3gp8: Difference between revisions

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-[[Image:3gp8.png|left|200px]]
-<!--
+==Crystal structure of the binary complex of RecD2 with DNA==
-The line below this paragraph, containing "STRUCTURE_3gp8", creates the "Structure Box" on the page.
+<StructureSection load='3gp8' size='340' side='right'caption='[[3gp8]], [[Resolution|resolution]] 2.50&Aring;' 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'>[[3gp8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GP8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GP8 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">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</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=3gp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gp8 OCA], [https://pdbe.org/3gp8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gp8 RCSB], [https://www.ebi.ac.uk/pdbsum/3gp8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gp8 ProSAT]</span></td></tr>
-{{STRUCTURE_3gp8|  PDB=3gp8  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RECDL_DEIRA RECDL_DEIRA] DNA-dependent ATPase (ssDNA better than dsDNA) and ATP-dependent 5'-3' DNA helicase. Appears to move along DNA in single base steps, powered by hydrolysis of 1 molecule of ATP. Has low processivity; short (20 bp) substrates with 5'-overhangs or forked ends are the best substrates, is much less efficient on 52 or 76 bp substrates with 5'- overhangs. The presence of single-stranded DNA-binding protein (SSB) increases unwinding 4-5 fold. Has no activity on blunt DNA or DNA with 3'-overhangs. Requires at least 10 bases of 5'-ssDNA for helicase activity.<ref>PMID:15466873</ref> <ref>PMID:19490894</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/gp/3gp8_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=3gp8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Superfamily 1B (SF1B) helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life. However, structural analyses to date have focused on how SF1A helicases achieve 3'-5' movement along nucleic acids. We present crystal structures of the complex between the SF1B helicase RecD2 from Deinococcus radiodurans and ssDNA in the presence and absence of an ATP analog. These snapshots of the reaction pathway reveal a nucleotide binding-induced conformational change of the two motor domains that is broadly reminiscent of changes observed in other SF1 and SF2 helicases. Together with biochemical data, the structures point to a step size for translocation of one base per ATP hydrolyzed. Moreover, the structures also reveal a mechanism for nucleic acid translocation in the 5'-3' direction by SF1B helicases that is surprisingly different from that of 3'-5' translocation by SF1A enzymes, and explains the molecular basis of directionality.
-===Crystal structure of the binary complex of RecD2 with DNA===
+Mechanistic basis of 5'-3' translocation in SF1B helicases.,Saikrishnan K, Powell B, Cook NJ, Webb MR, Wigley DB Cell. 2009 May 29;137(5):849-59. PMID:19490894<ref>PMID:19490894</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3gp8" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19490894}}, adds the Publication Abstract to the page
+*[[Exonuclease 3D structures|Exonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19490894 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19490894}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Deinococcus radiodurans R1]]
-[[3gp8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans_r1 Deinococcus radiodurans r1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GP8 OCA].
+[[Category: Large Structures]]
+[[Category: Cook N]]
-==Reference==
+[[Category: Saikrishnan K]]
-<ref group="xtra">PMID:19490894</ref><ref group="xtra">PMID:18668125</ref><references group="xtra"/>
+[[Category: Wigley DB]]
-[[Category: Deinococcus radiodurans r1]]
-[[Category: Cook, N.]]
-[[Category: Saikrishnan, K.]]
-[[Category: Wigley, D B.]]
-[[Category: Alpha and beta protein]]
-[[Category: Atp-binding]]
-[[Category: Helicase]]
-[[Category: Hydrolase/dna complex]]
-[[Category: Nucleotide-binding]]