|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Crystal structure of the binary complex of RecD2 with DNA== | | ==Crystal structure of the binary complex of RecD2 with DNA== |
| - | <StructureSection load='3gp8' size='340' side='right' caption='[[3gp8]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='3gp8' size='340' side='right'caption='[[3gp8]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3gp8]] is a 2 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=3GP8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GP8 FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gpl|3gpl]], [[3e1s|3e1s]]</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]] 2.5Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_1902, recD ([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'>[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> |
| - | <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=3gp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gp8 OCA], [http://pdbe.org/3gp8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gp8 RCSB], [http://www.ebi.ac.uk/pdbsum/3gp8 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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> | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/3gp8_consurf.spt"</scriptWhenChecked> | + | <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> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| Line 30: |
Line 30: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Exonuclease|Exonuclease]] | + | *[[Exonuclease 3D structures|Exonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Deira]] | + | [[Category: Deinococcus radiodurans R1]] |
| - | [[Category: Cook, N]] | + | [[Category: Large Structures]] |
| - | [[Category: Saikrishnan, K]] | + | [[Category: Cook N]] |
| - | [[Category: Wigley, D B]] | + | [[Category: Saikrishnan K]] |
| - | [[Category: Alpha and beta protein]] | + | [[Category: Wigley DB]] |
| - | [[Category: Atp-binding]]
| + | |
| - | [[Category: Helicase]]
| + | |
| - | [[Category: Hydrolase-dna complex]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| 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 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.
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 Also
References
- ↑ Wang J, Julin DA. DNA helicase activity of the RecD protein from Deinococcus radiodurans. J Biol Chem. 2004 Dec 10;279(50):52024-32. Epub 2004 Oct 4. PMID:15466873 doi:http://dx.doi.org/10.1074/jbc.M408645200
- ↑ Saikrishnan K, Powell B, Cook NJ, Webb MR, Wigley DB. Mechanistic basis of 5'-3' translocation in SF1B helicases. Cell. 2009 May 29;137(5):849-59. PMID:19490894 doi:10.1016/j.cell.2009.03.036
- ↑ Saikrishnan K, Powell B, Cook NJ, Webb MR, Wigley DB. Mechanistic basis of 5'-3' translocation in SF1B helicases. Cell. 2009 May 29;137(5):849-59. PMID:19490894 doi:10.1016/j.cell.2009.03.036
|
