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PDBsum entry 1pmd
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Peptidoglycan synthesis
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PDB id
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1pmd
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Contents |
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* Residue conservation analysis
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* C-alpha coords only
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Nat Struct Biol
3:284-289
(1996)
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PubMed id:
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X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme.
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S.Pares,
N.Mouz,
Y.Pétillot,
R.Hakenbeck,
O.Dideberg.
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ABSTRACT
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All beta-lactam antibiotics exert their biological effects by interacting with a
unique class of proteins, the penicillin-binding proteins (PBPs). These membrane
proteins are involved in the biosynthesis of the murein or peptidoglycan, a
mesh-like structure which completely surrounds the bacterial cell. Sequence
similarities indicate that one domain of these proteins belongs to a large
family of beta-lactam-recognizing proteins, which includes the active-site
serine beta-lactamases. We here report the first three-dimensional crystal
structure of a high molecular weight penicillin-binding protein, PBP2x of
Streptococcus pneumoniae, at 3.5 A resolution. The molecule has three domains,
the central domain being a transpeptidase, which is a suitable target for
antibiotic development.
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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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A.Ruggiero,
F.Squeglia,
D.Marasco,
R.Marchetti,
A.Molinaro,
and
R.Berisio
(2011).
X-ray structural studies of the entire extracellular region of the serine/threonine kinase PrkC from Staphylococcus aureus.
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Biochem J,
435,
33-41.
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PDB code:
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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.
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J Mol Biol,
398,
54-65.
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PDB code:
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P.Barthe,
G.V.Mukamolova,
C.Roumestand,
and
M.Cohen-Gonsaud
(2010).
The structure of PknB extracellular PASTA domain from mycobacterium tuberculosis suggests a ligand-dependent kinase activation.
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Structure,
18,
606-615.
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PDB codes:
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A.J.Powell,
J.Tomberg,
A.M.Deacon,
R.A.Nicholas,
and
C.Davies
(2009).
Crystal Structures of Penicillin-binding Protein 2 from Penicillin-susceptible and -resistant Strains of Neisseria gonorrhoeae Reveal an Unexpectedly Subtle Mechanism for Antibiotic Resistance.
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J Biol Chem,
284,
1202-1212.
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PDB codes:
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M.Débarbouillé,
S.Dramsi,
O.Dussurget,
M.A.Nahori,
E.Vaganay,
G.Jouvion,
A.Cozzone,
T.Msadek,
and
B.Duclos
(2009).
Characterization of a serine/threonine kinase involved in virulence of Staphylococcus aureus.
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J Bacteriol,
191,
4070-4081.
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S.F.Pereira,
A.O.Henriques,
M.G.Pinho,
H.de Lencastre,
and
A.Tomasz
(2009).
Evidence for a dual role of PBP1 in the cell division and cell separation of Staphylococcus aureus.
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Mol Microbiol,
72,
895-904.
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S.Hower,
K.Wolf,
and
K.A.Fields
(2009).
Evidence that CT694 is a novel Chlamydia trachomatis T3S substrate capable of functioning during invasion or early cycle development.
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Mol Microbiol,
72,
1423-1437.
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A.Zapun,
C.Contreras-Martel,
and
T.Vernet
(2008).
Penicillin-binding proteins and beta-lactam resistance.
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FEMS Microbiol Rev,
32,
361-385.
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E.Sauvage,
F.Kerff,
M.Terrak,
J.A.Ayala,
and
P.Charlier
(2008).
The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis.
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FEMS Microbiol Rev,
32,
234-258.
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M.Yamada,
T.Watanabe,
N.Baba,
T.Miyara,
J.Saito,
and
Y.Takeuchi
(2008).
Crystallization and preliminary crystallographic analysis of the transpeptidase domain of penicillin-binding protein 2B from Streptococcus pneumoniae.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
284-288.
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M.Yamada,
T.Watanabe,
N.Baba,
Y.Takeuchi,
F.Ohsawa,
and
S.Gomi
(2008).
Crystal structures of biapenem and tebipenem complexed with penicillin-binding proteins 2X and 1A from Streptococcus pneumoniae.
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Antimicrob Agents Chemother,
52,
2053-2060.
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PDB codes:
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M.Yamada,
T.Watanabe,
T.Miyara,
N.Baba,
J.Saito,
Y.Takeuchi,
and
F.Ohsawa
(2007).
