9wm2: Difference between revisions

Latest revision as of 08:07, 9 September 2026

Crystal structure of Escherichia coli RecG in complex with a partial replication fork and ADPAlF4

Structural highlights

9wm2 is a 4 chain structure with sequence from Escherichia coli K-12 and Chemical production metagenome. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:	ADP, ALF, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RECG_ECOLI Genetic interactions indicate that RecG or RadD are required for DNA repair in every replication cycle; they function in different pathways, each is essential in the absence of the other (PubMed:32644157). Plays a critical role in recombination and DNA repair (PubMed:8428576, PubMed:7957087, PubMed:8127666, PubMed:9265736, PubMed:10871364, PubMed:32644157). RecG or RadD are required for DNA maintenance in every replication cycle (PubMed:32644157). Helps process Holliday junction (HJ) intermediates to mature products by catalyzing branch migration (PubMed:8428576, PubMed:7957087, PubMed:8127666, PubMed:10871364). Has replication fork regression activity, unwinds stalled or blocked replication forks to make a HJ that can be resolved by RuvC or RusA (PubMed:10778854, PubMed:11459957). Also rewinds unwound dsDNA in an ATP-dependent manner (PubMed:24013402). Has double-stranded (ds)DNA unwinding activity characteristic of a DNA helicase with 3'-5' polarity in vitro on linear dsDNA; branched duplex DNA (Y-DNA) substrates adopt different conformations that influence which of the two arms are unwound (PubMed:7957087). Binds and unwinds HJ and Y-DNA but not linear duplex DNA; binds no more than 10 nucleotides of ssDNA at a fork (PubMed:8428576, PubMed:7957087, PubMed:8127666, PubMed:10871364, PubMed:11459957, PubMed:15533834). Has a role in constitutive stable DNA replication (cSDR, DNA replication in the absence of protein synthesis) and R-loop (RNA annealed with dsDNA) formation (PubMed:7774596). Unwinds R-loops but not RNA:DNA hybrids (PubMed:8980680, PubMed:15533834). Is genetically synergistic to RadA and RuvABC (PubMed:12446634, PubMed:25484163).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] Uup probably acts upstream of RecG; they are important in repair of stalled replication forks and postreplication gaps (PubMed:32644157). Lethal double radD-recG deletions are suppressed by a reduction in recA expression, by point mutations in priA helicase, by deletions in recF, recO or uup, suggesting all these proteins create branched DNA intermediates requiring RadD or RecG for resolution (PubMed:32644157).^[14]

