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| | ==CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA== | | ==CRYSTAL STRUCTURE DETERMINATION OF ASPARTATE RACEMASE FROM AN ARCHAEA== |
| - | <StructureSection load='1jfl' size='340' side='right' caption='[[1jfl]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='1jfl' size='340' side='right'caption='[[1jfl]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1jfl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JFL FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH0670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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=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> |
| - | <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=1jfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jfl OCA], [http://pdbe.org/1jfl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jfl RCSB], [http://www.ebi.ac.uk/pdbsum/1jfl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jfl ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RACD_PYRHO RACD_PYRHO] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jf/1jfl_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jf/1jfl_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aspartate racemase]] | + | [[Category: Large Structures]] |
| - | [[Category: Pyrococcus horikoshii]] | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | [[Category: Iwata, K]] | + | [[Category: Iwata K]] |
| - | [[Category: Kawarabayasi, Y]] | + | [[Category: Kawarabayasi Y]] |
| - | [[Category: Kita, A]] | + | [[Category: Kita A]] |
| - | [[Category: Liu, L J]] | + | [[Category: Liu LJ]] |
| - | [[Category: Miki, K]] | + | [[Category: Miki K]] |
| - | [[Category: Yohda, M]] | + | [[Category: Yohda M]] |
| - | [[Category: Alpha-beta structure]]
| + | |
| - | [[Category: Homo-dimer]]
| + | |
| - | [[Category: Homologous domain]]
| + | |
| - | [[Category: Isomerase]]
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| Structural highlights
Function
RACD_PYRHO
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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:12051922[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Liu L, Iwata K, Kita A, Kawarabayasi Y, Yohda M, Miki K. Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization. J Mol Biol. 2002 May 31;319(2):479-89. PMID:12051922 doi:10.1016/S0022-2836(02)00296-6
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