Crystal structure of cefditoren complexed with Streptococcus pneumoniae penicillin-binding protein 2X: structural basis for its high antimicrobial activity.
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Antimicrob Agents Chemother,
51,
3902-3907.
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PDB codes:
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S.Tristram,
M.R.Jacobs,
and
P.C.Appelbaum
(2007).
Antimicrobial resistance in Haemophilus influenzae.
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Clin Microbiol Rev,
20,
368-389.
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B.Zuber,
M.Haenni,
T.Ribeiro,
K.Minnig,
F.Lopes,
P.Moreillon,
and
J.Dubochet
(2006).
Granular layer in the periplasmic space of gram-positive bacteria and fine structures of Enterococcus gallinarum and Streptococcus gordonii septa revealed by cryo-electron microscopy of vitreous sections.
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J Bacteriol,
188,
6652-6660.
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G.Jones,
and
P.Dyson
(2006).
Evolution of transmembrane protein kinases implicated in coordinating remodeling of gram-positive peptidoglycan: inside versus outside.
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J Bacteriol,
188,
7470-7476.
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M.Haenni,
P.A.Majcherczyk,
J.L.Barblan,
and
P.Moreillon
(2006).
Mutational analysis of class A and class B penicillin-binding proteins in Streptococcus gordonii.
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Antimicrob Agents Chemother,
50,
4062-4069.
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M.Haenni,
and
P.Moreillon
(2006).
Mutations in penicillin-binding protein (PBP) genes and in non-PBP genes during selection of penicillin-resistant Streptococcus gordonii.
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Antimicrob Agents Chemother,
50,
4053-4061.
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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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R.Carapito,
L.Chesnel,
T.Vernet,
and
A.Zapun
(2006).
Pneumococcal beta-lactam resistance due to a conformational change in penicillin-binding protein 2x.
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J Biol Chem,
281,
1771-1777.
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T.Mascher,
M.Heintz,
D.Zähner,
M.Merai,
and
R.Hakenbeck
(2006).
The CiaRH system of Streptococcus pneumoniae prevents lysis during stress induced by treatment with cell wall inhibitors and by mutations in pbp2x involved in beta-lactam resistance.
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J Bacteriol,
188,
1959-1968.
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C.Morlot,
L.Pernot,
A.Le Gouellec,
A.M.Di Guilmi,
T.Vernet,
O.Dideberg,
and
A.Dessen
(2005).
Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae.
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J Biol Chem,
280,
15984-15991.
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PDB code:
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D.J.Scheffers,
and
M.G.Pinho
(2005).
Bacterial cell wall synthesis: new insights from localization studies.
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Microbiol Mol Biol Rev,
69,
585-607.
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E.Sauvage,
R.Herman,
S.Petrella,
C.Duez,
F.Bouillenne,
J.M.Frère,
and
P.Charlier
(2005).
Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins.
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J Biol Chem,
280,
31249-31256.
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PDB codes:
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J.O.Korbel,
T.Doerks,
L.J.Jensen,
C.Perez-Iratxeta,
S.Kaczanowski,
S.D.Hooper,
M.A.Andrade,
and
P.Bork
(2005).
Systematic association of genes to phenotypes by genome and literature mining.
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PLoS Biol,
3,
e134.
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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.
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Proc Natl Acad Sci U S A,
102,
577-582.
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PDB codes:
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R.Kobayashi,
M.Konomi,
K.Hasegawa,
M.Morozumi,
K.Sunakawa,
and
K.Ubukata
(2005).
In vitro activity of tebipenem, a new oral carbapenem antibiotic, against penicillin-nonsusceptible Streptococcus pneumoniae.
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Antimicrob Agents Chemother,
49,
889-894.
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V.R.Matias,
and
T.J.Beveridge
(2005).
Cryo-electron microscopy reveals native polymeric cell wall structure in Bacillus subtilis 168 and the existence of a periplasmic space.
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Mol Microbiol,
56,
240-251.
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E.Pagliero,
L.Chesnel,
J.Hopkins,
J.Croizé,
O.Dideberg,
T.Vernet,
and
A.M.Di Guilmi
(2004).
Biochemical characterization of Streptococcus pneumoniae penicillin-binding protein 2b and its implication in beta-lactam resistance.
