5b19: Difference between revisions
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The | ==Picrophilus torridus aspartate racemase== | ||
<StructureSection load='5b19' size='340' side='right' caption='[[5b19]], [[Resolution|resolution]] 1.85Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5b19]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B19 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B19 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5b19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b19 OCA], [http://pdbe.org/5b19 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b19 RCSB], [http://www.ebi.ac.uk/pdbsum/5b19 PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Functional and structural characterizations of pyridoxal 5'-phosphate-independent aspartate racemase of the acidothermophilic archaeon Picrophilus torridus were performed. Picrophilus aspartate racemase exhibited high substrate specificity to aspartic acid. The optimal reaction temperature was 60 degrees C, which is almost the same as the optimal growth temperature. Reflecting the low pH in the cytosol, the optimal reaction pH of Picrophilus aspartate racemase was approximately 5.5. However, the activity at the putative cytosolic pH of 4.6 was approximately 6 times lower than that at the optimal pH of 5.5. The crystal structure of Picrophilus aspartate racemase was almost the same as that of other pyridoxal 5'-phosphate -independent aspartate racemases. In two molecules of the dimer, one molecule contained a tartaric acid molecule in the catalytic site; the structure of the other molecule was relatively flexible. Finally, we examined the intracellular existence of D-amino acids. Unexpectedly, the proportion of D-aspartate to total aspartate was not very high. In contrast, both D-proline and D-alanine were observed. Because Picrophilus aspartate racemase is highly specific to aspartate, other amino acid racemases might exist in Picrophilus torridus. | |||
Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus.,Aihara T, Ito T, Yamanaka Y, Noguchi K, Odaka M, Sekine M, Homma H, Yohda M Extremophiles. 2016 Apr 19. PMID:27094682<ref>PMID:27094682</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 5b19" style="background-color:#fffaf0;"></div> | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Aspartate racemase]] | |||
[[Category: Aihara, T]] | [[Category: Aihara, T]] | ||
[[Category: Homma, H]] | [[Category: Homma, H]] | ||
[[Category: Ito, T]] | |||
[[Category: Noguchi, K]] | |||
[[Category: Odaka, M]] | |||
[[Category: Sekine, M]] | |||
[[Category: Yamanaka, Y]] | [[Category: Yamanaka, Y]] | ||
[[Category: Yohda, M]] | [[Category: Yohda, M]] | ||
[[Category: | [[Category: Archaea]] | ||
[[Category: D-amino acid]] | |||
[[Category: Isomerase]] | |||
[[Category: Picrophilus torridus]] | |||
Revision as of 02:20, 24 June 2016
Picrophilus torridus aspartate racemasePicrophilus torridus aspartate racemase
Structural highlights
Publication Abstract from PubMedFunctional and structural characterizations of pyridoxal 5'-phosphate-independent aspartate racemase of the acidothermophilic archaeon Picrophilus torridus were performed. Picrophilus aspartate racemase exhibited high substrate specificity to aspartic acid. The optimal reaction temperature was 60 degrees C, which is almost the same as the optimal growth temperature. Reflecting the low pH in the cytosol, the optimal reaction pH of Picrophilus aspartate racemase was approximately 5.5. However, the activity at the putative cytosolic pH of 4.6 was approximately 6 times lower than that at the optimal pH of 5.5. The crystal structure of Picrophilus aspartate racemase was almost the same as that of other pyridoxal 5'-phosphate -independent aspartate racemases. In two molecules of the dimer, one molecule contained a tartaric acid molecule in the catalytic site; the structure of the other molecule was relatively flexible. Finally, we examined the intracellular existence of D-amino acids. Unexpectedly, the proportion of D-aspartate to total aspartate was not very high. In contrast, both D-proline and D-alanine were observed. Because Picrophilus aspartate racemase is highly specific to aspartate, other amino acid racemases might exist in Picrophilus torridus. Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus.,Aihara T, Ito T, Yamanaka Y, Noguchi K, Odaka M, Sekine M, Homma H, Yohda M Extremophiles. 2016 Apr 19. PMID:27094682[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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