3wuh: Difference between revisions

Revision as of 05:31, 10 August 2022

Qri7 and AMP complex

Structural highlights

3wuh is a 2 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	AMP, ZN
Gene:	QRI7, YDL104C, D2366 (Baker's yeast)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[QRI7_YEAST] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine. Involved in mitochondrial genome maintenance.^[1] ^[2]

Publication Abstract from PubMed

N(6)-Threonylcarbamoyladenosine (t(6)A) is a modified tRNA base required for accuracy in translation. Qri7 is localized in yeast mitochondria and is involved in t(6)A biosynthesis. In t(6)A biosynthesis, threonylcarbamoyl-adenylate (TCA) is synthesized from threonine, bicarbonate and ATP, and the threonyl-carbamoyl group is transferred to adenine 37 of tRNA by Qri7. Qri7 alone is sufficient to catalyze the second step of the reaction, whereas the Qri7 homologues YgjD (in bacteria) and Kae1 (in archaea and eukaryotes) function as parts of multi-protein complexes. In this study, the crystal structure of Qri7 complexed with AMP (a part of TCA) has been determined at 2.94 A resolution in a new crystal form. The manner of AMP recognition is similar, with some minor variations, among the Qri7/Kae1/YgjD family proteins. The previously reported dimer formation was also observed in this new crystal form. Furthermore, a comparison with the structure of TobZ, which catalyzes a similar reaction to t(6)A biosynthesis, revealed the presence of a flexible loop that may be involved in tRNA binding.

Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP.,Tominaga T, Kobayashi K, Ishii R, Ishitani R, Nureki O Acta Crystallogr F Struct Biol Commun. 2014 Aug;70(Pt 8):1009-14. doi:, 10.1107/S2053230X14014046. Epub 2014 Jul 23. PMID:25084372^[3]

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

References

↑ Srinivasan M, Mehta P, Yu Y, Prugar E, Koonin EV, Karzai AW, Sternglanz R. The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. EMBO J. 2011 Mar 2;30(5):873-81. doi: 10.1038/emboj.2010.343. Epub 2010 Dec 24. PMID:21183954 doi:10.1038/emboj.2010.343
↑ El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crecy-Lagard V. A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J. 2011 Mar 2;30(5):882-93. doi: 10.1038/emboj.2010.363. Epub 2011 Feb 1. PMID:21285948 doi:10.1038/emboj.2010.363
↑ Tominaga T, Kobayashi K, Ishii R, Ishitani R, Nureki O. Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP. Acta Crystallogr F Struct Biol Commun. 2014 Aug;70(Pt 8):1009-14. doi:, 10.1107/S2053230X14014046. Epub 2014 Jul 23. PMID:25084372 doi:https://dx.doi.org/10.1107/S2053230X14014046

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OCA

[1] Srinivasan M, Mehta P, Yu Y, Prugar E, Koonin EV, Karzai AW, Sternglanz R. The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. EMBO J. 2011 Mar 2;30(5):873-81. doi: 10.1038/emboj.2010.343. Epub 2010 Dec 24. PMID:21183954 doi:10.1038/emboj.2010.343

[2] El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crecy-Lagard V. A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J. 2011 Mar 2;30(5):882-93. doi: 10.1038/emboj.2010.363. Epub 2011 Feb 1. PMID:21285948 doi:10.1038/emboj.2010.363

[3] Tominaga T, Kobayashi K, Ishii R, Ishitani R, Nureki O. Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP. Acta Crystallogr F Struct Biol Commun. 2014 Aug;70(Pt 8):1009-14. doi:, 10.1107/S2053230X14014046. Epub 2014 Jul 23. PMID:25084372 doi:https://dx.doi.org/10.1107/S2053230X14014046

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Qri7 and AMP complex==
-<StructureSection load='3wuh' size='340' side='right' caption='[[3wuh]], [[Resolution|resolution]] 2.94&Aring;' scene=''>
+<StructureSection load='3wuh' size='340' side='right'caption='[[3wuh]], [[Resolution|resolution]] 2.94&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3wuh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WUH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3wuh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">QRI7, YDL104C, D2366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">QRI7, YDL104C, D2366 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=3wuh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wuh OCA], [http://pdbe.org/3wuh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wuh RCSB], [http://www.ebi.ac.uk/pdbsum/3wuh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wuh ProSAT]</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=3wuh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wuh OCA], [https://pdbe.org/3wuh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wuh RCSB], [https://www.ebi.ac.uk/pdbsum/3wuh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wuh ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/QRI7_YEAST QRI7_YEAST]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine. Involved in mitochondrial genome maintenance.<ref>PMID:21183954</ref> <ref>PMID:21285948</ref>
+[[https://www.uniprot.org/uniprot/QRI7_YEAST QRI7_YEAST]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine. Involved in mitochondrial genome maintenance.<ref>PMID:21183954</ref> <ref>PMID:21285948</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Baker's yeast]]
+[[Category: Large Structures]]
 [[Category: Ishii, R]]
 [[Category: Ishitani, R]]

3wuh: Difference between revisions

Revision as of 05:31, 10 August 2022

Qri7 and AMP complex

Structural highlights

Function

Publication Abstract from PubMed

References

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