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PDBsum entry 1bmc
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Hydrolase (acting in cyclic amides)
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PDB id
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1bmc
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Contents |
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* Residue conservation analysis
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Embo J
14:4914-4921
(1995)
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PubMed id:
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The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold.
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A.Carfi,
S.Pares,
E.Duée,
M.Galleni,
C.Duez,
J.M.Frère,
O.Dideberg.
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ABSTRACT
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The 3-D structure of Bacillus cereus (569/H/9) beta-lactamase (EC 3.5.2.6),
which catalyses the hydrolysis of nearly all beta-lactams, has been solved at
2.5 A resolution by the multiple isomorphous replacement method, with density
modification and phase combination, from crystals of the native protein and of a
specially designed mutant (T97C). The current model includes 212 of the 227
amino acid residues, the zinc ion and 10 water molecules. The protein is folded
into a beta beta sandwich with helices on each external face. To our knowledge,
this fold has never been observed. An approximate internal molecular symmetry is
found, with a 2-fold axis passing roughly through the zinc ion and suggesting a
possible gene duplication. The active site is located at one edge of the beta
beta sandwich and near the N-terminal end of a helix. The zinc ion is
coordinated by three histidine residues (86, 88 and 149) and a water molecule. A
sequence comparison of the relevant metallo-beta-lactamases, based on this
protein structure, highlights a few well-conserved amino acid residues. The
structure shows that most of these residues are in the active site. Among these,
aspartic acid 90 and histidine 210 participate in a proposed catalytic mechanism
for beta-lactam hydrolysis.
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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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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.
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FEBS J,
278,
1252-1263.
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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.
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Biochemistry (Mosc),
76,
350-358.
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A.L.Stamp,
P.Owen,
K.E.Omari,
C.E.Nichols,
M.Lockyer,
H.K.Lamb,
I.G.Charles,
A.R.Hawkins,
and
D.K.Stammers
(2010).
Structural and functional characterization of Salmonella enterica serovar Typhimurium YcbL: an unusual Type II glyoxalase.
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Protein Sci,
19,
1897-1905.
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PDB code:
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D.C.Cantu,
Y.Chen,
and
P.J.Reilly
(2010).
Thioesterases: a new perspective based on their primary and tertiary structures.
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Protein Sci,
19,
1281-1295.
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J.D.Docquier,
M.Benvenuti,
V.Calderone,
M.Stoczko,
N.Menciassi,
G.M.Rossolini,
and
S.Mangani
(2010).
High-resolution crystal structure of the subclass B3 metallo-beta-lactamase BJP-1: rational basis for substrate specificity and interaction with sulfonamides.
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Antimicrob Agents Chemother,
54,
4343-4351.
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PDB codes:
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M.N.Lisa,
L.Hemmingsen,
and
A.J.Vila
(2010).
Catalytic role of the metal ion in the metallo-beta-lactamase GOB.
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J Biol Chem,
285,
4570-4577.
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P.Oelschlaeger,
N.Ai,
K.T.Duprez,
W.J.Welsh,
and
J.H.Toney
(2010).
Evolving carbapenemases: can medicinal chemists advance one step ahead of the coming storm?
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J Med Chem,
53,
3013-3027.
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V.A.Campos-Bermudez,
J.M.González,
D.L.Tierney,
and
A.J.Vila
(2010).
Spectroscopic signature of a ubiquitous metal binding site in the metallo-β-lactamase superfamily.
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J Biol Inorg Chem,
15,
1209-1218.
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B.Meier,
L.J.Barber,
Y.Liu,
L.Shtessel,
S.J.Boulton,
A.Gartner,
and
S.Ahmed
(2009).
The MRT-1 nuclease is required for DNA crosslink repair and telomerase activity in vivo in Caenorhabditis elegans.
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EMBO J,
28,
3549-3563.
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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.
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Antimicrob Agents Chemother,
53,
4464-4471.
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PDB codes:
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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.
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J Biol Chem,
284,
28164-28171.
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J.Morán-Barrio,
A.S.Limansky,
and
A.M.Viale
(2009).
Secretion of GOB metallo-beta-lactamase in Escherichia coli depends strictly on the cooperation between the cytoplasmic DnaK chaperone system and the Sec machinery: completion of folding and Zn(II) ion acquisition occur in the bacterial periplasm.
