6sjb

From Proteopedia

(Difference between revisions)

Revision as of 06:11, 11 April 2020

Cryo-EM structure of the RecBCD Chi recognised complex

6sjb, resolution 3.70Å

Structural highlights

6sjb is a 4 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	recB_1, recB, AUQ13_17740, BANRA_01341, BANRA_04284, BHS81_16925, BUE81_06765, BvCms2454_02089, BvCmsHHP001_01116, BvCmsHHP056_02020, BvCmsNSNP006_02180, BvCmsNSNP027_02943, BvCmsSINP011_00475, BvCmsSIP044_01651, C4J69_11455, C5N07_06355, D9I18_10890, DNQ41_19170, E5M00_06020, EAI44_21005, EAI52_16505, EC3234A_49c00050, ECTO6_01026, EFV07_08645, EPS71_15035, ERL57_14525, EXX32_11785, EXX39_20385, EXX71_16045, EYD11_05005, NCTC11022_02903, NCTC13462_04762, NCTC9117_01550, NCTC9706_03254, RG28_07470, SAMEA3472080_03114, SAMEA3752559_02953, SAMEA3753300_01149 ("Bacillus coli" Migula 1895), recC, b2822, JW2790 ("Bacillus coli" Migula 1895), recD, recD_2, ACU57_24225, AM464_05810, AUQ13_17735, BHS81_16920, BUE81_06770, BvCms2454_02088, BvCmsHHP001_01117, BvCmsHHP056_02019, BvCmsKSP036_04400, BvCmsNSNP006_02181, BvCmsNSNP027_02942, BvCmsSINP011_00476, BvCmsSINP012_00057, BvCmsSIP044_01650, BVL39_12765, C4J69_11460, C5N07_06350, C7B02_19600, CG692_06815, CRM83_26155, D3821_10935, D9G42_05835, D9H94_17780, D9I18_10885, D9K48_23640, DNQ41_19165, E4Z89_04655, EAI44_21010, EC3234A_49c00040, ECTO6_01027, EEP23_14080, EFB45_23490, EL75_0877, EL79_0879, EL80_0882, ERL57_14520, EXX24_12005, EXX32_11780, EXX71_16050, EYD11_05010, EYY78_03865, HW43_18500, NCTC11022_02902, NCTC13148_02729, NCTC8500_01037, NCTC9036_01094, NCTC9037_01202, NCTC9062_02173, NCTC9117_01551, NCTC9706_03255, RG28_07475, RK56_023370, SAMEA3472047_00298, SAMEA3472080_03115, SAMEA3484427_03257, SAMEA3484429_03374, SAMEA3752559_02954, SAMEA3753300_01148, SK85_03061 ("Bacillus coli" Migula 1895)
Activity:	Exodeoxyribonuclease V, with EC number 3.1.11.5
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[A0A024LB08_ECOLX] A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit contributes ATPase, 3'-5' helicase, exonuclease activity and loads RecA onto ssDNA.[HAMAP-Rule:MF_01485] [A0A061K747_ECOLX] A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD.[HAMAP-Rule:MF_01487] [RECC_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 almost certainly recognizes the wild-type Chi sequence, when added to isolated RecB increases its ATP-dependent helicase processivity. The RecBC complex requires the RecD subunit for nuclease activity, but can translocate along ssDNA in both directions.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18]

Publication Abstract from PubMed

The RecBCD complex plays key roles in phage DNA degradation, CRISPR array acquisition (adaptation) and host DNA repair. The switch between these roles is regulated by a DNA sequence called Chi. We report cryo-EM structures of the Escherichia coli RecBCD complex bound to several different DNA forks containing a Chi sequence, including one in which Chi is recognized and others in which it is not. The Chi-recognized structure shows conformational changes in regions of the protein that contact Chi and reveals a tortuous path taken by the DNA. Sequence specificity arises from interactions with both the RecC subunit and the sequence itself. These structures provide molecular details for how Chi is recognized and insights into the changes that occur in response to Chi binding that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition to constructive host DNA repair.

