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1jfl

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(New page: 200px<br /><applet load="1jfl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jfl, resolution 1.90&Aring;" /> '''CRYSTAL STRUCTURE DE...)
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[[Image:1jfl.gif|left|200px]]<br /><applet load="1jfl" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1jfl, resolution 1.90&Aring;" />
 
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'''CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA==
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There exists a d-enantiomer of aspartic acid in lactic acid bacteria and, several hyperthermophilic archaea, which is biosynthesized from the, l-enantiomer by aspartate racemase. Aspartate racemase is a representative, pyridoxal 5'-phosphate (PLP)-independent amino acid racemase. The, "two-base" catalytic mechanism has been proposed for this type of, racemase, in which a pair of cysteine residues are utilized as the, conjugated catalytic acid and base. We have determined the, three-dimensional structure of aspartate racemase from the, hyperthermophilic archaeum Pyrococcus horikoshii OT3 at 1.9 A resolution, by X-ray crystallography and refined it to a crystallographic R factor of, 19.4% (R(free) of 22.2%). This is the first structure reported for, aspartate racemase, indeed for any amino acid racemase from archaea. The, crystal structure revealed that this enzyme forms a stable dimeric, structure with a strong three-layered inter-subunit interaction, and that, its subunit consists of two structurally homologous alpha/beta domains, each containing a four-stranded parallel beta-sheet flanked by six, alpha-helices. Two strictly conserved cysteine residues (Cys82 and, Cys194), which have been shown biochemically to act as catalytic acid and, base, are located on both sides of a cleft between the two domains. The, spatial arrangement of these two cysteine residues supports the "two-base", mechanism but disproves the previous hypothesis that the active site of, aspartate racemase is located at the dimeric interface. The structure, revealed a unique pseudo mirror-symmetry in the spatial arrangement of the, residues around the active site, which may explain the molecular, recognition mechanism of the mirror-symmetric aspartate enantiomers by the, non-mirror-symmetric aspartate racemase.
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<StructureSection load='1jfl' size='340' side='right'caption='[[1jfl]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1jfl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JFL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JFL FirstGlance]. <br>
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1JFL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Active as [http://en.wikipedia.org/wiki/Aspartate_racemase Aspartate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.13 5.1.1.13] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JFL OCA].
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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]] 1.9&#8491;</td></tr>
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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=1jfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jfl OCA], [https://pdbe.org/1jfl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jfl RCSB], [https://www.ebi.ac.uk/pdbsum/1jfl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jfl ProSAT]</span></td></tr>
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==Reference==
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</table>
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Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization., Liu L, Iwata K, Kita A, Kawarabayasi Y, Yohda M, Miki K, J Mol Biol. 2002 May 31;319(2):479-89. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12051922 12051922]
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== Function ==
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[[Category: Aspartate racemase]]
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[https://www.uniprot.org/uniprot/RACD_PYRHO RACD_PYRHO]
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[[Category: Pyrococcus horikoshii]]
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== Evolutionary Conservation ==
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[[Category: Single protein]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Iwata, K.]]
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Check<jmol>
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[[Category: Kawarabayasi, Y.]]
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<jmolCheckbox>
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[[Category: Kita, A.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jf/1jfl_consurf.spt"</scriptWhenChecked>
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[[Category: Liu, L.J.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: Miki, K.]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: Yohda, M.]]
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</jmolCheckbox>
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[[Category: alpha-beta structure]]
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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=1jfl ConSurf].
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[[Category: homo-dimer]]
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<div style="clear:both"></div>
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[[Category: homologous domains]]
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__TOC__
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</StructureSection>
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:34:17 2007''
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[[Category: Large Structures]]
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[[Category: Pyrococcus horikoshii OT3]]
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[[Category: Iwata K]]
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[[Category: Kawarabayasi Y]]
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[[Category: Kita A]]
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[[Category: Liu LJ]]
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[[Category: Miki K]]
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[[Category: Yohda M]]

Current revision

CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA

PDB ID 1jfl

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