1w79: Difference between revisions

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-[[Image:1w79.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1w79", creates the "Structure Box" on the page.
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-{{STRUCTURE_1w79|  PDB=1w79  |  SCENE=  }}
-'''CRYSTAL STRUCTURE OF THE DD-TRANSPEPTIDASE-CARBOXYPEPTIDASE FROM ACTINOMADURA R39'''
+==Crystal structure of the DD-transpeptidase-carboxypeptidase from Actinomadura R39==
+<StructureSection load='1w79' size='340' side='right'caption='[[1w79]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1w79]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomadura_sp._R39 Actinomadura sp. R39]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W79 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1w79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w79 OCA], [https://pdbe.org/1w79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w79 RCSB], [https://www.ebi.ac.uk/pdbsum/1w79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w79 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DAC_ACTSP DAC_ACTSP] 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/w7/1w79_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/main_output.php?pdb_ID=1w79 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Actinomadura sp. R39 produces an exocellular DD-peptidase/penicillin-binding protein (PBP) whose primary structure is similar to that of Escherichia coli PBP4. It is characterized by a high beta-lactam-binding activity (second order rate constant for the acylation of the active site serine by benzylpenicillin: k2/K = 300 mm(-1) s(-1)). The crystal structure of the DD-peptidase from Actinomadura R39 was solved at a resolution of 1.8 angstroms by single anomalous dispersion at the cobalt resonance wavelength. The structure is composed of three domains: a penicillin-binding domain similar to the penicillin-binding domain of E. coli PBP5 and two domains of unknown function. In most multimodular PBPs, additional domains are generally located at the C or N termini of the penicillin-binding domain. In R39, the other two domains are inserted in the penicillin-binding domain, between the SXXK and SXN motifs, in a manner similar to "Matryoshka dolls." One of these domains is composed of a five-stranded beta-sheet with two helices on one side, and the other domain is a double three-stranded beta-sheet inserted in the previous domain. Additionally, the 2.4-angstroms structure of the acyl-enzyme complex of R39 with nitrocefin reveals the absence of active site conformational change upon binding the beta-lactams.
-==Overview==
+Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins.,Sauvage E, Herman R, Petrella S, Duez C, Bouillenne F, Frere JM, Charlier P J Biol Chem. 2005 Sep 2;280(35):31249-56. Epub 2005 Jun 29. PMID:15987687<ref>PMID:15987687</ref>
-Actinomadura sp. R39 produces an exocellular DD-peptidase/penicillin-binding protein (PBP) whose primary structure is similar to that of Escherichia coli PBP4. It is characterized by a high beta-lactam-binding activity (second order rate constant for the acylation of the active site serine by benzylpenicillin: k2/K = 300 mm(-1) s(-1)). The crystal structure of the DD-peptidase from Actinomadura R39 was solved at a resolution of 1.8 angstroms by single anomalous dispersion at the cobalt resonance wavelength. The structure is composed of three domains: a penicillin-binding domain similar to the penicillin-binding domain of E. coli PBP5 and two domains of unknown function. In most multimodular PBPs, additional domains are generally located at the C or N termini of the penicillin-binding domain. In R39, the other two domains are inserted in the penicillin-binding domain, between the SXXK and SXN motifs, in a manner similar to "Matryoshka dolls." One of these domains is composed of a five-stranded beta-sheet with two helices on one side, and the other domain is a double three-stranded beta-sheet inserted in the previous domain. Additionally, the 2.4-angstroms structure of the acyl-enzyme complex of R39 with nitrocefin reveals the absence of active site conformational change upon binding the beta-lactams.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-W79 is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W79 OCA].
+</div>
+<div class="pdbe-citations 1w79" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins., Sauvage E, Herman R, Petrella S, Duez C, Bouillenne F, Frere JM, Charlier P, J Biol Chem. 2005 Sep 2;280(35):31249-56. Epub 2005 Jun 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15987687 15987687]
+*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]]
-[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
-[[Category: Single protein]]
+== References ==
-[[Category: Charlier, P.]]
+<references/>
-[[Category: Duez, C.]]
+__TOC__
-[[Category: Frere, J M.]]
+</StructureSection>
-[[Category: Herman, R.]]
+[[Category: Actinomadura sp. R39]]
-[[Category: Petrella, S.]]
+[[Category: Large Structures]]
-[[Category: Sauvage, E.]]
+[[Category: Charlier P]]
-[[Category: Actinomadura]]
+[[Category: Duez C]]
-[[Category: Antibiotic resistance]]
+[[Category: Frere JM]]
-[[Category: Hydrolase]]
+[[Category: Herman R]]
-[[Category: Penicillin-binding]]
+[[Category: Petrella S]]
-[[Category: Peptidoglycan]]
+[[Category: Sauvage E]]
-[[Category: Transpeptidase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 13:15:14 2008''