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Chapter 9 : Class B β-Lactamases
Authors:
Gian Maria Rossolini1,
Jean-Denis Docquier2
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Affiliations:
1: Dipartimento di Biologia Molecolare, Università di Siena, Siena, I-53100, Italy;
2: Centre d’Ingénierie des Protéines & Laboratoire d’Enzymologie, Université de Liège, Liège, B-4000, Belgium
Content Type: Monograph
Publication Year:
2007
Category: Bacterial Pathogenesis
Book DOI:
10.1128/9781555815615
Chapter DOI:
10.1128/9781555815615.ch9
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Abstract:
This chapter provides an overview of class B β-lactamases (CBBLs), considering both fundamental and clinical aspects. Class B is one of the four classes in the structural classification of β-lactamases, which was created to accommodate the metallo-β-lactamases (MBLs). Expression of the CBBL genes carried on gene cassettes is normally under the control of the integron promoters (Pc and, possibly, P2) located in the 5'-conserved segment of the integron. The constant features of CBBLs include (i) good to excellent carbapenemase activity; (ii) lack of activity on monobactams, which apparently do not interact with these enzymes; and (iii) inhibition by EDTA and other metal ion chelators, and lack of inhibition by the conventional serine-β-lactamase inhibitors. Concerning the structure of the zinc center, which is located at the bottom of a shallow groove between the two β-sheets, in subclass B1 and B3 CBBLs it can accommodate two zinc ions (dinuclear zinc center): a tetrahedrally coordinated zinc ion (Zn1) and a trigonal bipyramidally coordinated zinc ion (Zn2), bridged by a water molecule/hydroxide ion (Wat1). Zn1 is coordinated by three His residues (His 116, His118, and His196) and the bridging Wat1 in all subclass B1 and B3 enzymes, while the strategy of Zn2 coordination is partially different in members of the two subclasses. The clinical relevance of resident CBBLs essentially reflects that of the host species, where these enzymes can variably contribute to intrinsic β-lactam resistance depending on their expression pattern and substrate specificity.
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
Figures
Class B β-Lactamases
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Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09fig01
Figure 9.1
Unrooted tree showing the structural relatedness among the major lineages of CBBLs. The names of the enzymes are the same as in
Table 9.1
. The tree was constructed using the TREEVIEW program (
121
) on the basis of a sequence alignment constructed with the CLUSTAL X program (
158
) using the sequences whose accession numbers are reported in the fourth column of
Table 9.1
.
10.1128/9781555815615/f0118-01_thmb.gif
10.1128/9781555815615/f0118-01.gif
Figure 9.1
Unrooted tree showing the structural relatedness among the major lineages of CBBLs. The names of the enzymes are the same as in Table 9.1 . The tree was constructed using the TREEVIEW program ( 121 ) on the basis of a sequence alignment constructed with the CLUSTAL X program ( 158 ) using the sequences whose accession numbers are reported in the fourth column of Table 9.1 .
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09fig02
Figure 9.2
Amino acid sequence alignment of CBBLs of subclass B1 (section A), subclass B2 (section B), and subclass B3 (section C). The alignments were constructed considering a single representative for each major lineage, using the sequences whose accession numbers are reported in the fourth column of
Table 9.1
. Structural elements are shown above the alignment for enzymes of each subclass, based on the three-dimensional structures of the Bc-II (
23
), CphA (
53
), and L1 (
167
) enzymes, respectively. The conserved residues shared by enzymes of subclass B1 and those shared by enzymes of subclass B3 are boxshaded in gray (note that the Trp244 is not conserved in IMP-18). The four residues conserved among all CBBLs are boxshaded in black. Numbering is according to the BBL scheme (
52
,
54
).
