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2zuk

From Proteopedia

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{{Seed}}
 
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[[Image:2zuk.jpg|left|200px]]
 
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==The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam (different binding mode)==
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The line below this paragraph, containing "STRUCTURE_2zuk", creates the "Structure Box" on the page.
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<StructureSection load='2zuk' size='340' side='right'caption='[[2zuk]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2zuk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_obae Achromobacter obae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZUK FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.41&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ICC:AZEPAN-2-ONE'>ICC</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
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{{STRUCTURE_2zuk| PDB=2zuk | SCENE= }}
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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=2zuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zuk OCA], [https://pdbe.org/2zuk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zuk RCSB], [https://www.ebi.ac.uk/pdbsum/2zuk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zuk ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ACLR_ACHOB ACLR_ACHOB] catalyzes the interconversion of L-alpha-amino-epsilon-caprolactam and D-alpha-amino-epsilon-caprolactam.<ref>PMID:19146406</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zu/2zuk_consurf.spt"</scriptWhenChecked>
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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=2zuk 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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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.
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===The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam (different binding mode)===
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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>
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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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The line below this paragraph, {{ABSTRACT_PUBMED_19146406}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2zuk" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19146406 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19146406}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2ZUK is a 2 chains structure of sequences 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=2ZUK OCA].
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==Reference==
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<ref group="xtra">PMID:19146406</ref><references group="xtra"/>
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[[Category: Achromobacter obae]]
[[Category: Achromobacter obae]]
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[[Category: Asano, Y.]]
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[[Category: Large Structures]]
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[[Category: Komeda, H.]]
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[[Category: Asano Y]]
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[[Category: Okazaki, S.]]
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[[Category: Komeda H]]
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[[Category: Suzuki, A.]]
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[[Category: Okazaki S]]
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[[Category: Yamane, T.]]
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[[Category: Suzuki A]]
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[[Category: Fold-type1]]
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[[Category: Yamane T]]
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[[Category: Isomerase]]
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[[Category: Pyridoxal phosphate]]
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[[Category: Pyridoxal-5'-phosphate dependent racemase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:06:58 2009''
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Current revision

The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam (different binding mode)

PDB ID 2zuk

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