4gyi: Difference between revisions

Revision as of 07:26, 26 October 2022

Crystal structure of the Rio2 kinase-ADP/Mg2+-phosphoaspartate complex from Chaetomium thermophilum

Structural highlights

4gyi is a 1 chain structure with sequence from Chaetomium thermophilum var. thermophilum DSM 1495. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ADP, EDO, MG, PHD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G0S5R3_CHATD

Publication Abstract from PubMed

Ribosome synthesis involves dynamic association of ribosome-biogenesis factors with evolving preribosomal particles. Rio2 is an atypical protein kinase required for pre-40S subunit maturation. We report the crystal structure of eukaryotic Rio2-ATP-Mg(2+) complex. The active site contains ADP-Mg(2+) and a phosphoaspartate intermediate typically found in Na(+), K(+) and Ca(2+) ATPases but not protein kinases. Consistent with this finding, ctRio2 exhibits a robust ATPase activity in vitro. In vivo, Rio2 docks on the ribosome, with its active site occluded and its flexible loop positioned to interact with the pre-40S subunit. Moreover, Rio2 catalytic activity is required for its dissociation from the ribosome, a necessary step in pre-40S maturation. We propose that phosphoryl transfer from ATP to Asp257 in Rio2's active site and subsequent hydrolysis of the aspartylphosphate could be a trigger to power late cytoplasmic 40S subunit biogenesis.

ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit.,Ferreira-Cerca S, Sagar V, Schafer T, Diop M, Wesseling AM, Lu H, Chai E, Hurt E, Laronde-Leblanc N Nat Struct Mol Biol. 2012 Dec;19(12):1316-23. doi: 10.1038/nsmb.2403. Epub 2012, Oct 28. PMID:23104056^[1]

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

References

↑ Ferreira-Cerca S, Sagar V, Schafer T, Diop M, Wesseling AM, Lu H, Chai E, Hurt E, Laronde-Leblanc N. ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit. Nat Struct Mol Biol. 2012 Dec;19(12):1316-23. doi: 10.1038/nsmb.2403. Epub 2012, Oct 28. PMID:23104056 doi:https://dx.doi.org/10.1038/nsmb.2403

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OCA

[1] Ferreira-Cerca S, Sagar V, Schafer T, Diop M, Wesseling AM, Lu H, Chai E, Hurt E, Laronde-Leblanc N. ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit. Nat Struct Mol Biol. 2012 Dec;19(12):1316-23. doi: 10.1038/nsmb.2403. Epub 2012, Oct 28. PMID:23104056 doi:https://dx.doi.org/10.1038/nsmb.2403

[1]

@@ Line 1: / Line 1: @@
 ==Crystal structure of the Rio2 kinase-ADP/Mg2+-phosphoaspartate complex from Chaetomium thermophilum==
-<StructureSection load='4gyi' size='340' side='right' caption='[[4gyi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='4gyi' size='340' side='right'caption='[[4gyi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4gyi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chatd Chatd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GYI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GYI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4gyi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum_var._thermophilum_DSM_1495 Chaetomium thermophilum var. thermophilum DSM 1495]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GYI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GYI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHD:ASPARTYL+PHOSPHATE'>PHD</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PHD:ASPARTYL+PHOSPHATE'>PHD</scene></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=4gyi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gyi OCA], [https://pdbe.org/4gyi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gyi RCSB], [https://www.ebi.ac.uk/pdbsum/4gyi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gyi ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gyg|4gyg]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CTHT_0033330, Rio2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=759272 CHATD])</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=4gyi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gyi OCA], [http://pdbe.org/4gyi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gyi RCSB], [http://www.ebi.ac.uk/pdbsum/4gyi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gyi ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/G0S5R3_CHATD G0S5R3_CHATD]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 18: @@
 </div>
 <div class="pdbe-citations 4gyi" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Serine/threonine protein kinase 3D structures|Serine/threonine protein kinase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Chatd]]
+[[Category: Chaetomium thermophilum var. thermophilum DSM 1495]]
-[[Category: Chai, E]]
+[[Category: Large Structures]]
-[[Category: Diop, M]]
+[[Category: Chai E]]
-[[Category: Ferreira-Cerca, S]]
+[[Category: Diop M]]
-[[Category: Hurt, E]]
+[[Category: Ferreira-Cerca S]]
-[[Category: LaRonde-LeBlanc, N]]
+[[Category: Hurt E]]
-[[Category: Lu, H]]
+[[Category: LaRonde-LeBlanc N]]
-[[Category: Sagar, V]]
+[[Category: Lu H]]
-[[Category: Schafer, T]]
+[[Category: Sagar V]]
-[[Category: Wesseling, A M]]
+[[Category: Schafer T]]
-[[Category: Acyl-phosphate]]
+[[Category: Wesseling AM]]
-[[Category: Adp complex]]
-[[Category: Phosphoaspartate]]
-[[Category: Phosphorylation]]
-[[Category: Pre-40]]
-[[Category: Pre-40s maturation]]
-[[Category: Protein kinase]]
-[[Category: Ribosomal rna processing]]
-[[Category: Ribosome biogenesis]]
-[[Category: Ser/thr protein kinase]]
-[[Category: Transferase]]

4gyi: Difference between revisions

Revision as of 07:26, 26 October 2022

Crystal structure of the Rio2 kinase-ADP/Mg2+-phosphoaspartate complex from Chaetomium thermophilum

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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