1qu6

From Proteopedia

(Difference between revisions)

Current revision

STRUCTURE OF THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF THE PROTEIN KINASE PKR REVEALS THE MOLECULAR BASIS OF ITS DSRNA-MEDIATED ACTIVATION

Structural highlights

1qu6 is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

E2AK2_HUMAN Following activation by double-stranded RNA in the presence of ATP, the kinase becomes autophosphorylated and can catalyze the phosphorylation of the translation initiation factor EIF2S1, which leads to an inhibition of the initiation of protein synthesis. Double-stranded RNA is generated during the course of a viral infection. In addition to serine/threonine-protein kinase activity, also has tyrosine-protein kinase activity: phosphorylates CDK1 upon DNA damage. CDK1 phosphorylation triggers CDK1 polyubiquitination and subsequent proteolysis, thus leading to G2 arrest.^[1]

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

Protein kinase PKR is an interferon-induced enzyme that plays a key role in the control of viral infections and cellular homeostasis. Compared with other known kinases, PKR is activated by a distinct mechanism that involves double-stranded RNA (dsRNA) binding in its N-terminal region in an RNA sequence-independent fashion. We report here the solution structure of the 20 kDa dsRNA-binding domain (dsRBD) of human PKR, which provides the first three-dimensional insight into the mechanism of its dsRNA-mediated activation. The structure of dsRBD exhibits a dumb-bell shape comprising two tandem linked dsRNA-binding motifs (dsRBMs) both with an alpha-beta-beta-beta-alpha fold. The structure, combined with previous mutational and biochemical data, reveals a highly conserved RNA-binding site on each dsRBM and suggests a novel mode of protein-RNA recognition. The central linker is highly flexible, which may enable the two dsRBMs to wrap around the RNA duplex for cooperative and high-affinity binding, leading to the overall change of PKR conformation and its activation.

Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation.,Nanduri S, Carpick BW, Yang Y, Williams BR, Qin J EMBO J. 1998 Sep 15;17(18):5458-65. PMID:9736623^[2]

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

References

↑ Yoon CH, Miah MA, Kim KP, Bae YS. New Cdc2 Tyr 4 phosphorylation by dsRNA-activated protein kinase triggers Cdc2 polyubiquitination and G2 arrest under genotoxic stresses. EMBO Rep. 2010 May;11(5):393-9. doi: 10.1038/embor.2010.45. Epub 2010 Apr 16. PMID:20395957 doi:http://dx.doi.org/10.1038/embor.2010.45
↑ Nanduri S, Carpick BW, Yang Y, Williams BR, Qin J. Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation. EMBO J. 1998 Sep 15;17(18):5458-65. PMID:9736623 doi:10.1093/emboj/17.18.5458

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/1qu6"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1qu6.png|left|200px]]
-<!--
+==STRUCTURE OF THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF THE PROTEIN KINASE PKR REVEALS THE MOLECULAR BASIS OF ITS DSRNA-MEDIATED ACTIVATION==
-The line below this paragraph, containing "STRUCTURE_1qu6", creates the "Structure Box" on the page.
+<StructureSection load='1qu6' size='340' side='right'caption='[[1qu6]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1qu6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QU6 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1qu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu6 OCA], [https://pdbe.org/1qu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qu6 RCSB], [https://www.ebi.ac.uk/pdbsum/1qu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qu6 ProSAT]</span></td></tr>
-{{STRUCTURE_1qu6|  PDB=1qu6  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/E2AK2_HUMAN E2AK2_HUMAN] Following activation by double-stranded RNA in the presence of ATP, the kinase becomes autophosphorylated and can catalyze the phosphorylation of the translation initiation factor EIF2S1, which leads to an inhibition of the initiation of protein synthesis. Double-stranded RNA is generated during the course of a viral infection. In addition to serine/threonine-protein kinase activity, also has tyrosine-protein kinase activity: phosphorylates CDK1 upon DNA damage. CDK1 phosphorylation triggers CDK1 polyubiquitination and subsequent proteolysis, thus leading to G2 arrest.<ref>PMID:20395957</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qu/1qu6_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <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/main_output.php?pdb_ID=1qu6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Protein kinase PKR is an interferon-induced enzyme that plays a key role in the control of viral infections and cellular homeostasis. Compared with other known kinases, PKR is activated by a distinct mechanism that involves double-stranded RNA (dsRNA) binding in its N-terminal region in an RNA sequence-independent fashion. We report here the solution structure of the 20 kDa dsRNA-binding domain (dsRBD) of human PKR, which provides the first three-dimensional insight into the mechanism of its dsRNA-mediated activation. The structure of dsRBD exhibits a dumb-bell shape comprising two tandem linked dsRNA-binding motifs (dsRBMs) both with an alpha-beta-beta-beta-alpha fold. The structure, combined with previous mutational and biochemical data, reveals a highly conserved RNA-binding site on each dsRBM and suggests a novel mode of protein-RNA recognition. The central linker is highly flexible, which may enable the two dsRBMs to wrap around the RNA duplex for cooperative and high-affinity binding, leading to the overall change of PKR conformation and its activation.
-===STRUCTURE OF THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF THE PROTEIN KINASE PKR REVEALS THE MOLECULAR BASIS OF ITS DSRNA-MEDIATED ACTIVATION===
+Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation.,Nanduri S, Carpick BW, Yang Y, Williams BR, Qin J EMBO J. 1998 Sep 15;17(18):5458-65. PMID:9736623<ref>PMID:9736623</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_9736623}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1qu6" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 9736623 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9736623}}
+__TOC__
+</StructureSection>
-==About this Structure==
-QU6 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU6 OCA].
-==Reference==
-<ref group="xtra">PMID:9736623</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Carpick, B W.]]
+[[Category: Large Structures]]
-[[Category: Nanduri, S.]]
+[[Category: Carpick BW]]
-[[Category: Qin, J.]]
+[[Category: Nanduri S]]
-[[Category: Williams, B R.G.]]
+[[Category: Qin J]]
-[[Category: Yang, Y.]]
+[[Category: Williams BRG]]
-[[Category: Dsrna-binding domain]]
+[[Category: Yang Y]]
-[[Category: Nmr]]
-[[Category: Pkr]]
-[[Category: Protein kinase]]
-[[Category: Solution structure]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:51:00 2009''

1qu6

From Proteopedia

Current revision

STRUCTURE OF THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF THE PROTEIN KINASE PKR REVEALS THE MOLECULAR BASIS OF ITS DSRNA-MEDIATED ACTIVATION

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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