10.1128/9781555815615/f0119-01_thmb.gif
10.1128/9781555815615/f0119-01.gif
Figure 9.2
Amino acid sequence alignment of CBBLs of subclass B1 (section A), subclass B2 (section B), and subclass B3 (section C). The alignments were constructed considering a single representative for each major lineage, using the sequences whose accession numbers are reported in the fourth column of Table 9.1 . Structural elements are shown above the alignment for enzymes of each subclass, based on the three-dimensional structures of the Bc-II ( 23 ), CphA ( 53 ), and L1 ( 167 ) enzymes, respectively. The conserved residues shared by enzymes of subclass B1 and those shared by enzymes of subclass B3 are boxshaded in gray (note that the Trp244 is not conserved in IMP-18). The four residues conserved among all CBBLs are boxshaded in black. Numbering is according to the BBL scheme ( 52 , 54 ).
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09fig03
Figure 9.3
Unrooted tree showing the structural relatedness among known IMP variants. The tree was constructed using the TREEVIEW program (
121
) on the basis of a sequence alignment constructed with the CLUSTAL X program (
158
) using the sequences whose accession numbers are reported in the third column of
Table 9.2
.
10.1128/9781555815615/f0121-01_thmb.gif
10.1128/9781555815615/f0121-01.gif
Figure 9.3
Unrooted tree showing the structural relatedness among known IMP variants. The tree was constructed using the TREEVIEW program ( 121 ) on the basis of a sequence alignment constructed with the CLUSTAL X program ( 158 ) using the sequences whose accession numbers are reported in the third column of Table 9.2 .
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09fig04
Figure 9.4
Unrooted tree showing the structural relatedness among known VIM variants. The tree was constructed using the TREEVIEW program (
121
) on the basis of a sequence alignment constructed with the CLUSTAL X program (
158
) using the sequences whose accession numbers are reported in the third column of
Table 9.3
.
10.1128/9781555815615/f0123-01_thmb.gif
10.1128/9781555815615/f0123-01.gif
Figure 9.4
Unrooted tree showing the structural relatedness among known VIM variants. The tree was constructed using the TREEVIEW program ( 121 ) on the basis of a sequence alignment constructed with the CLUSTAL X program ( 158 ) using the sequences whose accession numbers are reported in the third column of Table 9.3 .
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09fig05
Figure 9.5a
Schematic representation of the structure of the variable region of class 1 integrons containing bla
IMP (section A) or bla
VIM(section B) gene cassettes. The gene cassettes are indicated by arrows (those carrying CBBL genes are filled). The presence of the integron 5′-conserved segment (5′-CS) and 3′-conserved segment (3′-CS), flanking the cassette array, is also indicated. Only integrons whose variable region has been completely sequenced are shown.
10.1128/9781555815615/f0124-01_thmb.gif
10.1128/9781555815615/f0124-01.gif
Figure 9.5a
Schematic representation of the structure of the variable region of class 1 integrons containing bla IMP (section A) or bla VIM(section B) gene cassettes. The gene cassettes are indicated by arrows (those carrying CBBL genes are filled). The presence of the integron 5′-conserved segment (5′-CS) and 3′-conserved segment (3′-CS), flanking the cassette array, is also indicated. Only integrons whose variable region has been completely sequenced are shown.
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09fig05b
Figure 9.5b
Schematic representation of the structure of the variable region of class 1 integrons containing bla
IMP (section A) or bla
VIM(section B) gene cassettes. The gene cassettes are indicated by arrows (those carrying CBBL genes are filled). The presence of the integron 5′-conserved segment (5′-CS) and 3′-conserved segment (3′-CS), flanking the cassette array, is also indicated. Only integrons whose variable region has been completely sequenced are shown.
10.1128/9781555815615/f0125-01_thmb.gif
10.1128/9781555815615/f0125-01.gif
Figure 9.5b
Schematic representation of the structure of the variable region of class 1 integrons containing bla IMP (section A) or bla VIM(section B) gene cassettes. The gene cassettes are indicated by arrows (those carrying CBBL genes are filled). The presence of the integron 5′-conserved segment (5′-CS) and 3′-conserved segment (3′-CS), flanking the cassette array, is also indicated. Only integrons whose variable region has been completely sequenced are shown.
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09fig05c
Figure 9.5c
Schematic representation of the structure of the variable region of class 1 integrons containing bla
IMP (section A) or bla
VIM(section B) gene cassettes. The gene cassettes are indicated by arrows (those carrying CBBL genes are filled). The presence of the integron 5′-conserved segment (5′-CS) and 3′-conserved segment (3′-CS), flanking the cassette array, is also indicated. Only integrons whose variable region has been completely sequenced are shown.