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Antimicrob Agents Chemother,
48,
1848-1855.
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G.Mallorquí-Fernández,
A.Marrero,
S.García-Piquè,
R.García-Castellanos,
and
F.X.Gomis-Rüth
(2004).
Staphylococcal methicillin resistance: fine focus on folds and functions.
|
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FEMS Microbiol Lett,
235,
1-8.
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K.Ubukata,
N.Chiba,
K.Hasegawa,
R.Kobayashi,
S.Iwata,
and
K.Sunakawa
(2004).
Antibiotic susceptibility in relation to penicillin-binding protein genes and serotype distribution of Streptococcus pneumoniae strains responsible for meningitis in Japan, 1999 to 2002.
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Antimicrob Agents Chemother,
48,
1488-1494.
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L.B.Rice,
S.Bellais,
L.L.Carias,
R.Hutton-Thomas,
R.A.Bonomo,
P.Caspers,
M.G.Page,
and
L.Gutmann
(2004).
Impact of specific pbp5 mutations on expression of beta-lactam resistance in Enterococcus faecium.
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Antimicrob Agents Chemother,
48,
3028-3032.
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L.Pernot,
L.Chesnel,
A.Le Gouellec,
J.Croizé,
T.Vernet,
O.Dideberg,
and
A.Dessen
(2004).
A PBP2x from a clinical isolate of Streptococcus pneumoniae exhibits an alternative mechanism for reduction of susceptibility to beta-lactam antibiotics.
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J Biol Chem,
279,
16463-16470.
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PDB code:
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M.C.Wissel,
and
D.S.Weiss
(2004).
Genetic analysis of the cell division protein FtsI (PBP3): amino acid substitutions that impair septal localization of FtsI and recruitment of FtsN.
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J Bacteriol,
186,
490-502.
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A.M.Di Guilmi,
A.Dessen,
O.Dideberg,
and
T.Vernet
(2003).
Functional characterization of penicillin-binding protein 1b from Streptococcus pneumoniae.
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J Bacteriol,
185,
1650-1658.
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J.Errington,
R.A.Daniel,
and
D.J.Scheffers
(2003).
Cytokinesis in bacteria.
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Microbiol Mol Biol Rev,
67,
52.
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L.Cravello,
D.Lascoux,
and
E.Forest
(2003).
Use of different proteases working in acidic conditions to improve sequence coverage and resolution in hydrogen/deuterium exchange of large proteins.
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Rapid Commun Mass Spectrom,
17,
2387-2393.
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C.Goffin,
and
J.M.Ghuysen
(2002).
Biochemistry and comparative genomics of SxxK superfamily acyltransferases offer a clue to the mycobacterial paradox: presence of penicillin-susceptible target proteins versus lack of efficiency of penicillin as therapeutic agent.
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Microbiol Mol Biol Rev,
66,
702.
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D.Lim,
and
N.C.Strynadka
(2002).
Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus.
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Nat Struct Biol,
9,
870-876.
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PDB codes:
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L.Chesnel,
A.Zapun,
N.Mouz,
O.Dideberg,
and
T.Vernet
(2002).
Increase of the deacylation rate of PBP2x from Streptococcus pneumoniae by single point mutations mimicking the class A beta-lactamases.
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Eur J Biochem,
269,
1678-1683.
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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.
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Biochemistry,
40,
6233-6239.
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PDB code:
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K.Ubukata,
Y.Shibasaki,
K.Yamamoto,
N.Chiba,
K.Hasegawa,
Y.Takeuchi,
K.Sunakawa,
M.Inoue,
and
M.Konno
(2001).
Association of amino acid substitutions in penicillin-binding protein 3 with beta-lactam resistance in beta-lactamase-negative ampicillin-resistant Haemophilus influenzae.
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Antimicrob Agents Chemother,
45,
1693-1699.
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M.Ishiguro,
T.Nishihara,
and
R.Tanaka
(2001).
[New orally active penem antibiotic: Farom]
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Yakugaku Zasshi,
121,
915-927.
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W.Lee,
M.A.McDonough,
L.Kotra,
Z.H.Li,
N.R.Silvaggi,
Y.Takeda,
J.A.Kelly,
and
S.Mobashery
(2001).
A 1.2-A snapshot of the final step of bacterial cell wall biosynthesis.
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Proc Natl Acad Sci U S A,
98,
1427-1431.