References

↑ McGlynn P, Lloyd RG. Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression. Cell. 2000 Mar 31;101(1):35-45. doi: 10.1016/S0092-8674(00)80621-2. PMID:10778854 doi:https://dx.doi.org/10.1016/S0092-8674(00)80621-2
↑ McGlynn P, Mahdi AA, Lloyd RG. Characterisation of the catalytically active form of RecG helicase. Nucleic Acids Res. 2000 Jun 15;28(12):2324-32. doi: 10.1093/nar/28.12.2324. PMID:10871364 doi:https://dx.doi.org/10.1093/nar/28.12.2324
↑ McGlynn P, Lloyd RG. Rescue of stalled replication forks by RecG: simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8227-34. doi: , 10.1073/pnas.111008698. PMID:11459957 doi:https://dx.doi.org/10.1073/pnas.111008698
↑ Beam CE, Saveson CJ, Lovett ST. Role for radA/sms in recombination intermediate processing in Escherichia coli. J Bacteriol. 2002 Dec;184(24):6836-44. doi: 10.1128/JB.184.24.6836-6844.2002. PMID:12446634 doi:https://dx.doi.org/10.1128/JB.184.24.6836-6844.2002
↑ Wen Q, Mahdi AA, Briggs GS, Sharples GJ, Lloyd RG. Conservation of RecG activity from pathogens to hyperthermophiles. DNA Repair (Amst). 2005 Jan 2;4(1):23-31. doi: 10.1016/j.dnarep.2004.07.008. PMID:15533834 doi:https://dx.doi.org/10.1016/j.dnarep.2004.07.008
↑ Manosas M, Perumal SK, Bianco PR, Ritort F, Benkovic SJ, Croquette V. RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue. Nat Commun. 2013;4:2368. doi: 10.1038/ncomms3368. PMID:24013402 doi:https://dx.doi.org/10.1038/ncomms3368
↑ Cooper DL, Boyle DC, Lovett ST. Genetic analysis of Escherichia coli RadA: functional motifs and genetic interactions. Mol Microbiol. 2015 Mar;95(5):769-79. doi: 10.1111/mmi.12899. Epub 2015 Jan 30. PMID:25484163 doi:https://dx.doi.org/10.1111/mmi.12899
↑ Romero ZJ, Chen SH, Armstrong T, Wood EA, van Oijen A, Robinson A, Cox MM. Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD. Nucleic Acids Res. 2020 Sep 4;48(15):8445-8460. doi: 10.1093/nar/gkaa579. PMID:32644157 doi:https://dx.doi.org/10.1093/nar/gkaa579
↑ Hong X, Cadwell GW, Kogoma T. Escherichia coli RecG and RecA proteins in R-loop formation. EMBO J. 1995 May 15;14(10):2385-92. doi: 10.1002/j.1460-2075.1995.tb07233.x. PMID:7774596 doi:https://dx.doi.org/10.1002/j.1460-2075.1995.tb07233.x
↑ Whitby MC, Vincent SD, Lloyd RG. Branch migration of Holliday junctions: identification of RecG protein as a junction specific DNA helicase. EMBO J. 1994 Nov 1;13(21):5220-8. doi: 10.1002/j.1460-2075.1994.tb06853.x. PMID:7957087 doi:https://dx.doi.org/10.1002/j.1460-2075.1994.tb06853.x
↑ Sharples GJ, Whitby MC, Ryder L, Lloyd RG. A mutation in helicase motif III of E. coli RecG protein abolishes branch migration of Holliday junctions. Nucleic Acids Res. 1994 Feb 11;22(3):308-13. doi: 10.1093/nar/22.3.308. PMID:8127666 doi:https://dx.doi.org/10.1093/nar/22.3.308
↑ Lloyd RG, Sharples GJ. Dissociation of synthetic Holliday junctions by E. coli RecG protein. EMBO J. 1993 Jan;12(1):17-22. PMID:8428576
↑ Ishioka K, Iwasaki H, Shinagawa H. Roles of the recG gene product of Escherichia coli in recombination repair: effects of the delta recG mutation on cell division and chromosome partition. Genes Genet Syst. 1997 Apr;72(2):91-9. doi: 10.1266/ggs.72.91. PMID:9265736 doi:https://dx.doi.org/10.1266/ggs.72.91
↑ Romero ZJ, Chen SH, Armstrong T, Wood EA, van Oijen A, Robinson A, Cox MM. Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD. Nucleic Acids Res. 2020 Sep 4;48(15):8445-8460. doi: 10.1093/nar/gkaa579. PMID:32644157 doi:https://dx.doi.org/10.1093/nar/gkaa579

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] McGlynn P, Lloyd RG. Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression. Cell. 2000 Mar 31;101(1):35-45. doi: 10.1016/S0092-8674(00)80621-2. PMID:10778854 doi:https://dx.doi.org/10.1016/S0092-8674(00)80621-2

[2] McGlynn P, Mahdi AA, Lloyd RG. Characterisation of the catalytically active form of RecG helicase. Nucleic Acids Res. 2000 Jun 15;28(12):2324-32. doi: 10.1093/nar/28.12.2324. PMID:10871364 doi:https://dx.doi.org/10.1093/nar/28.12.2324

[3] McGlynn P, Lloyd RG. Rescue of stalled replication forks by RecG: simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8227-34. doi: , 10.1073/pnas.111008698. PMID:11459957 doi:https://dx.doi.org/10.1073/pnas.111008698

[4] Beam CE, Saveson CJ, Lovett ST. Role for radA/sms in recombination intermediate processing in Escherichia coli. J Bacteriol. 2002 Dec;184(24):6836-44. doi: 10.1128/JB.184.24.6836-6844.2002. PMID:12446634 doi:https://dx.doi.org/10.1128/JB.184.24.6836-6844.2002

[5] Wen Q, Mahdi AA, Briggs GS, Sharples GJ, Lloyd RG. Conservation of RecG activity from pathogens to hyperthermophiles. DNA Repair (Amst). 2005 Jan 2;4(1):23-31. doi: 10.1016/j.dnarep.2004.07.008. PMID:15533834 doi:https://dx.doi.org/10.1016/j.dnarep.2004.07.008

