3dxw: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
Line 1: Line 1:
{{STRUCTURE_3dxw|  PDB=3dxw  |  SCENE=  }}
==The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam==
===The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam===
<StructureSection load='3dxw' size='340' side='right' caption='[[3dxw]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
{{ABSTRACT_PUBMED_19146406}}
== Structural highlights ==
<table><tr><td colspan='2'>[[3dxw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_obae Achromobacter obae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DXW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DXW FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ICC:AZEPAN-2-ONE'>ICC</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dxv|3dxv]]</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dxw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dxw RCSB], [http://www.ebi.ac.uk/pdbsum/3dxw PDBsum]</span></td></tr>
</table>
== 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/dx/3dxw_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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Alpha-amino-epsilon-caprolactam (ACL) racemase (ACLR) from Achromobacter obae catalyzes the interconversion of l- and d-ACL. ACLR belongs to the fold-type I group of pyridoxal 5'-phosphate (PLP) dependent enzymes. In this study, the first crystal structures of a fold-type I racemase are solved for the native form and epsilon-caprolactam-complexed form of ACLR at 2.21 and 2.40 A resolution, respectively. Based on the location of epsilon-caprolactam in the complex structure, the substrate-binding site is assigned between Trp49 and Tyr137. The carboxyl group of Asp210 is a reasonable candidate that recognizes the nitrogen atom of a lactam or amide in the substrate. Based on a structural comparison with fold-type III alanine racemase, Tyr137 is potentially the acid/base catalytic residue that is essential for the two-base racemization mechanism. The overall structure of ACLR is similar to that of fold-type I enzymes. A structural comparison with these enzymes explains the different reaction specificities.


==About this Structure==
The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae.,Okazaki S, Suzuki A, Mizushima T, Kawano T, Komeda H, Asano Y, Yamane T Biochemistry. 2009 Feb 10;48(5):941-50. PMID:19146406<ref>PMID:19146406</ref>
[[3dxw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_obae Achromobacter obae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DXW OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<ref group="xtra">PMID:019146406</ref><references group="xtra"/><references/>
</div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Achromobacter obae]]
[[Category: Achromobacter obae]]
[[Category: Asano, Y.]]
[[Category: Asano, Y]]
[[Category: Komeda, H.]]
[[Category: Komeda, H]]
[[Category: Okazaki, S.]]
[[Category: Okazaki, S]]
[[Category: Suzuki, A.]]
[[Category: Suzuki, A]]
[[Category: Yamane, T.]]
[[Category: Yamane, T]]
[[Category: Fold-type1]]
[[Category: Fold-type1]]
[[Category: Isomerase]]
[[Category: Isomerase]]
[[Category: Pyridoxal phosphate]]
[[Category: Pyridoxal phosphate]]
[[Category: Pyridoxal-5'-phosphate dependent racemase]]
[[Category: Pyridoxal-5'-phosphate dependent racemase]]
Retrieved from "https://proteopedia.org/3dxw"