3k70

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{{Seed}}
 
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[[Image:3k70.png|left|200px]]
 
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==Crystal structure of the complete initiation complex of RecBCD==
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The line below this paragraph, containing "STRUCTURE_3k70", creates the "Structure Box" on the page.
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<StructureSection load='3k70' size='340' side='right'caption='[[3k70]], [[Resolution|resolution]] 3.59&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3k70]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K70 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.59&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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{{STRUCTURE_3k70| PDB=3k70 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3k70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k70 OCA], [https://pdbe.org/3k70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k70 RCSB], [https://www.ebi.ac.uk/pdbsum/3k70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k70 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RECB_ECOLI RECB_ECOLI] A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a rapid (>1 kb/second) and highly processive (>30 kb) ATP-dependent bidirectional helicase. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator, 5'-GCTGGTGG-3') sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to Chi site, by nicking one strand or switching the strand degraded (depending on the reaction conditions). The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang which facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination (PubMed:4562392, PubMed:4552016, PubMed:123277). In the holoenzyme this subunit contributes ATPase, 3'-5' helicase, exonuclease activity and loads RecA onto ssDNA. The RecBC complex requires the RecD subunit for nuclease activity, but can translocate along ssDNA in both directions.<ref>PMID:10197988</ref> <ref>PMID:10518611</ref> <ref>PMID:10766864</ref> <ref>PMID:123277</ref> <ref>PMID:12815437</ref> <ref>PMID:12815438</ref> <ref>PMID:1535156</ref> <ref>PMID:16041061</ref> <ref>PMID:1618858</ref> <ref>PMID:16388588</ref> <ref>PMID:18079176</ref> <ref>PMID:20852646</ref> <ref>PMID:23851395</ref> <ref>PMID:25073102</ref> <ref>PMID:4268693</ref> <ref>PMID:4552016</ref> <ref>PMID:4562392</ref> <ref>PMID:7608206</ref> <ref>PMID:9192629</ref> <ref>PMID:9230304</ref> <ref>PMID:9448271</ref> <ref>PMID:9790841</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k7/3k70_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3k70 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The molecular mechanism of superfamily 1Balpha helicases remains unclear. We present here the crystal structure of the RecD2 helicase from Deinococcus radiodurans at 2.2-A resolution. The structure reveals the folds of the 1B and 2B domains of RecD that were poorly ordered in the structure of the Escherichia coli RecBCD enzyme complex reported previously. The 2B domain adopts an SH3 fold which, although common in eukaryotes, is extremely rare in bacterial systems. In addition, the D. radiodurans RecD2 structure has aided us in deciphering lower resolution (3.6 A) electron density maps for the E. coli RecBCD enzyme in complex with a long DNA substrate that interacts with the RecD subunit. Taken together, these structures indicated an important role for the 1B domain of RecD, a beta-hairpin that extends from the surface of the 1A domain and interacts with the DNA substrate. On the basis of these structural data, we designed a mutant RecD2 helicase that lacks this pin. The 'pin-less' mutant protein is a fully active ssDNA-dependent ATPase but totally lacks helicase activity.
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===Crystal structure of the complete initiation complex of RecBCD===
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DNA binding to RecD: role of the 1B domain in SF1B helicase activity.,Saikrishnan K, Griffiths SP, Cook N, Court R, Wigley DB EMBO J. 2008 Aug 20;27(16):2222-9. Epub 2008 Jul 31. PMID:18668125<ref>PMID:18668125</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3k70" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18668125}}, adds the Publication Abstract to the page
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*[[Exonuclease 3D structures|Exonuclease 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18668125 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18668125}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia coli K-12]]
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3K70 is a 8 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K70 OCA].
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[[Category: Large Structures]]
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[[Category: Saikrishnan K]]
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==Reference==
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[[Category: Wigley DB]]
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<ref group="xtra">PMID:18668125</ref><ref group="xtra">PMID:15538360</ref><references group="xtra"/>
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[[Category: Escherichia coli k-12]]
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[[Category: Exodeoxyribonuclease V]]
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[[Category: Saikrishnan, K.]]
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[[Category: Wigley, D B.]]
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[[Category: Atp-binding]]
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[[Category: Dna damage]]
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[[Category: Dna repair]]
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[[Category: Endonuclease]]
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[[Category: Exonuclease]]
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[[Category: Helicase]]
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[[Category: Hydrolase]]
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[[Category: Hydrolase/dna complex]]
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[[Category: Nuclease]]
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[[Category: Nucleotide-binding]]
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[[Category: Recombination]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:42:21 2010''
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Current revision

Crystal structure of the complete initiation complex of RecBCD

PDB ID 3k70

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OCA

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