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2efx

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[[Image:2efx.jpg|left|200px]]<br /><applet load="2efx" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2efx, resolution 2.20&Aring;" />
 
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'''The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine amide'''<br />
 
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==About this Structure==
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==The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine amide==
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2EFX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Ochrobactrum_anthropi Ochrobactrum anthropi] with <scene name='pdbligand=BA:'>BA</scene> and <scene name='pdbligand=NFA:'>NFA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Ba+Binding+Site+For+Residue+C+3001'>AC1</scene>, <scene name='pdbsite=AC2:Ba+Binding+Site+For+Residue+B+3002'>AC2</scene>, <scene name='pdbsite=AC3:Ba+Binding+Site+For+Residue+A+3003'>AC3</scene>, <scene name='pdbsite=AC4:Ba+Binding+Site+For+Residue+A+3004'>AC4</scene>, <scene name='pdbsite=AC5:Ba+Binding+Site+For+Residue+C+3005'>AC5</scene>, <scene name='pdbsite=AC6:Ba+Binding+Site+For+Residue+B+3007'>AC6</scene>, <scene name='pdbsite=AC7:Ba+Binding+Site+For+Residue+A+3008'>AC7</scene>, <scene name='pdbsite=AC8:Ba+Binding+Site+For+Residue+B+3009'>AC8</scene>, <scene name='pdbsite=AC9:Ba+Binding+Site+For+Residue+C+3010'>AC9</scene>, <scene name='pdbsite=BC1:Ba+Binding+Site+For+Residue+E+3011'>BC1</scene>, <scene name='pdbsite=BC2:Ba+Binding+Site+For+Residue+C+3012'>BC2</scene>, <scene name='pdbsite=BC3:Ba+Binding+Site+For+Residue+D+3013'>BC3</scene>, <scene name='pdbsite=BC4:Ba+Binding+Site+For+Residue+E+3014'>BC4</scene>, <scene name='pdbsite=BC5:Ba+Binding+Site+For+Residue+D+3015'>BC5</scene>, <scene name='pdbsite=BC6:Ba+Binding+Site+For+Residue+D+3016'>BC6</scene>, <scene name='pdbsite=BC7:Ba+Binding+Site+For+Residue+A+3017'>BC7</scene>, <scene name='pdbsite=BC8:Ba+Binding+Site+For+Residue+E+3019'>BC8</scene>, <scene name='pdbsite=BC9:Ba+Binding+Site+For+Residue+D+3020'>BC9</scene>, <scene name='pdbsite=CC1:Nfa+Binding+Site+For+Residue+A+2001'>CC1</scene>, <scene name='pdbsite=CC2:Nfa+Binding+Site+For+Residue+B+2002'>CC2</scene>, <scene name='pdbsite=CC3:Nfa+Binding+Site+For+Residue+C+2003'>CC3</scene>, <scene name='pdbsite=CC4:Nfa+Binding+Site+For+Residue+D+2004'>CC4</scene>, <scene name='pdbsite=CC5:Nfa+Binding+Site+For+Residue+E+2005'>CC5</scene> and <scene name='pdbsite=CC6:Nfa+Binding+Site+For+Residue+F+2006'>CC6</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFX OCA].
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<StructureSection load='2efx' size='340' side='right'caption='[[2efx]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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[[Category: Ochrobactrum anthropi]]
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== Structural highlights ==
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[[Category: Single protein]]
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<table><tr><td colspan='2'>[[2efx]] 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=2EFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EFX FirstGlance]. <br>
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[[Category: Asano, Y.]]
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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]] 2.2&#8491;</td></tr>
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[[Category: Komeda, H.]]
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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=NFA:PHENYLALANINE+AMIDE'>NFA</scene></td></tr>
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[[Category: Mizushima, T.]]
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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=2efx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efx OCA], [https://pdbe.org/2efx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2efx RCSB], [https://www.ebi.ac.uk/pdbsum/2efx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2efx ProSAT]</span></td></tr>
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[[Category: Okazaki, S.]]
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</table>
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[[Category: Suzuki, A.]]
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== Function ==
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[[Category: Yamane, T.]]
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[https://www.uniprot.org/uniprot/Q9LCC8_BRUAN Q9LCC8_BRUAN]
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[[Category: BA]]
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== Evolutionary Conservation ==
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[[Category: NFA]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: d-stereospecific amidase]]
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Check<jmol>
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[[Category: hydrolase]]
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<jmolCheckbox>
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[[Category: l-phenylalanine amide]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ef/2efx_consurf.spt"</scriptWhenChecked>
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[[Category: penicillin recognizing protein]]
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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=2efx 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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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 5 13:25:23 2008''
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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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</div>
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<div class="pdbe-citations 2efx" style="background-color:#fffaf0;"></div>
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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: Brucella anthropi]]
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[[Category: Large Structures]]
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[[Category: Asano Y]]
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[[Category: Komeda H]]
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[[Category: Mizushima T]]
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[[Category: Okazaki S]]
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[[Category: Suzuki A]]
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[[Category: Yamane T]]

Current revision

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

PDB ID 2efx

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