A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair.,Cheng K, Wilkinson M, Chaban Y, Wigley DB Nat Struct Mol Biol. 2020 Jan;27(1):71-77. doi: 10.1038/s41594-019-0355-2. Epub, 2020 Jan 6. PMID:31907455^[19]

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

References

↑ Taylor AF, Smith GR. Regulation of homologous recombination: Chi inactivates RecBCD enzyme by disassembly of the three subunits. Genes Dev. 1999 Apr 1;13(7):890-900. PMID:10197988
↑ Arnold DA, Handa N, Kobayashi I, Kowalczykowski SC. A novel, 11 nucleotide variant of chi, chi*: one of a class of sequences defining the Escherichia coli recombination hotspot chi. J Mol Biol. 2000 Jul 14;300(3):469-79. PMID:10884344 doi:http://dx.doi.org/10.1006/jmbi.2000.3861
↑ Benzinger R, Enquist LW, Skalka A. Transfection of Escherichia coli spheroplasts. V. Activity of recBC nuclease in rec+ and rec minus spheroplasts measured with different forms of bacteriophage DNA. J Virol. 1975 Apr;15(4):861-71. PMID:123277
↑ Taylor AF, Smith GR. RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity. Nature. 2003 Jun 19;423(6942):889-93. PMID:12815437 doi:http://dx.doi.org/10.1038/nature01674
↑ Dillingham MS, Spies M, Kowalczykowski SC. RecBCD enzyme is a bipolar DNA helicase. Nature. 2003 Jun 19;423(6942):893-7. PMID:12815438 doi:http://dx.doi.org/10.1038/nature01673
↑ Taylor AF, Smith GR. RecBCD enzyme is altered upon cutting DNA at a chi recombination hotspot. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5226-30. PMID:1535156
↑ Dillingham MS, Webb MR, Kowalczykowski SC. Bipolar DNA translocation contributes to highly processive DNA unwinding by RecBCD enzyme. J Biol Chem. 2005 Nov 4;280(44):37069-77. Epub 2005 Jul 22. PMID:16041061 doi:http://dx.doi.org/10.1074/jbc.M505520200
↑ Masterson C, Boehmer PE, McDonald F, Chaudhuri S, Hickson ID, Emmerson PT. Reconstitution of the activities of the RecBCD holoenzyme of Escherichia coli from the purified subunits. J Biol Chem. 1992 Jul 5;267(19):13564-72. PMID:1618858
↑ Wu CG, Bradford C, Lohman TM. Escherichia coli RecBC helicase has two translocase activities controlled by a single ATPase motor. Nat Struct Mol Biol. 2010 Oct;17(10):1210-7. doi: 10.1038/nsmb.1901. Epub 2010, Sep 19. PMID:20852646 doi:http://dx.doi.org/10.1038/nsmb.1901
↑ Liu B, Baskin RJ, Kowalczykowski SC. DNA unwinding heterogeneity by RecBCD results from static molecules able to equilibrate. Nature. 2013 Aug 22;500(7463):482-5. doi: 10.1038/nature12333. Epub 2013 Jul 14. PMID:23851395 doi:http://dx.doi.org/10.1038/nature12333
↑ Karu AE, MacKay V, Goldmark PJ, Linn S. The recBC deoxyribonuclease of Escherichia coli K-12. Substrate specificity and reaction intermediates. J Biol Chem. 1973 Jul 25;248(14):4874-84. PMID:4268693
↑ Goldmark PJ, Linn S. Purification and properties of the recBC DNase of Escherichia coli K-12. J Biol Chem. 1972 Mar 25;247(6):1849-60. PMID:4552016
↑ Simmon VF, Lederberg S. Degradation of bacteriophage lambda deoxyribonucleic acid after restriction by Escherichia coli K-12. J Bacteriol. 1972 Oct;112(1):161-9. PMID:4562392
↑ Dixon DA, Kowalczykowski SC. Role of the Escherichia coli recombination hotspot, chi, in RecABCD-dependent homologous pairing. J Biol Chem. 1995 Jul 7;270(27):16360-70. PMID:7608206
↑ Bianco PR, Kowalczykowski SC. The recombination hotspot Chi is recognized by the translocating RecBCD enzyme as the single strand of DNA containing the sequence 5'-GCTGGTGG-3'. Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6706-11. PMID:9192629
↑ Anderson DG, Kowalczykowski SC. The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a chi-regulated manner. Cell. 1997 Jul 11;90(1):77-86. PMID:9230304
↑ Yu M, Souaya J, Julin DA. The 30-kDa C-terminal domain of the RecB protein is critical for the nuclease activity, but not the helicase activity, of the RecBCD enzyme from Escherichia coli. Proc Natl Acad Sci U S A. 1998 Feb 3;95(3):981-6. PMID:9448271
↑ Yu M, Souaya J, Julin DA. Identification of the nuclease active site in the multifunctional RecBCD enzyme by creation of a chimeric enzyme. J Mol Biol. 1998 Nov 6;283(4):797-808. PMID:9790841 doi:http://dx.doi.org/10.1006/jmbi.1998.2127
↑ Cheng K, Wilkinson M, Chaban Y, Wigley DB. A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair. Nat Struct Mol Biol. 2020 Jan;27(1):71-77. doi: 10.1038/s41594-019-0355-2. Epub, 2020 Jan 6. PMID:31907455 doi:http://dx.doi.org/10.1038/s41594-019-0355-2

