1j9m: Difference between revisions
New page: left|200px<br /><applet load="1j9m" size="450" color="white" frame="true" align="right" spinBox="true" caption="1j9m, resolution 1.65Å" /> '''K38H mutant of Strep... |
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[[Image:1j9m.jpg|left|200px]]<br /><applet load="1j9m" size=" | [[Image:1j9m.jpg|left|200px]]<br /><applet load="1j9m" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1j9m, resolution 1.65Å" /> | caption="1j9m, resolution 1.65Å" /> | ||
'''K38H mutant of Streptomyces K15 DD-transpeptidase'''<br /> | '''K38H mutant of Streptomyces K15 DD-transpeptidase'''<br /> | ||
==Overview== | ==Overview== | ||
The Streptomyces K15 penicillin-binding DD-transpeptidase is presumed to | The Streptomyces K15 penicillin-binding DD-transpeptidase is presumed to be involved in peptide cross-linking during bacterial cell wall peptidoglycan assembly. To gain insight into the catalytic mechanism, the roles of residues Lys38, Ser96, and Cys98, belonging to the structural elements defining the active site cleft, have been investigated by site-directed mutagenesis, biochemical studies, and X-ray diffraction analysis. The Lys38His and Ser96Ala mutations almost completely abolished the penicillin binding and severely impaired the transpeptidase activities while the geometry of the active site was essentially the same as in the wild-type enzyme. It is proposed that Lys38 acts as the catalytic base that abstracts a proton from the active serine Ser35 during nucleophilic attack and that Ser96 is a key intermediate in the proton transfer from the Ogamma of Ser35 to the substrate leaving group nitrogen. The role of these two residues should be conserved among penicillin-binding proteins containing the Ser-Xaa-Asn/Cys sequence in motif 2. Conversion of Cys98 into Asn decreased the transpeptidase activity and increased hydrolysis of the thiolester substrate and the acylation rate with most beta-lactam antibiotics. Cys98 is proposed to play the same role as Asn in motif 2 of other penicilloyl serine transferases in properly positioning the substrate for the catalytic process. | ||
==About this Structure== | ==About this Structure== | ||
1J9M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.] with NA and CL as [http://en.wikipedia.org/wiki/ligands ligands]. This structure | 1J9M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.] with <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1EQS. Active as [http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9M OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: serine peptidase]] | [[Category: serine peptidase]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:20:09 2008'' | ||
Revision as of 14:20, 21 February 2008
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K38H mutant of Streptomyces K15 DD-transpeptidase
OverviewOverview
The Streptomyces K15 penicillin-binding DD-transpeptidase is presumed to be involved in peptide cross-linking during bacterial cell wall peptidoglycan assembly. To gain insight into the catalytic mechanism, the roles of residues Lys38, Ser96, and Cys98, belonging to the structural elements defining the active site cleft, have been investigated by site-directed mutagenesis, biochemical studies, and X-ray diffraction analysis. The Lys38His and Ser96Ala mutations almost completely abolished the penicillin binding and severely impaired the transpeptidase activities while the geometry of the active site was essentially the same as in the wild-type enzyme. It is proposed that Lys38 acts as the catalytic base that abstracts a proton from the active serine Ser35 during nucleophilic attack and that Ser96 is a key intermediate in the proton transfer from the Ogamma of Ser35 to the substrate leaving group nitrogen. The role of these two residues should be conserved among penicillin-binding proteins containing the Ser-Xaa-Asn/Cys sequence in motif 2. Conversion of Cys98 into Asn decreased the transpeptidase activity and increased hydrolysis of the thiolester substrate and the acylation rate with most beta-lactam antibiotics. Cys98 is proposed to play the same role as Asn in motif 2 of other penicilloyl serine transferases in properly positioning the substrate for the catalytic process.
About this StructureAbout this Structure
1J9M is a Single protein structure of sequence from Streptomyces sp. with and as ligands. This structure supersedes the now removed PDB entry 1EQS. Active as Serine-type D-Ala-D-Ala carboxypeptidase, with EC number 3.4.16.4 Full crystallographic information is available from OCA.
ReferenceReference
Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis., Rhazi N, Charlier P, Dehareng D, Engher D, Vermeire M, Frere JM, Nguyen-Disteche M, Fonze E, Biochemistry. 2003 Mar 18;42(10):2895-906. PMID:12627955
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