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2db3

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Revision as of 10:53, 11 September 2015

Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa

Structural highlights

2db3 is a 8 chain structure with sequence from Drome. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	VASA (DROME)
Activity:	Adenosinetriphosphatase, with EC number 3.6.1.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, TOPSAN

Function

[VASA1_DROME] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles during germ cell formation. Required for gus, Fsn and aub accumulation at the posterior pole of the embryo. Required for the localization of vas to the perinuclear region of nurse cells.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

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

DEAD-box RNA helicases, which regulate various processes involving RNA, have two RecA-like domains as a catalytic core to alter higher-order RNA structures. We determined the 2.2 A resolution structure of the core of the Drosophila DEAD-box protein Vasa in complex with a single-stranded RNA and an ATP analog. The ATP analog intensively interacts with both of the domains, thereby bringing them into the closed form, with many interdomain interactions of conserved residues. The bound RNA is sharply bent, avoiding a clash with a conserved alpha helix in the N-terminal domain. This "wedge" helix should disrupt base pairs by bending one of the strands when a duplex is bound. Mutational analyses indicated that the interdomain interactions couple ATP hydrolysis to RNA unwinding, probably through fine positioning of the duplex relative to the wedge helix. This mechanism, which differs from those for canonical translocating helicases, may enable the targeted modulation of intricate RNA structures.

Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.,Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S Cell. 2006 Apr 21;125(2):287-300. PMID:16630817^[12]

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

References

↑ Carrera P, Johnstone O, Nakamura A, Casanova J, Jackle H, Lasko P. VASA mediates translation through interaction with a Drosophila yIF2 homolog. Mol Cell. 2000 Jan;5(1):181-7. PMID:10678180
↑ Harris AN, Macdonald PM. Aubergine encodes a Drosophila polar granule component required for pole cell formation and related to eIF2C. Development. 2001 Jul;128(14):2823-32. PMID:11526087
↑ Styhler S, Nakamura A, Lasko P. VASA localization requires the SPRY-domain and SOCS-box containing protein, GUSTAVUS. Dev Cell. 2002 Dec;3(6):865-76. PMID:12479811
↑ Liu N, Dansereau DA, Lasko P. Fat facets interacts with vasa in the Drosophila pole plasm and protects it from degradation. Curr Biol. 2003 Oct 28;13(21):1905-9. PMID:14588248
↑ Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell. 2006 Apr 21;125(2):287-300. PMID:16630817 doi:10.1016/j.cell.2006.01.054
↑ Thomson T, Liu N, Arkov A, Lehmann R, Lasko P. Isolation of new polar granule components in Drosophila reveals P body and ER associated proteins. Mech Dev. 2008 Sep-Oct;125(9-10):865-73. doi: 10.1016/j.mod.2008.06.005. Epub, 2008 Jun 12. PMID:18590813 doi:http://dx.doi.org/10.1016/j.mod.2008.06.005
↑ Kugler JM, Woo JS, Oh BH, Lasko P. Regulation of Drosophila vasa in vivo through paralogous cullin-RING E3 ligase specificity receptors. Mol Cell Biol. 2010 Apr;30(7):1769-82. doi: 10.1128/MCB.01100-09. Epub 2010 Feb, 1. PMID:20123973 doi:http://dx.doi.org/10.1128/MCB.01100-09
↑ Hay B, Jan LY, Jan YN. A protein component of Drosophila polar granules is encoded by vasa and has extensive sequence similarity to ATP-dependent helicases. Cell. 1988 Nov 18;55(4):577-87. PMID:3052853
↑ Lasko PF, Ashburner M. The product of the Drosophila gene vasa is very similar to eukaryotic initiation factor-4A. Nature. 1988 Oct 13;335(6191):611-7. PMID:3140040 doi:http://dx.doi.org/10.1038/335611a0
↑ Liang L, Diehl-Jones W, Lasko P. Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-binding and helicase activities. Development. 1994 May;120(5):1201-11. PMID:8026330
↑ Styhler S, Nakamura A, Swan A, Suter B, Lasko P. vasa is required for GURKEN accumulation in the oocyte, and is involved in oocyte differentiation and germline cyst development. Development. 1998 May;125(9):1569-78. PMID:9521895
↑ Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell. 2006 Apr 21;125(2):287-300. PMID:16630817 doi:10.1016/j.cell.2006.01.054

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2db3"

@@ Line 2: / Line 2: @@
 <StructureSection load='2db3' size='340' side='right' caption='[[2db3]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DB3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2db3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DB3 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VASA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VASA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosinetriphosphatase Adenosinetriphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.3 3.6.1.3] </span></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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [http://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [http://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</span></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=2db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db3 OCA], [http://pdbe.org/2db3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2db3 RCSB], [http://www.ebi.ac.uk/pdbsum/2db3 PDBsum], [http://www.topsan.org/Proteins/RSGI/2db3 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VASA_DROME VASA_DROME]] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles.<ref>PMID:3140040</ref> <ref>PMID:3052853</ref> <ref>PMID:8026330</ref> <ref>PMID:9521895</ref> <ref>PMID:10678180</ref> <ref>PMID:12479811</ref> <ref>PMID:14588248</ref> <ref>PMID:16630817</ref>
+[[http://www.uniprot.org/uniprot/VASA1_DROME VASA1_DROME]] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles during germ cell formation. Required for gus, Fsn and aub accumulation at the posterior pole of the embryo. Required for the localization of vas to the perinuclear region of nurse cells.<ref>PMID:10678180</ref> <ref>PMID:11526087</ref> <ref>PMID:12479811</ref> <ref>PMID:14588248</ref> <ref>PMID:16630817</ref> <ref>PMID:18590813</ref> <ref>PMID:20123973</ref> <ref>PMID:3052853</ref> <ref>PMID:3140040</ref> <ref>PMID:8026330</ref> <ref>PMID:9521895</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2db3" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 36: / Line 37: @@
 </StructureSection>
 [[Category: Adenosinetriphosphatase]]
-[[Category: Drosophila melanogaster]]
+[[Category: Drome]]
 [[Category: Kobayashi, S]]
 [[Category: Nakamura, A]]

2db3

From Proteopedia

Revision as of 10:53, 11 September 2015

Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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