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6sjb"

@@ Line 3: / Line 3: @@
 <SX load='6sjb' size='340' side='right' viewer='molstar' caption='[[6sjb]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6sjb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SJB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SJB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6sjb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SJB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SJB FirstGlance]. <br>
 </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">recB_1, recB, AUQ13_17740, BANRA_01341, BANRA_04284, BHS81_16925, BUE81_06765, BvCms2454_02089, BvCmsHHP001_01116, BvCmsHHP056_02020, BvCmsNSNP006_02180, BvCmsNSNP027_02943, BvCmsSINP011_00475, BvCmsSIP044_01651, C4J69_11455, C5N07_06355, D9I18_10890, DNQ41_19170, E5M00_06020, EAI44_21005, EAI52_16505, EC3234A_49c00050, ECTO6_01026, EFV07_08645, EPS71_15035, ERL57_14525, EXX32_11785, EXX39_20385, EXX71_16045, EYD11_05005, NCTC11022_02903, NCTC13462_04762, NCTC9117_01550, NCTC9706_03254, RG28_07470, SAMEA3472080_03114, SAMEA3752559_02953, SAMEA3753300_01149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), recC, b2822, JW2790 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), recD, recD_2, ACU57_24225, AM464_05810, AUQ13_17735, BHS81_16920, BUE81_06770, BvCms2454_02088, BvCmsHHP001_01117, BvCmsHHP056_02019, BvCmsKSP036_04400, BvCmsNSNP006_02181, BvCmsNSNP027_02942, BvCmsSINP011_00476, BvCmsSINP012_00057, BvCmsSIP044_01650, BVL39_12765, C4J69_11460, C5N07_06350, C7B02_19600, CG692_06815, CRM83_26155, D3821_10935, D9G42_05835, D9H94_17780, D9I18_10885, D9K48_23640, DNQ41_19165, E4Z89_04655, EAI44_21010, EC3234A_49c00040, ECTO6_01027, EEP23_14080, EFB45_23490, EL75_0877, EL79_0879, EL80_0882, ERL57_14520, EXX24_12005, EXX32_11780, EXX71_16050, EYD11_05010, EYY78_03865, HW43_18500, NCTC11022_02902, NCTC13148_02729, NCTC8500_01037, NCTC9036_01094, NCTC9037_01202, NCTC9062_02173, NCTC9117_01551, NCTC9706_03255, RG28_07475, RK56_023370, SAMEA3472047_00298, SAMEA3472080_03115, SAMEA3484427_03257, SAMEA3484429_03374, SAMEA3752559_02954, SAMEA3753300_01148, SK85_03061 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_V Exodeoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.5 3.1.11.5] </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=6sjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sjb OCA], [http://pdbe.org/6sjb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sjb RCSB], [http://www.ebi.ac.uk/pdbsum/6sjb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sjb ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6sjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sjb OCA], [http://pdbe.org/6sjb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sjb RCSB], [http://www.ebi.ac.uk/pdbsum/6sjb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sjb ProSAT]</span></td></tr>
 </table>
 == Function ==

6sjb

From Proteopedia

Revision as of 06:11, 11 April 2020

Cryo-EM structure of the RecBCD Chi recognised complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox