5mbv

From Proteopedia

(Difference between revisions)

Current revision

Cryo-EM structure of Lambda Phage protein GamS bound to RecBCD.

5mbv, resolution 3.80Å

Structural highlights

5mbv is a 5 chain structure with sequence from Escherichia coli and Escherichia virus Lambda. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.8Å
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18] ^[19] ^[20] ^[21] ^[22]

Publication Abstract from PubMed

Our previous paper (Wilkinson et al, 2016) used high-resolution cryo-electron microscopy to solve the structure of the Escherichia coli RecBCD complex, which acts in both the repair of double-stranded DNA breaks and the degradation of bacteriophage DNA. To counteract the latter activity, bacteriophage lambda encodes a small protein inhibitor called Gam that binds to RecBCD and inactivates the complex. Here, we show that Gam inhibits RecBCD by competing at the DNA-binding site. The interaction surface is extensive and involves molecular mimicry of the DNA substrate. We also show that expression of Gam in E. coli or Klebsiella pneumoniae increases sensitivity to fluoroquinolones; antibacterials that kill cells by inhibiting topoisomerases and inducing double-stranded DNA breaks. Furthermore, fluoroquinolone-resistance in K. pneumoniae clinical isolates is reversed by expression of Gam. Together, our data explain the synthetic lethality observed between topoisomerase-induced DNA breaks and the RecBCD gene products, suggesting a new co-antibacterial strategy.

Structural basis for the inhibition of RecBCD by Gam and its synergistic antibacterial effect with quinolones.,Wilkinson M, Troman L, Wan Nur Ismah WA, Chaban Y, Avison MB, Dillingham MS, Wigley DB Elife. 2016 Dec 23;5. pii: e22963. doi: 10.7554/eLife.22963. PMID:28009252^[23]

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
↑ Zhang XJ, Julin DA. Isolation and characterization of the C-terminal nuclease domain from the RecB protein of Escherichia coli. Nucleic Acids Res. 1999 Nov 1;27(21):4200-7. PMID:10518611
↑ Arnold DA, Kowalczykowski SC. Facilitated loading of RecA protein is essential to recombination by RecBCD enzyme. J Biol Chem. 2000 Apr 21;275(16):12261-5. PMID:10766864
↑ 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
↑ Sun JZ, Julin DA, Hu JS. The nuclease domain of the Escherichia coli RecBCD enzyme catalyzes degradation of linear and circular single-stranded and double-stranded DNA. Biochemistry. 2006 Jan 10;45(1):131-40. PMID:16388588 doi:http://dx.doi.org/10.1021/bi051150v
↑ Amundsen SK, Taylor AF, Reddy M, Smith GR. Intersubunit signaling in RecBCD enzyme, a complex protein machine regulated by Chi hot spots. Genes Dev. 2007 Dec 15;21(24):3296-307. PMID:18079176 doi:http://dx.doi.org/10.1101/gad.1605807
↑ 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
↑ Taylor AF, Amundsen SK, Guttman M, Lee KK, Luo J, Ranish J, Smith GR. Control of RecBCD enzyme activity by DNA binding- and Chi hotspot-dependent conformational changes. J Mol Biol. 2014 Oct 23;426(21):3479-99. doi: 10.1016/j.jmb.2014.07.017. Epub, 2014 Jul 27. PMID:25073102 doi:http://dx.doi.org/10.1016/j.jmb.2014.07.017
↑ 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
↑ Wilkinson M, Troman L, Wan Nur Ismah WA, Chaban Y, Avison MB, Dillingham MS, Wigley DB. Structural basis for the inhibition of RecBCD by Gam and its synergistic antibacterial effect with quinolones. Elife. 2016 Dec 23;5. pii: e22963. doi: 10.7554/eLife.22963. PMID:28009252 doi:http://dx.doi.org/10.7554/eLife.22963

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5mbv"

@@ Line 3: / Line 3: @@
 <SX load='5mbv' size='340' side='right' viewer='molstar' caption='[[5mbv]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5mbv]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MBV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MBV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5mbv]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MBV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MBV FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ld2|5ld2]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">recB, ior, rorA, b2820, JW2788 ([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, hopE, b2819, JW2787 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), gam, gamma ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</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=5mbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mbv OCA], [https://pdbe.org/5mbv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mbv RCSB], [https://www.ebi.ac.uk/pdbsum/5mbv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mbv ProSAT]</span></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://proteopedia.org/fgij/fg.htm?mol=5mbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mbv OCA], [http://pdbe.org/5mbv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mbv RCSB], [http://www.ebi.ac.uk/pdbsum/5mbv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mbv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GAM_LAMBD GAM_LAMBD]] Binds to host RecBCD nuclease and inhibits it thereby protecting the viral DNA against recBCD mediated degradation.<ref>PMID:17544443</ref>  [[http://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>  [[http://www.uniprot.org/uniprot/RECD_ECOLI RECD_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. In the holoenzyme this subunit contributes ssDNA-dependent ATPase and fast 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.<ref>PMID:10197988</ref> <ref>PMID:10840065</ref> <ref>PMID:12815437</ref> <ref>PMID:12815438</ref> <ref>PMID:1535156</ref> <ref>PMID:16041061</ref> <ref>PMID:1618858</ref> <ref>PMID:18079176</ref> <ref>PMID:23851395</ref> <ref>PMID:7608206</ref> <ref>PMID:9192629</ref> <ref>PMID:9230304</ref> <ref>PMID:9448271</ref> <ref>PMID:9790841</ref>  [[http://www.uniprot.org/uniprot/RECC_ECOLI 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.<ref>PMID:10197988</ref> <ref>PMID:10884344</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:20852646</ref> <ref>PMID:23851395</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>
+[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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 18: @@
 </div>
 <div class="pdbe-citations 5mbv" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Exonuclease 3D structures|Exonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </SX>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Bacteriophage lambda]]
+[[Category: Escherichia virus Lambda]]
-[[Category: Exodeoxyribonuclease V]]
 [[Category: Large Structures]]
-[[Category: Chaban, Y]]
+[[Category: Chaban Y]]
-[[Category: Wigley, D B]]
+[[Category: Wigley DB]]
-[[Category: Wilkinson, M]]
+[[Category: Wilkinson M]]
-[[Category: Complex]]
-[[Category: Dna binding protein]]
-[[Category: Dna repair]]
-[[Category: Helicase/nuclease]]
-[[Category: Inhibitor]]

5mbv

From Proteopedia

Current revision

Cryo-EM structure of Lambda Phage protein GamS bound to RecBCD.

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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