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PDBsum entry 1bvt
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* Residue conservation analysis
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DOI no:
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Acta Crystallogr D Biol Crystallogr
54:313-323
(1998)
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PubMed id:
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1.85 A resolution structure of the zinc (II) beta-lactamase from Bacillus cereus.
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A.Carfi,
E.Duée,
M.Galleni,
J.M.Frère,
O.Dideberg.
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ABSTRACT
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Class B beta-lactamases are wide spectrum enzymes which require bivalent metal
ions for activity. The structure of the class B zinc-ion-dependent
beta-lactamase from Bacillus cereus (BCII) has been refined at 1.85 A resolution
using data collected on cryocooled crystals (100 K). The enzyme from B. cereus
has a molecular mass of 24 946 Da and is folded into a beta-sandwich structure
with helices on the external faces. The active site is located in a groove
running between the two beta-sheets [Carfi et al. (1995). EMBO J. 14,
4914-4921]. The 100 K high-resolution BCII structure shows one fully and one
partially occupied zinc sites. The zinc ion in the fully occupied site (the
catalytic zinc) is coordinated by three histidines and one water molecule. The
second zinc ion is at 3.7 A from the first one and is coordinated by one
histidine, one cysteine, one aspartate and one unknown molecule (most likely a
carbonate ion). In the B. cereus zinc beta-lactamase the affinity for the second
metal-ion is low at the pH of crystallization (Kd = 25 mM, 293 K; [Baldwin et
al. (1978). Biochem. J. 175, 441-447] and the dissociation constant of the
second zinc ion was thus apparently decreased at the cryogenic temperature. In
addition, the structure of the apo enzyme was determined at 2.5 A resolution.
The removal of the zinc ion by chelating agents causes small changes in the
active-site environment.
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Selected figure(s)
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Figure 6.
Ball-and-stick representation of the active-sites environment of BCII and B. fragilis
zinc [\beta] -lactamases. The same orientation was used for the two views.
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Figure 7.
Ball-and-stick representation of the active sites environment of holo and apo BCII. The
same orientation was used for the two views.
[Figure 8]-[gr0751fig8thm.gif]
Figure 8
Stereoview of the C [\alpha] superposition of the apo (dotted lines) and holo (solid
line) BCII.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1998,
54,
313-323)
copyright 1998.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.Beck,
L.Maton,
J.L.Habib Jiwan,
and
J.Marchand-Brynaert
(2011).
Calcium and zinc complexes of pyrroglutamate analogs detected by electrospray ionization mass spectrometry.
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Amino Acids,
40,
679-687.
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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.
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J Biochem,
147,
905-915.
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PDB code:
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F.R.Salsbury,
M.W.Crowder,
S.F.Kingsmore,
and
J.J.Huntley
(2009).
Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor.
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J Mol Model,
15,
133-145.
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N.Selevsek,
S.Rival,
A.Tholey,
E.Heinzle,
U.Heinz,
L.Hemmingsen,
and
H.W.Adolph
(2009).
Zinc Ion-induced Domain Organization in Metallo-{beta}-lactamases: A FLEXIBLE "ZINC ARM" FOR RAPID METAL ION TRANSFER?
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J Biol Chem,
284,
16419-16431.
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A.Badarau,
and
M.I.Page
(2008).
Loss of enzyme activity during turnover of the Bacillus cereus beta-lactamase catalysed hydrolysis of beta-lactams due to loss of zinc ion.
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J Biol Inorg Chem,
13,
919-928.
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A.Tamilselvi,
and
G.Mugesh
(2008).
Zinc and antibiotic resistance: metallo-beta-lactamases and their synthetic analogues.
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J Biol Inorg Chem,
13,
1039-1053.
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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.
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Org Biomol Chem,
6,
2282-2294.
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PDB codes:
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L.I.Llarrull,
M.F.Tioni,
J.Kowalski,
B.Bennett,
and
A.J.Vila
(2007).
Evidence for a dinuclear active site in the metallo-beta-lactamase BcII with substoichiometric Co(II). A new model for metal uptake.
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J Biol Chem,
282,
30586-30595.
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G.Estiu,
D.Suárez,
and
K.M.Merz
(2006).
Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases.
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J Comput Chem,
27,
1240-1262.
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B.Bauer-Siebenlist,
S.Dechert,
and
F.Meyer
(2005).
Biomimetic hydrolysis of penicillin G catalyzed by dinuclear zinc(II) complexes: structure-activity correlations in beta-lactamase model systems.
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Chemistry,
11,
5343-5352.
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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.
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J Biol Chem,
280,
28195-28202.
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T.R.Walsh,
M.A.Toleman,
L.Poirel,
and
P.Nordmann
(2005).
Metallo-beta-lactamases: the quiet before the storm?
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Clin Microbiol Rev,
18,
306-325.
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G.Garau,
I.García-Sáez,
C.Bebrone,
C.Anne,
P.Mercuri,
M.Galleni,
J.M.Frère,
and
O.Dideberg
(2004).
Update of the standard numbering scheme for class B beta-lactamases.
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Antimicrob Agents Chemother,
48,
2347-2349.
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M.Dal Peraro,
A.J.Vila,
and
P.Carloni
(2004).
Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus.
