2efu: Difference between revisions

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{{Seed}}
[[Image:2efu.png|left|200px]]


<!--
==The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine==
The line below this paragraph, containing "STRUCTURE_2efu", creates the "Structure Box" on the page.
<StructureSection load='2efu' size='340' side='right'caption='[[2efu]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
-->
<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>
{{STRUCTURE_2efu|  PDB=2efu  |  SCENE=  }}
<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.


===The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine===
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>
The line below this paragraph, {{ABSTRACT_PUBMED_18323628}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2efu" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 18323628 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18323628}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Brucella anthropi]]
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].
[[Category: Large Structures]]
 
[[Category: Asano Y]]
==Reference==
[[Category: Komeda H]]
<ref group="xtra">PMID:18323628</ref><references group="xtra"/>
[[Category: Mizushima T]]
[[Category: Ochrobactrum anthropi]]
[[Category: Okazaki S]]
[[Category: Asano, Y.]]
[[Category: Suzuki A]]
[[Category: Komeda, H.]]
[[Category: Yamane T]]
[[Category: Mizushima, T.]]
[[Category: Okazaki, S.]]
[[Category: Suzuki, A.]]
[[Category: Yamane, T.]]
[[Category: Amidase]]
[[Category: D-stereospecific]]
[[Category: Hydrolase]]
[[Category: L-phenylalanine]]
[[Category: Penicillin recognizing protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 11:13:34 2009''

Latest revision as of 08:39, 25 October 2023

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

2efu, resolution 2.30Å

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