2efu: Difference between revisions

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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 2.30&Aring;" />
'''The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine'''<br />


==About this Structure==
==The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine==
2EFU 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=PHE:'>PHE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFU OCA].
<StructureSection load='2efu' size='340' side='right'caption='[[2efu]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
[[Category: Ochrobactrum anthropi]]
== Structural highlights ==
[[Category: Single protein]]
<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>
[[Category: Asano, Y.]]
</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>
[[Category: Komeda, H.]]
<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>
[[Category: Mizushima, T.]]
<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>
[[Category: Okazaki, S.]]
</table>
[[Category: Suzuki, A.]]
== Function ==
[[Category: Yamane, T.]]
[https://www.uniprot.org/uniprot/Q9LCC8_BRUAN Q9LCC8_BRUAN]  
[[Category: BA]]
== Evolutionary Conservation ==
[[Category: PHE]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: amidase]]
Check<jmol>
[[Category: d-stereospecific]]
  <jmolCheckbox>
[[Category: l-phenylalanine]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ef/2efu_consurf.spt"</scriptWhenChecked>
[[Category: penicillin recognizing proteins]]
    <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.


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:09:33 2008''
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&reg;/PubMed&reg;, 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]]
Retrieved from "https://proteopedia.org/2efu"