6ezc: Difference between revisions
New page: '''Unreleased structure''' The entry 6ezc is ON HOLD until Paper Publication Authors: Charles, B.N., Damien, B., Ludovic, P., Vincent, G., Marc, F., Djemel, H. Description: Crystal Str... |
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==Crystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain E294K Q305K double mutant== | |||
<StructureSection load='6ezc' size='340' side='right' caption='[[6ezc]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6ezc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EZC FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6eza|6eza]], [[6ezb|6ezb]]</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=6ezc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ezc OCA], [http://pdbe.org/6ezc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ezc RCSB], [http://www.ebi.ac.uk/pdbsum/6ezc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ezc ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/DUS2L_HUMAN DUS2L_HUMAN]] Dihydrouridine synthase. Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. Negatively regulates the activation of EIF2AK2/PKR.<ref>PMID:15994936</ref> <ref>PMID:18096616</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Dihydrouridine (D) is an abundant modified base of tRNA found in the majority of living organisms. This base is synthesized via an NADPH-dependent reduction of specific uridines by the dihydrouridine synthases (Dus), a large family of flavoenzymes comprising eight subfamilies. Almost all of these enzymes function with only two conserved domains, an N-terminal catalytic domain (TBD) adopting a TIM barrel fold and a unique C-terminal helical domain (HD) devoted to tRNA recognition, except for the animal U20-specific Dus2 enzyme. Curiously, this enzyme is distinguished from paralogues and its fungi orthologues by the acquisition of an additional domain, a double stranded RNA binding domain (dsRBD), which serves as the main tRNA binding module. On the basis of a homology model of yeast Dus2 and the crystallographic structure of a human Dus2 variant (TBD + HD) lacking dsRBD, we herein show that the HD surface of the human enzyme is less electropositive than that of its yeast orthologue. This is partly due to two positively charged residues, K304 and K315, present in yeast and more broadly in fungi Dus2 that are replaced by E294 and Q305 in human and conserved among animals Dus2. By artificially reintroducing these positive charges in human Dus2 lacking dsRBD, we restored a functional tRNA binding in this enzyme variant. Altogether, these results suggest that the electrostatic potential changes of HD have likely played a key role in the emergence of a new tRNA binding mode among Dus2 enzymes. | |||
Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases.,Bou-Nader C, Bregeon D, Pecqueur L, Fontecave M, Hamdane D Biochemistry. 2018 Sep 18;57(37):5407-5414. doi: 10.1021/acs.biochem.8b00584., Epub 2018 Aug 31. PMID:30149704<ref>PMID:30149704</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6ezc" style="background-color:#fffaf0;"></div> | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bou-Nader, C]] | |||
[[Category: Bregeon, D]] | |||
[[Category: Fontecave, M]] | |||
[[Category: Hamdane, D]] | |||
[[Category: Vincent, G]] | [[Category: Vincent, G]] | ||
[[Category: | [[Category: Flavoprotein]] | ||
[[Category: | [[Category: Oxidoreductase]] | ||
[[Category: | [[Category: Rna binding protein]] | ||
[[Category: | [[Category: Trna processing]] | ||
Latest revision as of 11:10, 26 September 2018
Crystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain E294K Q305K double mutantCrystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain E294K Q305K double mutant
Structural highlights
Function[DUS2L_HUMAN] Dihydrouridine synthase. Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. Negatively regulates the activation of EIF2AK2/PKR.[1] [2] Publication Abstract from PubMedDihydrouridine (D) is an abundant modified base of tRNA found in the majority of living organisms. This base is synthesized via an NADPH-dependent reduction of specific uridines by the dihydrouridine synthases (Dus), a large family of flavoenzymes comprising eight subfamilies. Almost all of these enzymes function with only two conserved domains, an N-terminal catalytic domain (TBD) adopting a TIM barrel fold and a unique C-terminal helical domain (HD) devoted to tRNA recognition, except for the animal U20-specific Dus2 enzyme. Curiously, this enzyme is distinguished from paralogues and its fungi orthologues by the acquisition of an additional domain, a double stranded RNA binding domain (dsRBD), which serves as the main tRNA binding module. On the basis of a homology model of yeast Dus2 and the crystallographic structure of a human Dus2 variant (TBD + HD) lacking dsRBD, we herein show that the HD surface of the human enzyme is less electropositive than that of its yeast orthologue. This is partly due to two positively charged residues, K304 and K315, present in yeast and more broadly in fungi Dus2 that are replaced by E294 and Q305 in human and conserved among animals Dus2. By artificially reintroducing these positive charges in human Dus2 lacking dsRBD, we restored a functional tRNA binding in this enzyme variant. Altogether, these results suggest that the electrostatic potential changes of HD have likely played a key role in the emergence of a new tRNA binding mode among Dus2 enzymes. Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases.,Bou-Nader C, Bregeon D, Pecqueur L, Fontecave M, Hamdane D Biochemistry. 2018 Sep 18;57(37):5407-5414. doi: 10.1021/acs.biochem.8b00584., Epub 2018 Aug 31. PMID:30149704[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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