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Antimicrob Agents Chemother,
53,
2908-2917.
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R.Singh,
A.Saxena,
and
H.Singh
(2009).
Identification of group specific motifs in Beta-lactamase family of proteins.
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J Biomed Sci,
16,
109.
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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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A.Yamamura,
J.Ohtsuka,
K.Kubota,
Y.Agari,
A.Ebihara,
N.Nakagawa,
K.Nagata,
and
M.Tanokura
(2008).
Crystal structure of TTHA1429, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8.
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Proteins,
73,
1053-1057.
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PDB code:
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B.Jeon,
W.Muraoka,
O.Sahin,
and
Q.Zhang
(2008).
Role of Cj1211 in natural transformation and transfer of antibiotic resistance determinants in Campylobacter jejuni.
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Antimicrob Agents Chemother,
52,
2699-2708.
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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.
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Biochemistry,
47,
8590-8599.
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M.I.Page,
and
A.Badarau
(2008).
The mechanisms of catalysis by metallo beta-lactamases.
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Bioinorg Chem Appl,
(),
576297.
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P.E.Tomatis,
S.M.Fabiane,
F.Simona,
P.Carloni,
B.J.Sutton,
and
A.J.Vila
(2008).
Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility.
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Proc Natl Acad Sci U S A,
105,
20605-20610.
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PDB code:
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V.Gupta
(2008).
Metallo beta lactamases in Pseudomonas aeruginosa and Acinetobacter species.
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Expert Opin Investig Drugs,
17,
131-143.
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Z.Hu,
G.Periyannan,
B.Bennett,
and
M.W.Crowder
(2008).
Role of the Zn1 and Zn2 sites in metallo-beta-lactamase L1.
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J Am Chem Soc,
130,
14207-14216.
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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.
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Proteins,
69,
595-605.
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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.
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J Biol Chem,
282,
18286-18293.
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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.
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Antimicrob Agents Chemother,
51,
2136-2142.
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PDB code:
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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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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.
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J Biol Chem,
282,
18276-18285.
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PDB code:
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A.Costello,
G.Periyannan,
K.W.Yang,
M.W.Crowder,
and
D.L.Tierney
(2006).
Site-selective binding of Zn(II) to metallo-beta-lactamase L1 from Stenotrophomonas maltophilia.
|
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J Biol Inorg Chem,
11,
351-358.
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B.A.Manjasetty,
K.Büssow,
M.Fieber-Erdmann,
Y.Roske,
J.Gobom,
C.Scheich,
F.Götz,
F.H.Niesen,
and
U.Heinemann
(2006).
Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold.
|
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Protein Sci,
15,
914-920.
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PDB code:
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D.Xu,
D.Xie,
and
H.Guo
(2006).
Catalytic mechanism of class B2 metallo-beta-lactamase.
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J Biol Chem,
281,
8740-8747.
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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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G.Hagelueken,
T.M.Adams,
L.Wiehlmann,
U.Widow,
H.Kolmar,
B.Tümmler,
D.W.Heinz,
and
W.D.Schubert
(2006).
The crystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, defines a third class of sulfatases.
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Proc Natl Acad Sci U S A,
103,
7631-7636.
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PDB codes:
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J.Wang,
Y.Okamoto,
J.Morishita,
K.Tsuboi,
A.Miyatake,
and
N.Ueda
(2006).
Functional analysis of the purified anandamide-generating phospholipase D as a member of the metallo-beta-lactamase family.
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J Biol Chem,
281,
12325-12335.
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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.
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J Am Soc Mass Spectrom,
17,
180-188.
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N.Selevsek,
A.Tholey,
E.Heinzle,
B.M.Liénard,
N.J.Oldham,
C.J.Schofield,
U.Heinz,
H.W.Adolph,
and
J.M.Frère
(2006).
Studies on ternary metallo-beta lactamase-inhibitor complexes using electrospray ionization mass spectrometry.
|
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J Am Soc Mass Spectrom,
17,
1000-1004.
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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.
|
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FEMS Microbiol Rev,
30,
673-691.
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A.Vogel,
O.Schilling,
B.Späth,
and
A.Marchfelder
(2005).
The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties.
