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2efu

From Proteopedia

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{{Seed}}
 
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[[Image:2efu.png|left|200px]]
 
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==The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine==
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The line below this paragraph, containing "STRUCTURE_2efu", creates the "Structure Box" on the page.
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<StructureSection load='2efu' size='340' side='right'caption='[[2efu]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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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]] 2.3&#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=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene></td></tr>
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{{STRUCTURE_2efu| PDB=2efu | SCENE= }}
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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=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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9LCC8_BRUAN Q9LCC8_BRUAN]
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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/ef/2efu_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=2efu 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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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.
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===The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==About this Structure==
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</div>
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2EFU is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Ochrobactrum_anthropi Ochrobactrum anthropi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFU OCA].
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<div class="pdbe-citations 2efu" style="background-color:#fffaf0;"></div>
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[[Category: Ochrobactrum anthropi]]
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== References ==
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[[Category: Asano, Y.]]
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<references/>
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[[Category: Komeda, H.]]
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__TOC__
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[[Category: Mizushima, T.]]
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</StructureSection>
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[[Category: Okazaki, S.]]
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[[Category: Brucella anthropi]]
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[[Category: Suzuki, A.]]
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[[Category: Large Structures]]
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[[Category: Yamane, T.]]
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[[Category: Asano Y]]
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[[Category: Amidase]]
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[[Category: Komeda H]]
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[[Category: D-stereospecific]]
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[[Category: Mizushima T]]
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[[Category: Hydrolase]]
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[[Category: Okazaki S]]
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[[Category: L-phenylalanine]]
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[[Category: Suzuki A]]
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[[Category: Penicillin recognizing protein]]
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[[Category: Yamane T]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:03:23 2009''
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Current revision

The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine

PDB ID 2efu

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