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2efu
From Proteopedia
(Difference between revisions)
(New page: 200px<br /><applet load="2efu" size="350" color="white" frame="true" align="right" spinBox="true" caption="2efu, resolution 2.30Å" /> '''The crystal structur...) |
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| - | [[Image:2efu.jpg|left|200px]]<br /><applet load="2efu" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2efu, resolution 2.30Å" /> | ||
| - | '''The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine'''<br /> | ||
| - | == | + | ==The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine== |
| - | + | <StructureSection load='2efu' size='340' side='right'caption='[[2efu]], [[Resolution|resolution]] 2.30Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | [ | + | <table><tr><td colspan='2'>[[2efu]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Brucella_anthropi Brucella anthropi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EFU 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]] 2.3Å</td></tr> |
| - | [ | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</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=2efu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efu OCA], [https://pdbe.org/2efu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2efu RCSB], [https://www.ebi.ac.uk/pdbsum/2efu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2efu ProSAT]</span></td></tr> |
| - | [[ | + | </table> |
| - | + | == Function == | |
| - | + | [https://www.uniprot.org/uniprot/Q9LCC8_BRUAN Q9LCC8_BRUAN] | |
| - | [ | + | == 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/ef/2efu_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=2efu ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The crystal structures of D-amino-acid amidase (DAA) from Ochrobactrum anthropi SV3 in complex with L-phenylalanine and with L-phenylalanine amide were determined at 2.3 and 2.2 A resolution, respectively. Comparison of the L-phenylalanine amide complex with the D-phenylalanine complex reveals that the D-stereospecificity of DAA might be achieved as a consequence of three structural factors: (i) the hydrophobic cavity in the region in which the hydrophobic side chain of the substrate is held, (ii) the spatial arrangement of Gln310 O and Glu114 O epsilon2 that fixes the amino N atom of the substrate and (iii) the existence of two cavities that keep the carboxyl/amide group of the substrate near or apart from Ser60 O gamma. | ||
| - | + | Structures of D-amino-acid amidase complexed with L-phenylalanine and with L-phenylalanine amide: insight into the D-stereospecificity of D-amino-acid amidase from Ochrobactrum anthropi SV3.,Okazaki S, Suzuki A, Mizushima T, Komeda H, Asano Y, Yamane T Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):331-4. Epub 2008, Feb 20. PMID:18323628<ref>PMID:18323628</ref> | |
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 2efu" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Brucella anthropi]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Asano Y]] | ||
| + | [[Category: Komeda H]] | ||
| + | [[Category: Mizushima T]] | ||
| + | [[Category: Okazaki S]] | ||
| + | [[Category: Suzuki A]] | ||
| + | [[Category: Yamane T]] | ||
Current revision
The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine
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