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1w8y

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(New page: 200px<br /> <applet load="1w8y" size="450" color="white" frame="true" align="right" spinBox="true" caption="1w8y, resolution 2.40&Aring;" /> '''CRYSTAL STRUCTURE O...)
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[[Image:1w8y.gif|left|200px]]<br />
 
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<applet load="1w8y" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1w8y, resolution 2.40&Aring;" />
 
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'''CRYSTAL STRUCTURE OF THE NITROCEFIN ACYL-DD-PEPTIDASE FROM ACTINOMADURA R39.'''<br />
 
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==Overview==
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==Crystal structure of the nitrocefin acyl-DD-peptidase 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, ... [[http://ispc.weizmann.ac.il/pmbin/getpm?15987687 (full description)]]
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<StructureSection load='1w8y' size='340' side='right'caption='[[1w8y]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1w8y]] 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=1W8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W8Y 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]] 2.4&#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=NCF:(2R)-2-{(1R)-2-OXO-1-[(2-THIENYLACETYL)AMINO]ETHYL}-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC+ACID'>NCF</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=1w8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w8y OCA], [https://pdbe.org/1w8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w8y RCSB], [https://www.ebi.ac.uk/pdbsum/1w8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w8y 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/w8/1w8y_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=1w8y 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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1W8Y is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Actinomadura Actinomadura]] with SO4, MG and NCF as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/ ]], 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1W8Y 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: Actinomadura]]
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<div class="pdbe-citations 1w8y" 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: NCF]]
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[[Category: SO4]]
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[[Category: actinomadura]]
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[[Category: nitrocefin]]
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[[Category: penicillin-binding]]
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[[Category: peptidoglycan]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Oct 29 21:24:23 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 nitrocefin acyl-DD-peptidase from Actinomadura R39.

PDB ID 1w8y

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