamases. 1997. J. Antimicrob. Chemother. 39:1-3.
  2. Ambler, R.P., A.F.W. Coulson, J.-M. Frère, J.-M. Ghuysen, B. Joris, M. Forsman, R.C. Levesque, G. Tiraby, and S.G. Waley. 1991. A standard numbering scheme for the class A β-lactamases. Biochem. J. 276:269-272.
  3. Livermore, D. M. 1995. β-Lactamases in laboratory and clinical resistance. Clin. Microbiol. Rev. 8:557-584.
  4. Bush, K., G.A. Jacoby, and A.A. Medeiros. 1995. A functional classification scheme for β-lactamases and its correlation with molecular structure. Antimicrob. Agents Chemother. 39:1211-1233.
  5. Knox, J.R. 1995. Extended-spectrum and inhibitor-resistant TEM-type β-lactamases: mutation, specificity, and three-dimensional structure. Antimicrob. Agents Chemother. 39:2593-2601.
  6. Bradford, P. A. 2001. Extended-spectrum β-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat. Clin. Microbiol. Rev. 14:933-951.
  7. Jacoby, G.A., and Munoz-Price, L.S. 2005. The new β-lactamases. New Engl. J. Med. 352:380-391.
  8. Paterson, D. L., and R. A. Bonomo. 2005. Extended-spectrum β-lactamases: a clinical update. Clin. Microbiol. Rev. 18:657-686.
  9. Jacoby, G.A. 2006. β-Lactamase nomenclature. Antimicrob Agents Chemother 50:1123-1129.
  10. Queenan, A.M., and K. Bush. 2007. Carbapenemases: the versatile β-lactamases. Clin. Microbiol. Rev. 20:440-458.
  11. Rodríguez-Baño J, Pascual A. 2008. Clinical significance of extended-spectrum β-lactamases. Expert Rev Anti Infect Ther. 2008; 6(5):671-83.
  12. Jacoby, G.A. AmpC β-Lactamases. 2009. Clin. Microbiol. Rev. 22:161-182.
  13. Bush, K, and G.A. Jacoby. 2010. Updated functional classification of β-lactamases. Antimicrob. Agents. Chemother. 54:969-976.
  14. Poirel, L., T. Naas, and P. Nordmann. 2010. Diversity, epidemiology, and genetics of class D β-lactamases. Antimicrob. Agents Chemother. 54:24-38.
  15. Drawz, S.M., Bonomo, R.A. Three decades of beta-lactamase inhibitors. Clin Microbiol Rev. 2010; 23(1):160-201. doi: 10.1128/CMR.00037-09. Review.
  16. Bush K. Proliferation and significance of clinically relevant β-lactamases. Ann N Y Acad Sci. 2013 Jan;1277:84-90. Review.
  17. Seiffert SN, Hilty M, Perreten V, Endimiani A. Extended-spectrum cephalosporin-resistant Gram-negative organisms in livestock: an emerging problem for human health?. Drug Resist Updat. 2013; 16(1-2):22-45. Review.
  18. D'Andrea MM, Arena F, Pallecchi L, Rossolini GM. CTX-M-type β-lactamases: a successful story of antibiotic resistance.. Int J Med Microbiol. 2013; 303(6-7):305-17. Review.
  19. Evans, B.A., and S.G.B.Amyes. 2014. OXA Beta-lactamases. Clin. Microbiol. Rev. 27:241-253.
  20. Liakopoulos A, Mevius D, Ceccarelli D. A Review of SHV Extended-Spectrum β-Lactamases: Neglected Yet Ubiquitous.. Front Microbiol. 2016; 7:1374. Review.
  21. Shahid M, Sobia F, Singh A, Malik A, Khan HM, Jonas D, Hawkey PM. Beta-lactams and beta-lactamase-inhibitors in current- or potential-clinical practice: a comprehensive update. Crit Rev Microbiol. 2009;35(2):81-108.
  22. TACKLING DRUG-RESISTANT INFECTIONS GLOBALLY: FINAL REPORT AND RECOMMENDATIONS. THE REVIEW ON ANTIMICROBIAL RESISTANCE CHAIRED BY JIM O’NEILL. 2016.