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Biol Chem,
386,
1253-1264.
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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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D.Liu,
B.W.Lepore,
G.A.Petsko,
P.W.Thomas,
E.M.Stone,
W.Fast,
and
D.Ringe
(2005).
Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis.
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Proc Natl Acad Sci U S A,
102,
11882-11887.
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PDB code:
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G.Garau,
A.M.Di Guilmi,
and
B.G.Hall
(2005).
Structure-based phylogeny of the metallo-beta-lactamases.
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Antimicrob Agents Chemother,
49,
2778-2784.
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G.Garau,
D.Lemaire,
T.Vernet,
O.Dideberg,
and
A.M.Di Guilmi
(2005).
Crystal structure of phosphorylcholine esterase domain of the virulence factor choline-binding protein e from streptococcus pneumoniae: new structural features among the metallo-beta-lactamase superfamily.
|
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J Biol Chem,
280,
28591-28600.
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PDB codes:
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I.L.de la Sierra-Gallay,
O.Pellegrini,
and
C.Condon
(2005).
Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z.
|
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Nature,
433,
657-661.
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PDB code:
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J.Antony,
J.P.Piquemal,
and
N.Gresh
(2005).
Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-beta-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry.
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J Comput Chem,
26,
1131-1147.
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N.Gresh,
J.P.Piquemal,
and
M.Krauss
(2005).
Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations.
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J Comput Chem,
26,
1113-1130.
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O.Schilling,
B.Späth,
B.Kostelecky,
A.Marchfelder,
W.Meyer-Klaucke,
and
A.Vogel
(2005).
Exosite modules guide substrate recognition in the ZiPD/ElaC protein family.
|
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J Biol Chem,
280,
17857-17862.
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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.
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P.Oelschlaeger,
S.L.Mayo,
and
J.Pleiss
(2005).
Impact of remote mutations on metallo-beta-lactamase substrate specificity: implications for the evolution of antibiotic resistance.
|
| |
Protein Sci,
14,
765-774.
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R.Ishii,
A.Minagawa,
H.Takaku,
M.Takagi,
M.Nashimoto,
and
S.Yokoyama
(2005).
Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima.
|
| |
J Biol Chem,
280,
14138-14144.
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PDB code:
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A.Minagawa,
H.Takaku,
M.Takagi,
and
M.Nashimoto
(2004).
A novel endonucleolytic mechanism to generate the CCA 3' termini of tRNA molecules in Thermotoga maritima.
|
| |
J Biol Chem,
279,
15688-15697.
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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.
|
| |
Antimicrob Agents Chemother,
48,
2347-2349.
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L.H.Wang,
L.X.Weng,
Y.H.Dong,
and
L.H.Zhang
(2004).
Specificity and enzyme kinetics of the quorum-quenching N-Acyl homoserine lactone lactonase (AHL-lactonase).
|
| |
J Biol Chem,
279,
13645-13651.
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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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P.S.Mercuri,
I.García-Sáez,
K.De Vriendt,
I.Thamm,
B.Devreese,
J.Van Beeumen,
O.Dideberg,
G.M.Rossolini,
J.M.Frère,
and
M.Galleni
(2004).
Probing the specificity of the subclass B3 FEZ-1 metallo-beta-lactamase by site-directed mutagenesis.
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J Biol Chem,
279,
33630-33638.
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R.M.Rasia,
and
A.J.Vila
(2004).
Structural determinants of substrate binding to Bacillus cereus metallo-beta-lactamase.
|
| |
J Biol Chem,
279,
26046-26051.
|
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Y.Okamoto,
J.Morishita,
K.Tsuboi,
T.Tonai,
and
N.Ueda
(2004).
Molecular characterization of a phospholipase D generating anandamide and its congeners.
|
| |
J Biol Chem,
279,
5298-5305.
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C.Damblon,
M.Jensen,
A.Ababou,
I.Barsukov,
C.Papamicael,
C.J.Schofield,
L.Olsen,
R.Bauer,
and
G.C.Roberts
(2003).
The inhibitor thiomandelic acid binds to both metal ions in metallo-beta-lactamase and induces positive cooperativity in metal binding.
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J Biol Chem,
278,
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PDB code:
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Where a reference describes a PDB structure, the PDB
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