3lmt

From Proteopedia

(Difference between revisions)

Revision as of 18:31, 9 February 2016

Crystal strucutre of DTD from Plasmodium falciparum

Structural highlights

3lmt is a 6 chain structure with sequence from Plaf7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3knf, 3knp, 3ko3, 3ko4, 3ko5, 3ko7, 3ko9, 3kob, 3koc, 3kod, 3lmu, 3lmv
Gene:	DTD, PF11_0095 (PLAF7)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[Q8IIS0_PLAF7] Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (By similarity).[RuleBase:RU003470]

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

D-Tyrosyl-tRNA(Tyr) deacylase (DTD) is an editing enzyme that removes D-amino acids from mischarged tRNAs. The crystal structure of Plasmodium falciparum DTD (PfDTD) was determined using the iodide-SAD phasing method. Iodide-derivatized PfDTD crystals were obtained using the quick cryo-soaking procedure in which native crystals were soaked for a short period of 10-30 s in cryoprotectant solution containing 0.2-1 M NaI. Iodide-SAD data sets were collected to 3.3 and 2.74 A resolution from PfDTD crystals that belonged to two different space groups, P4(3) and P1, using an in-house X-ray copper-anode source. This is the first report to detail structure solution using low iodide anomalous signal, modest resolution and redundancy and average solvent content for SAD phasing of 984 and 1312 amino acids in the triclinic P1 and tetragonal P4(3) space groups, respectively. A total of 85% and 56% of the residues were automatically built into the iodide-phased electron-density maps using PHENIX AutoBuild. The structure of HEPES-bound PfDTD was subsequently determined by molecular replacement and refined to 2.83 A resolution. The crystals obtained from various batches of crystallization trials of PfDTD exhibited polymorphism in terms of belonging to different crystal forms and space groups. Even within a given crystal system the unit-cell parameters showed high non-isomorphism. These packing variations were exploited in order to conduct a systematic study of conformational changes in PfDTD. It is shown that the disposition of a ten-residue insertion loop affects packing within the PfDTD crystals and seems to determine the non-isomorphism in unit-cell parameters. By tracking the changes in PfDTD unit cells, it was possible to map conformational differences within PfDTD that may be of significance for enzyme activity.

Structure of D-tyrosyl-tRNATyr deacylase using home-source Cu Kalpha and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme states.,Yogavel M, Khan S, Bhatt TK, Sharma A Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):584-92. Epub 2010, Apr 21. PMID:20445234^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yogavel M, Khan S, Bhatt TK, Sharma A. Structure of D-tyrosyl-tRNATyr deacylase using home-source Cu Kalpha and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme states. Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):584-92. Epub 2010, Apr 21. PMID:20445234 doi:10.1107/S0907444910006062

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3lmt"

@@ Line 2: / Line 2: @@
 <StructureSection load='3lmt' size='340' side='right' caption='[[3lmt]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lmt]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LMT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LMT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lmt]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Plaf7 Plaf7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LMT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LMT FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3knf|3knf]], [[3knp|3knp]], [[3ko3|3ko3]], [[3ko4|3ko4]], [[3ko5|3ko5]], [[3ko7|3ko7]], [[3ko9|3ko9]], [[3kob|3kob]], [[3koc|3koc]], [[3kod|3kod]], [[3lmu|3lmu]], [[3lmv|3lmv]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DTD, PF11_0095 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5833 Plasmodium falciparum])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DTD, PF11_0095 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36329 PLAF7])</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=3lmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lmt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lmt RCSB], [http://www.ebi.ac.uk/pdbsum/3lmt PDBsum]</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=3lmt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lmt OCA], [http://pdbe.org/3lmt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lmt RCSB], [http://www.ebi.ac.uk/pdbsum/3lmt PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 18: @@
     <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].
+</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=3lmt ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3lmt" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Plasmodium falciparum]]
+[[Category: Plaf7]]
 [[Category: Bhatt, T K]]
 [[Category: Khan, S]]

3lmt

From Proteopedia

Revision as of 18:31, 9 February 2016

Crystal strucutre of DTD from Plasmodium falciparum

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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