5hci: Difference between revisions

Latest revision as of 07:30, 9 August 2023

GPN-loop GTPase Npa3 in complex with GDP

Structural highlights

5hci is a 6 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	GDP, GOL, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GPN1_YEAST Small GTPase required for proper nuclear import of RNA polymerase II (RNAPII) (PubMed:20855544, PubMed:21844196). May act at an RNAP assembly step prior to nuclear import (PubMed:23267056). Promotes sister chromatid separation during anaphase (PubMed:21532343).^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Biogenesis of the 12-subunit RNA polymerase II (Pol II) transcription complex requires so-called GPN-loop GTPases, but the function of these enzymes is unknown. Here we report the first crystal structure of a eukaryotic GPN-loop GTPase, the S. cerevisiae enzyme Npa3 (a homolog of human GPN1, also called RPAP4, XAB1, MBDin), and analyze its catalytic mechanism. The enzyme was trapped in a GDP-bound, closed conformation, and in a novel GTP analogue-bound, open conformation displaying a conserved hydrophobic pocket distant from the active site. We show that Npa3 has chaperone activity and interacts with hydrophobic peptide regions of Pol II subunits that form interfaces in the assembled Pol II complex. Biochemical results are consistent with a model that the hydrophobic pocket binds peptides, and that this can allosterically stimulate GTPase activity and subsequent peptide release. These results suggest that GPN-loop GTPases are assembly chaperones for Pol II and other protein complexes.

Structure of GPN-loop GTPase Npa3 and implications for RNA polymerase II assembly.,Niesser J, Wagner FR, Kostrewa D, Muhlbacher W, Cramer P Mol Cell Biol. 2015 Dec 28. pii: MCB.01009-15. PMID:26711263^[6]

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

References

↑ Keniry ME, Kemp HA, Rivers DM, Sprague GF Jr. The identification of Pcl1-interacting proteins that genetically interact with Cla4 may indicate a link between G1 progression and mitotic exit. Genetics. 2004 Mar;166(3):1177-86. PMID:15082539
↑ Forget D, Lacombe AA, Cloutier P, Al-Khoury R, Bouchard A, Lavallee-Adam M, Faubert D, Jeronimo C, Blanchette M, Coulombe B. The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Mol Cell Proteomics. 2010 Dec;9(12):2827-39. doi: 10.1074/mcp.M110.003616. Epub, 2010 Sep 20. PMID:20855544 doi:https://dx.doi.org/10.1074/mcp.M110.003616
↑ Alonso B, Chaussinand G, Armengaud J, Godon C. A role for GPN-loop GTPase yGPN1 in sister chromatid cohesion. Cell Cycle. 2011 Jun 1;10(11):1828-37. Epub 2011 Jun 1. PMID:21532343
↑ Staresincic L, Walker J, Dirac-Svejstrup AB, Mitter R, Svejstrup JQ. GTP-dependent binding and nuclear transport of RNA polymerase II by Npa3 protein. J Biol Chem. 2011 Oct 14;286(41):35553-61. doi: 10.1074/jbc.M111.286161. Epub, 2011 Aug 15. PMID:21844196 doi:https://dx.doi.org/10.1074/jbc.M111.286161
↑ Minaker SW, Filiatrault MC, Ben-Aroya S, Hieter P, Stirling PC. Biogenesis of RNA polymerases II and III requires the conserved GPN small GTPases in Saccharomyces cerevisiae. Genetics. 2013 Mar;193(3):853-64. doi: 10.1534/genetics.112.148726. Epub 2012 Dec, 24. PMID:23267056 doi:https://dx.doi.org/10.1534/genetics.112.148726
↑ Niesser J, Wagner FR, Kostrewa D, Muhlbacher W, Cramer P. Structure of GPN-loop GTPase Npa3 and implications for RNA polymerase II assembly. Mol Cell Biol. 2015 Dec 28. pii: MCB.01009-15. PMID:26711263 doi:https://dx.doi.org/10.1128/MCB.01009-15

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OCA

[1] Keniry ME, Kemp HA, Rivers DM, Sprague GF Jr. The identification of Pcl1-interacting proteins that genetically interact with Cla4 may indicate a link between G1 progression and mitotic exit. Genetics. 2004 Mar;166(3):1177-86. PMID:15082539

