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| | <StructureSection load='1w8q' size='340' side='right'caption='[[1w8q]], [[Resolution|resolution]] 2.85Å' scene=''> | | <StructureSection load='1w8q' size='340' side='right'caption='[[1w8q]], [[Resolution|resolution]] 2.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1w8q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W8Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W8Q FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1w8q]] 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=1W8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W8Q FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.85Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1w79|1w79]], [[1w8y|1w8y]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1w8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w8q OCA], [https://pdbe.org/1w8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w8q RCSB], [https://www.ebi.ac.uk/pdbsum/1w8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w8q 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=1w8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w8q OCA], [http://pdbe.org/1w8q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w8q RCSB], [http://www.ebi.ac.uk/pdbsum/1w8q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1w8q ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DAC_ACTSP DAC_ACTSP]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors. | + | [https://www.uniprot.org/uniprot/DAC_ACTSP DAC_ACTSP] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Actinomadura sp]] | + | [[Category: Actinomadura sp. R39]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
| + | [[Category: Charlier P]] |
| - | [[Category: Charlier, P]] | + | [[Category: Duez C]] |
| - | [[Category: Duez, C]] | + | [[Category: Frere JM]] |
| - | [[Category: Frere, J M]] | + | [[Category: Herman R]] |
| - | [[Category: Herman, R]] | + | [[Category: Petrella S]] |
| - | [[Category: Petrella, S]] | + | [[Category: Sauvage E]] |
| - | [[Category: Sauvage, E]] | + | |
| - | [[Category: Actinomadura]]
| + | |
| - | [[Category: Antibiotic resistance]]
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| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Penicillin-binding]]
| + | |
| - | [[Category: Peptidoglycan]]
| + | |
| - | [[Category: Transpeptidase]]
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| Structural highlights
Function
DAC_ACTSP Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sauvage E, Herman R, Petrella S, Duez C, Bouillenne F, Frere JM, Charlier P. Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins. J Biol Chem. 2005 Sep 2;280(35):31249-56. Epub 2005 Jun 29. PMID:15987687 doi:10.1074/jbc.M503271200
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