10.1128/9781555815615/f0126-01_thmb.gif
10.1128/9781555815615/f0126-01.gif
Figure 9.5c
Schematic representation of the structure of the variable region of class 1 integrons containing bla IMP (section A) or bla VIM(section B) gene cassettes. The gene cassettes are indicated by arrows (those carrying CBBL genes are filled). The presence of the integron 5′-conserved segment (5′-CS) and 3′-conserved segment (3′-CS), flanking the cassette array, is also indicated. Only integrons whose variable region has been completely sequenced are shown.
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09fig06
Figure 9.6
(Upper panels) Ribbon diagram of the three-dimensional structure of the CfiA/CcrA enzyme from B. fragilis strain QMCN3 (PDB accession no., 1ZNB), of the CphA enzyme from A. hydrophila AE036 (PDB accession no., 1X8G), and of the L1 enzyme from S. maltophilia strain IID 1275 (PDB accession, 1SML). The diagrams were constructed using the MOLMOL program (
86
). (Lower panels) Structure of the zinc centers of the corresponding enzymes (the water molecule is replaced by a carbonate in the CphA structure, and a single oxygen atom, involved in zinc coordination, is shown for clarity).
10.1128/9781555815615/f0131-01_thmb.gif
10.1128/9781555815615/f0131-01.gif
Figure 9.6
(Upper panels) Ribbon diagram of the three-dimensional structure of the CfiA/CcrA enzyme from B. fragilis strain QMCN3 (PDB accession no., 1ZNB), of the CphA enzyme from A. hydrophila AE036 (PDB accession no., 1X8G), and of the L1 enzyme from S. maltophilia strain IID 1275 (PDB accession, 1SML). The diagrams were constructed using the MOLMOL program ( 86 ). (Lower panels) Structure of the zinc centers of the corresponding enzymes (the water molecule is replaced by a carbonate in the CphA structure, and a single oxygen atom, involved in zinc coordination, is shown for clarity).
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
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Tables
Class B β-Lactamases
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Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09tab01
Table 9.1
Class B β-lactamases
Table 9.1
Class B β-lactamases
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09tab02
Table 9.2
IMP-type enzymes: sublineages, allelic variants, and distribution
Table 9.2
IMP-type enzymes: sublineages, allelic variants, and distribution
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09tab03
Table 9.3
VIM-type enzymes: sublineages, allelic variants, and distribution
Table 9.3
VIM-type enzymes: sublineages, allelic variants, and distribution
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09tab04
Table 9.4
Kinetic parameters of CBBLs against relevant β-lactam substrates
Table 9.4
Kinetic parameters of CBBLs against relevant β-lactam substrates
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09tab05
Table 9.5
Kinetic parameters of different IMP variants for selected β-lactam substrates
Table 9.5
Kinetic parameters of different IMP variants for selected β-lactam substrates
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09tab06
Table 9.6
Inactivation parameters of different CBBLs for selected chelating agents
Table 9.6
Inactivation parameters of different CBBLs for selected chelating agents
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09tab07
Table 9.7
Tests for phenotypic detection of acquired MBL production in gram-negative pathogens
Table 9.7
Tests for phenotypic detection of acquired MBL production in gram-negative pathogens
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9
/content/10.1128/9781555815615.ch09.ch09tab08
Table 9.8
Primers for detection of bla
IMP and bla
VIM genes by multiplex PCR assay, and strategy for presumptive identification of the sublineage by means of RFLP analysis of PCR products
a
Table 9.8
Primers for detection of bla IMP and bla VIM genes by multiplex PCR assay, and strategy for presumptive identification of the sublineage by means of RFLP analysis of PCR products a
Citation:
Rossolini G, Docquier J.
2007.
Class B β-Lactamases,
p 115-144.
In
Bonomo R, Tolmasky M (ed),
Enzyme-Mediated Resistance to Antibiotics.
ASM Press, Washington, DC.
doi: 10.1128/9781555815615.ch9