[2] Forget D, Lacombe AA, Cloutier P, Al-Khoury R, Bouchard A, Lavallee-Adam M, Faubert D, Jeronimo C, Blanchette M, Coulombe B. The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Mol Cell Proteomics. 2010 Dec;9(12):2827-39. doi: 10.1074/mcp.M110.003616. Epub, 2010 Sep 20. PMID:20855544 doi:https://dx.doi.org/10.1074/mcp.M110.003616

[3] Alonso B, Chaussinand G, Armengaud J, Godon C. A role for GPN-loop GTPase yGPN1 in sister chromatid cohesion. Cell Cycle. 2011 Jun 1;10(11):1828-37. Epub 2011 Jun 1. PMID:21532343

[4] Staresincic L, Walker J, Dirac-Svejstrup AB, Mitter R, Svejstrup JQ. GTP-dependent binding and nuclear transport of RNA polymerase II by Npa3 protein. J Biol Chem. 2011 Oct 14;286(41):35553-61. doi: 10.1074/jbc.M111.286161. Epub, 2011 Aug 15. PMID:21844196 doi:https://dx.doi.org/10.1074/jbc.M111.286161

[5] Minaker SW, Filiatrault MC, Ben-Aroya S, Hieter P, Stirling PC. Biogenesis of RNA polymerases II and III requires the conserved GPN small GTPases in Saccharomyces cerevisiae. Genetics. 2013 Mar;193(3):853-64. doi: 10.1534/genetics.112.148726. Epub 2012 Dec, 24. PMID:23267056 doi:https://dx.doi.org/10.1534/genetics.112.148726

[6] Niesser J, Wagner FR, Kostrewa D, Muhlbacher W, Cramer P. Structure of GPN-loop GTPase Npa3 and implications for RNA polymerase II assembly. Mol Cell Biol. 2015 Dec 28. pii: MCB.01009-15. PMID:26711263 doi:https://dx.doi.org/10.1128/MCB.01009-15

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[6]

@@ Line 3: / Line 3: @@
 <StructureSection load='5hci' size='340' side='right'caption='[[5hci]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5hci]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HCI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HCI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5hci]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HCI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HCI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NPA3, EPA1, GPN1, YJR072C, J1821 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5hci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hci OCA], [http://pdbe.org/5hci PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hci RCSB], [http://www.ebi.ac.uk/pdbsum/5hci PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hci 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=5hci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hci OCA], [https://pdbe.org/5hci PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hci RCSB], [https://www.ebi.ac.uk/pdbsum/5hci PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hci ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GPN1_YEAST GPN1_YEAST]] Small GTPase required for proper nuclear import of RNA polymerase II (RNAPII) (PubMed:20855544, PubMed:21844196). May act at an RNAP assembly step prior to nuclear import (PubMed:23267056). Promotes sister chromatid separation during anaphase (PubMed:21532343).<ref>PMID:15082539</ref> <ref>PMID:20855544</ref> <ref>PMID:21532343</ref> <ref>PMID:21844196</ref> <ref>PMID:23267056</ref>
+[https://www.uniprot.org/uniprot/GPN1_YEAST GPN1_YEAST] Small GTPase required for proper nuclear import of RNA polymerase II (RNAPII) (PubMed:20855544, PubMed:21844196). May act at an RNAP assembly step prior to nuclear import (PubMed:23267056). Promotes sister chromatid separation during anaphase (PubMed:21532343).<ref>PMID:15082539</ref> <ref>PMID:20855544</ref> <ref>PMID:21532343</ref> <ref>PMID:21844196</ref> <ref>PMID:23267056</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Cramer, P]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Kostrewa, D]]
+[[Category: Cramer P]]
-[[Category: Muehlbacher, W]]
+[[Category: Kostrewa D]]
-[[Category: Niesser, J]]
+[[Category: Muehlbacher W]]
-[[Category: Wagner, F R]]
+[[Category: Niesser J]]
-[[Category: Assembly]]
+[[Category: Wagner FR]]
-[[Category: Chaperone]]
-[[Category: Gpn-loop gtpase]]
-[[Category: Hydrolase]]
-[[Category: Rna polymerase]]

5hci: Difference between revisions

Latest revision as of 07:30, 9 August 2023

GPN-loop GTPase Npa3 in complex with GDP

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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