3gpl: Difference between revisions
No edit summary |
No edit summary |
||
| Line 2: | Line 2: | ||
<StructureSection load='3gpl' size='340' side='right' caption='[[3gpl]], [[Resolution|resolution]] 2.50Å' scene=''> | <StructureSection load='3gpl' size='340' side='right' caption='[[3gpl]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3gpl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3gpl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GPL 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> | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gp8|3gp8]], [[3e1s|3e1s]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gp8|3gp8]], [[3e1s|3e1s]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_1902, recD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_1902, recD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</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=3gpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gpl RCSB], [http://www.ebi.ac.uk/pdbsum/3gpl PDBsum]</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=3gpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpl OCA], [http://pdbe.org/3gpl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpl RCSB], [http://www.ebi.ac.uk/pdbsum/3gpl PDBsum]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/ | [[http://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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 18: | Line 18: | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=3gpl ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 28: | Line 28: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3gpl" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
| Line 35: | Line 36: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Deira]] | ||
[[Category: Cook, N]] | [[Category: Cook, N]] | ||
[[Category: Saikrishnan, K]] | [[Category: Saikrishnan, K]] | ||
Revision as of 19:18, 9 February 2016
Crystal structure of the ternary complex of RecD2 with DNA and ADPNPCrystal structure of the ternary complex of RecD2 with DNA and ADPNP
Structural highlights
Function[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.[1] [2] 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 PubMedSuperfamily 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. 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[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||||