1j9m: Difference between revisions

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 ==K38H mutant of Streptomyces K15 DD-transpeptidase==
-<StructureSection load='1j9m' size='340' side='right' caption='[[1j9m]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+<StructureSection load='1j9m' size='340' side='right'caption='[[1j9m]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1j9m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strsk Strsk]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1eqs 1eqs]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J9M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1j9m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._K15 Streptomyces sp. K15]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1eqs 1eqs]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J9M FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1skf|1skf]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9m OCA], [https://pdbe.org/1j9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j9m RCSB], [https://www.ebi.ac.uk/pdbsum/1j9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j9m ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9m OCA], [http://pdbe.org/1j9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j9m RCSB], [http://www.ebi.ac.uk/pdbsum/1j9m PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DACX_STRSK DACX_STRSK]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
+[https://www.uniprot.org/uniprot/DACX_STRSK DACX_STRSK] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j9/1j9m_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j9/1j9m_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1j9m ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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<ref>PMID:12627955</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1j9m" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Penicillin-binding protein|Penicillin-binding protein]]
+*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]]
-== References ==
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
+[[Category: Large Structures]]
-[[Category: Strsk]]
+[[Category: Streptomyces sp. K15]]
-[[Category: Charlier, P]]
+[[Category: Charlier P]]
-[[Category: Fonze, E]]
+[[Category: Fonze E]]
-[[Category: Nguyen-Disteche, M]]
+[[Category: Nguyen-Disteche M]]
-[[Category: Rhazi, N]]
+[[Category: Rhazi N]]
-[[Category: Beta-lactamase]]
-[[Category: Dd-transpeptidase]]
-[[Category: Hydrolase]]
-[[Category: Hydrolase carboxypeptidase]]
-[[Category: Penicillin-binding]]
-[[Category: Serine peptidase]]