2efx

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "2efx" [edit=sysop:move=sysop])
Current revision (08:39, 25 October 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2efx.png|left|200px]]
 
-
{{STRUCTURE_2efx| PDB=2efx | SCENE= }}
+
==The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine amide==
 +
<StructureSection load='2efx' size='340' side='right'caption='[[2efx]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 +
== Structural highlights ==
 +
<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>
 +
</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>
 +
<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>
 +
<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>
 +
</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/2efx_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=2efx 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 amide===
+
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>
-
{{ABSTRACT_PUBMED_18323628}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 2efx" style="background-color:#fffaf0;"></div>
-
[[2efx]] is a 6 chain structure with sequence 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=2EFX OCA].
+
== References ==
-
 
+
<references/>
-
==Reference==
+
__TOC__
-
<ref group="xtra">PMID:018323628</ref><references group="xtra"/>
+
</StructureSection>
-
[[Category: Ochrobactrum anthropi]]
+
[[Category: Brucella anthropi]]
-
[[Category: Asano, Y.]]
+
[[Category: Large Structures]]
-
[[Category: Komeda, H.]]
+
[[Category: Asano Y]]
-
[[Category: Mizushima, T.]]
+
[[Category: Komeda H]]
-
[[Category: Okazaki, S.]]
+
[[Category: Mizushima T]]
-
[[Category: Suzuki, A.]]
+
[[Category: Okazaki S]]
-
[[Category: Yamane, T.]]
+
[[Category: Suzuki A]]
-
[[Category: D-stereospecific amidase]]
+
[[Category: Yamane T]]
-
[[Category: Hydrolase]]
+
-
[[Category: L-phenylalanine amide]]
+
-
[[Category: Penicillin recognizing protein]]
+

Current revision

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

PDB ID 2efx

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2efx"
Personal tools