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| <StructureSection load='4y7p' size='340' side='right'caption='[[4y7p]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='4y7p' size='340' side='right'caption='[[4y7p]], [[Resolution|resolution]] 2.10Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[4y7p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y7P FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4y7p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y7P FirstGlance]. <br> |
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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]] 2.1Å</td></tr> |
- | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1396 ATCC 14579])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></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=4y7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y7p OCA], [http://pdbe.org/4y7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y7p RCSB], [http://www.ebi.ac.uk/pdbsum/4y7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y7p ProSAT]</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=4y7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y7p OCA], [https://pdbe.org/4y7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y7p RCSB], [https://www.ebi.ac.uk/pdbsum/4y7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y7p ProSAT]</span></td></tr> |
| </table> | | </table> |
| + | == Function == |
| + | [https://www.uniprot.org/uniprot/P94288_BACCE P94288_BACCE] |
| <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
- | [[Category: Atcc 14579]] | + | [[Category: Bacillus cereus]] |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
- | [[Category: Asano, Y]] | + | [[Category: Asano Y]] |
- | [[Category: Ishitsubo, E]] | + | [[Category: Ishitsubo E]] |
- | [[Category: Kawahara, N]] | + | [[Category: Kawahara N]] |
- | [[Category: Komeda, H]] | + | [[Category: Komeda H]] |
- | [[Category: Nakano, S]] | + | [[Category: Nakano S]] |
- | [[Category: Okazaki, S]] | + | [[Category: Okazaki S]] |
- | [[Category: Tokiwa, H]] | + | [[Category: Tokiwa H]] |
- | [[Category: Apo form]]
| + | |
- | [[Category: Hydrolase]]
| + | |
- | [[Category: Penicillin binding protein]]
| + | |
| Structural highlights
Function
P94288_BACCE
Publication Abstract from PubMed
Alkaline D-peptidase from Bacillus cereus DF4-B, called ADP, is a D-stereospecific endopeptidase reacting with oligopeptides containing D-phenylalanine (D-Phe) at N-terminal penultimate residue. ADP has attracted increasing attention because it is useful as a catalyst for synthesis of D-Phe oligopeptides or, with the help of substrate mimetics, L-amino acid peptides and proteins. Structure and functional analysis of ADP is expected to elucidate molecular mechanism of ADP. In this study, the crystal structure of ADP (apo) form was determined at 2.1 A resolution. The fold of ADP is similar to that of the class C penicillin-binding proteins of type-AmpH. Docking simulations and fragment molecular orbital analyses of two peptides, (D-Phe)4 and (D-Phe)2-(L-Phe)2, with the putative substrate binding sites of ADP indicated that the P1 residue of the peptide interacts with hydrophobic residues at the S1 site of ADP. Furthermore, molecular dynamics simulation of ADP for 50 nsec suggested that the ADP forms large cavity at the active site. Formation of the cavity suggested that the ADP has open state in the solution. For the ADP, having the open state is convenient to bind the peptides having bulky side chain, such as (D-Phe)4. Taken together, we predicted peptide recognition mechanism of ADP.
Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B.,Nakano S, Okazaki S, Ishitsubo E, Kawahara N, Komeda H, Tokiwa H, Asano Y Sci Rep. 2015 Sep 15;5:13836. doi: 10.1038/srep13836. PMID:26370172[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nakano S, Okazaki S, Ishitsubo E, Kawahara N, Komeda H, Tokiwa H, Asano Y. Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B. Sci Rep. 2015 Sep 15;5:13836. doi: 10.1038/srep13836. PMID:26370172 doi:http://dx.doi.org/10.1038/srep13836
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