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Proteins,
54,
412-423.
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R.M.Rasia,
and
A.J.Vila
(2004).
Structural determinants of substrate binding to Bacillus cereus metallo-beta-lactamase.
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J Biol Chem,
279,
26046-26051.
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C.Moali,
C.Anne,
J.Lamotte-Brasseur,
S.Groslambert,
B.Devreese,
J.Van Beeumen,
M.Galleni,
and
J.M.Frère
(2003).
Analysis of the importance of the metallo-beta-lactamase active site loop in substrate binding and catalysis.
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Chem Biol,
10,
319-329.
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I.García-Saez,
J.Hopkins,
C.Papamicael,
N.Franceschini,
G.Amicosante,
G.M.Rossolini,
M.Galleni,
J.M.Frère,
and
O.Dideberg
(2003).
The 1.5-A structure of Chryseobacterium meningosepticum zinc beta-lactamase in complex with the inhibitor, D-captopril.
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J Biol Chem,
278,
23868-23873.
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PDB code:
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U.Heinz,
R.Bauer,
S.Wommer,
W.Meyer-Klaucke,
C.Papamichaels,
J.Bateson,
and
H.W.Adolph
(2003).
Coordination geometries of metal ions in d- or l-captopril-inhibited metallo-beta-lactamases.
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J Biol Chem,
278,
20659-20666.
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A.L.Carenbauer,
J.D.Garrity,
G.Periyannan,
R.B.Yates,
and
M.W.Crowder
(2002).
Probing substrate binding to metallo-beta-lactamase L1 from Stenotrophomonas maltophilia by using site-directed mutagenesis.
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BMC Biochem,
3,
4.
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A.M.Simm,
C.S.Higgins,
A.L.Carenbauer,
M.W.Crowder,
J.H.Bateson,
P.M.Bennett,
A.R.Clarke,
S.E.Halford,
and
T.R.Walsh
(2002).
Characterization of monomeric L1 metallo-beta -lactamase and the role of the N-terminal extension in negative cooperativity and antibiotic hydrolysis.
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J Biol Chem,
277,
24744-24752.
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F.R.Salsbury,
M.F.Crowley,
and
C.L.Brooks
(2001).
Modeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding.
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Proteins,
44,
448-459.
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G.M.Rossolini,
M.A.Condemi,
F.Pantanella,
J.D.Docquier,
G.Amicosante,
and
M.C.Thaller
(2001).
Metallo-beta-lactamase producers in environmental microbiota: new molecular class B enzyme in Janthinobacterium lividum.
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Antimicrob Agents Chemother,
45,
837-844.
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I.Ponsard,
M.Galleni,
P.Soumillion,
and
J.Fastrez
(2001).
Selection of metalloenzymes by catalytic activity using phage display and catalytic elution.
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Chembiochem,
2,
253-259.
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M.Galleni,
J.Lamotte-Brasseur,
G.M.Rossolini,
J.Spencer,
O.Dideberg,
and
J.M.Frère
(2001).
Standard numbering scheme for class B beta-lactamases.
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Antimicrob Agents Chemother,
45,
660-663.
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L.Boschi,
P.S.Mercuri,
M.L.Riccio,
G.Amicosante,
M.Galleni,
J.M.Frère,
and
G.M.Rossolini
(2000).
The Legionella (Fluoribacter) gormanii metallo-beta-lactamase: a new member of the highly divergent lineage of molecular-subclass B3 beta-lactamases.
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Antimicrob Agents Chemother,
44,
1538-1543.
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L.Chantalat,
E.Duée,
M.Galleni,
J.M.Frère,
and
O.Dideberg
(2000).
Structural effects of the active site mutation cysteine to serine in Bacillus cereus zinc-beta-lactamase.
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Protein Sci,
9,
1402-1406.
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PDB code:
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M.L.Riccio,
N.Franceschini,
L.Boschi,
B.Caravelli,
G.Cornaglia,
R.Fontana,
G.Amicosante,
and
G.M.Rossolini
(2000).
Characterization of the metallo-beta-lactamase determinant of Acinetobacter baumannii AC-54/97 reveals the existence of bla(IMP) allelic variants carried by gene cassettes of different phylogeny.
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Antimicrob Agents Chemother,
44,
1229-1235.
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A.D.Cameron,
M.Ridderström,
B.Olin,
and
B.Mannervik
(1999).
Crystal structure of human glyoxalase II and its complex with a glutathione thiolester substrate analogue.
|
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Structure,
7,
1067-1078.
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PDB codes:
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G.G.Hammond,
J.L.Huber,
M.L.Greenlee,
J.B.Laub,
K.Young,
L.L.Silver,
J.M.Balkovec,
K.D.Pryor,
J.K.Wu,
B.Leiting,
D.L.Pompliano,
and
J.H.Toney
(1999).
Inhibition of IMP-1 metallo-beta-lactamase and sensitization of IMP-1-producing bacteria by thioester derivatives.
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FEMS Microbiol Lett,
179,
289-296.
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Z.Wang,
W.Fast,
A.M.Valentine,
and
S.J.Benkovic
(1999).
Metallo-beta-lactamase: structure and mechanism.
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Curr Opin Chem Biol,
3,
614-622.
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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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Links