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PDB code:
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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.
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Structure,
8,
971-980.
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PDB code:
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G.Zhao,
T.I.Meier,
J.Hoskins,
and
K.A.McAllister
(2000).
Identification and characterization of the penicillin-binding protein 2a of Streptococcus pneumoniae and its possible role in resistance to beta-lactam antibiotics.
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Antimicrob Agents Chemother,
44,
1745-1748.
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H.Jiang,
and
K.E.Kendrick
(2000).
Cloning and characterization of the gene encoding penicillin-binding protein A of Streptomyces griseus.
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FEMS Microbiol Lett,
193,
63-68.
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J.W.Anderson,
and
R.F.Pratt
(2000).
Dipeptide binding to the extended active site of the Streptomyces R61 D-alanyl-D-alanine-peptidase: the path to a specific substrate.
|
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Biochemistry,
39,
12200-12209.
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A.M.di Guilmi,
N.Mouz,
L.Martin,
J.Hoskins,
S.R.Jaskunas,
O.Dideberg,
and
T.Vernet
(1999).
Glycosyltransferase domain of penicillin-binding protein 2a from Streptococcus pneumoniae is membrane associated.
|
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J Bacteriol,
181,
2773-2781.
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E.Fonzé,
M.Vermeire,
M.Nguyen-Distèche,
R.Brasseur,
and
P.Charlier
(1999).
The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity. The DD-transpeptidase of streptomyces K15.
|
| |
J Biol Chem,
274,
21853-21860.
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PDB code:
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J.M.Ghuysen,
and
C.Goffin
(1999).
Lack of cell wall peptidoglycan versus penicillin sensitivity: new insights into the chlamydial anomaly.
|
| |
Antimicrob Agents Chemother,
43,
2339-2344.
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J.Paik,
I.Kern,
R.Lurz,
and
R.Hakenbeck
(1999).
Mutational analysis of the Streptococcus pneumoniae bimodular class A penicillin-binding proteins.
|
| |
J Bacteriol,
181,
3852-3856.
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N.Mouz,
A.M.Di Guilmi,
E.Gordon,
R.Hakenbeck,
O.Dideberg,
and
T.Vernet
(1999).
Mutations in the active site of penicillin-binding protein PBP2x from Streptococcus pneumoniae. Role in the specificity for beta-lactam antibiotics.
|
| |
J Biol Chem,
274,
19175-19180.
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R.Hakenbeck,
K.Kaminski,
A.König,
M.van der Linden,
J.Paik,
P.Reichmann,
and
D.Zähner
(1999).
Penicillin-binding proteins in beta-lactam-resistant streptococcus pneumoniae.
|
| |
Microb Drug Resist,
5,
91-99.
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Y.Asahi,
Y.Takeuchi,
and
K.Ubukata
(1999).
Diversity of substitutions within or adjacent to conserved amino acid motifs of penicillin-binding protein 2X in cephalosporin-resistant Streptococcus pneumoniae isolates.
|
| |
Antimicrob Agents Chemother,
43,
1252-1255.
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A.M.Di Guilmi,
N.Mouz,
J.P.Andrieu,
J.Hoskins,
S.R.Jaskunas,
J.Gagnon,
O.Dideberg,
and
T.Vernet
(1998).
Identification, purification, and characterization of transpeptidase and glycosyltransferase domains of Streptococcus pneumoniae penicillin-binding protein 1a.
|
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J Bacteriol,
180,
5652-5659.
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C.Goffin,
and
J.M.Ghuysen
(1998).
Multimodular penicillin-binding proteins: an enigmatic family of orthologs and paralogs.
|
| |
Microbiol Mol Biol Rev,
62,
1079-1093.
|
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I.Massova,
and
S.Mobashery
(1998).
Kinship and diversification of bacterial penicillin-binding proteins and beta-lactamases.
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| |
Antimicrob Agents Chemother,
42,
1.
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N.Mouz,
E.Gordon,
A.M.Di Guilmi,
I.Petit,
Y.Pétillot,
Y.Dupont,
R.Hakenbeck,
T.Vernet,
and
O.Dideberg
(1998).
Identification of a structural determinant for resistance to beta-lactam antibiotics in Gram-positive bacteria.
|
| |
Proc Natl Acad Sci U S A,
95,
13403-13406.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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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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