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1w79

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[[Image:1w79.gif|left|200px]]<br />
 
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<applet load="1w79" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1w79, resolution 1.80&Aring;" />
 
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'''CRYSTAL STRUCTURE OF THE DD-TRANSPEPTIDASE-CARBOXYPEPTIDASE FROM ACTINOMADURA R39'''<br />
 
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==Overview==
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==Crystal structure of the DD-transpeptidase-carboxypeptidase from Actinomadura R39==
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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.
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<StructureSection load='1w79' size='340' side='right'caption='[[1w79]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</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>
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<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>
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DAC_ACTSP DAC_ACTSP] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w7/1w79_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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>
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1W79 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with SO4 and MG as [http://en.wikipedia.org/wiki/ligands ligands]. 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] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1W79 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=15987687 15987687]
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</div>
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[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
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<div class="pdbe-citations 1w79" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Charlier, P.]]
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[[Category: Duez, C.]]
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[[Category: Frere, J.M.]]
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[[Category: Herman, R.]]
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[[Category: Petrella, S.]]
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[[Category: Sauvage, E.]]
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[[Category: MG]]
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[[Category: SO4]]
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[[Category: actinomadura]]
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[[Category: antibiotic resistance]]
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[[Category: hydrolase]]
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[[Category: penicillin-binding]]
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[[Category: peptidoglycan]]
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[[Category: transpeptidase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 17:27:59 2007''
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==See Also==
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*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]]
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*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Actinomadura sp. R39]]
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[[Category: Large Structures]]
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[[Category: Charlier P]]
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[[Category: Duez C]]
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[[Category: Frere JM]]
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[[Category: Herman R]]
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[[Category: Petrella S]]
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[[Category: Sauvage E]]

Current revision

Crystal structure of the DD-transpeptidase-carboxypeptidase from Actinomadura R39

PDB ID 1w79

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