[6] Manosas M, Perumal SK, Bianco PR, Ritort F, Benkovic SJ, Croquette V. RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue. Nat Commun. 2013;4:2368. doi: 10.1038/ncomms3368. PMID:24013402 doi:https://dx.doi.org/10.1038/ncomms3368

[7] Cooper DL, Boyle DC, Lovett ST. Genetic analysis of Escherichia coli RadA: functional motifs and genetic interactions. Mol Microbiol. 2015 Mar;95(5):769-79. doi: 10.1111/mmi.12899. Epub 2015 Jan 30. PMID:25484163 doi:https://dx.doi.org/10.1111/mmi.12899

[8] Romero ZJ, Chen SH, Armstrong T, Wood EA, van Oijen A, Robinson A, Cox MM. Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD. Nucleic Acids Res. 2020 Sep 4;48(15):8445-8460. doi: 10.1093/nar/gkaa579. PMID:32644157 doi:https://dx.doi.org/10.1093/nar/gkaa579

[9] Hong X, Cadwell GW, Kogoma T. Escherichia coli RecG and RecA proteins in R-loop formation. EMBO J. 1995 May 15;14(10):2385-92. doi: 10.1002/j.1460-2075.1995.tb07233.x. PMID:7774596 doi:https://dx.doi.org/10.1002/j.1460-2075.1995.tb07233.x

[10] Whitby MC, Vincent SD, Lloyd RG. Branch migration of Holliday junctions: identification of RecG protein as a junction specific DNA helicase. EMBO J. 1994 Nov 1;13(21):5220-8. doi: 10.1002/j.1460-2075.1994.tb06853.x. PMID:7957087 doi:https://dx.doi.org/10.1002/j.1460-2075.1994.tb06853.x

[11] Sharples GJ, Whitby MC, Ryder L, Lloyd RG. A mutation in helicase motif III of E. coli RecG protein abolishes branch migration of Holliday junctions. Nucleic Acids Res. 1994 Feb 11;22(3):308-13. doi: 10.1093/nar/22.3.308. PMID:8127666 doi:https://dx.doi.org/10.1093/nar/22.3.308

[12] Lloyd RG, Sharples GJ. Dissociation of synthetic Holliday junctions by E. coli RecG protein. EMBO J. 1993 Jan;12(1):17-22. PMID:8428576

[13] Ishioka K, Iwasaki H, Shinagawa H. Roles of the recG gene product of Escherichia coli in recombination repair: effects of the delta recG mutation on cell division and chromosome partition. Genes Genet Syst. 1997 Apr;72(2):91-9. doi: 10.1266/ggs.72.91. PMID:9265736 doi:https://dx.doi.org/10.1266/ggs.72.91

[14] Romero ZJ, Chen SH, Armstrong T, Wood EA, van Oijen A, Robinson A, Cox MM. Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD. Nucleic Acids Res. 2020 Sep 4;48(15):8445-8460. doi: 10.1093/nar/gkaa579. PMID:32644157 doi:https://dx.doi.org/10.1093/nar/gkaa579

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9wm2 is ON HOLD  until Paper Publication
+==Crystal structure of Escherichia coli RecG in complex with a partial replication fork and ADPAlF4==
+<StructureSection load='9wm2' size='340' side='right'caption='[[9wm2]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9wm2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Chemical_production_metagenome Chemical production metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9WM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9WM2 FirstGlance]. <br>
-Description:
+</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&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=9wm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9wm2 OCA], [https://pdbe.org/9wm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9wm2 RCSB], [https://www.ebi.ac.uk/pdbsum/9wm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9wm2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RECG_ECOLI RECG_ECOLI] Genetic interactions indicate that RecG or RadD are required for DNA repair in every replication cycle; they function in different pathways, each is essential in the absence of the other (PubMed:32644157). Plays a critical role in recombination and DNA repair (PubMed:8428576, PubMed:7957087, PubMed:8127666, PubMed:9265736, PubMed:10871364, PubMed:32644157). RecG or RadD are required for DNA maintenance in every replication cycle (PubMed:32644157). Helps process Holliday junction (HJ) intermediates to mature products by catalyzing branch migration (PubMed:8428576, PubMed:7957087, PubMed:8127666, PubMed:10871364). Has replication fork regression activity, unwinds stalled or blocked replication forks to make a HJ that can be resolved by RuvC or RusA (PubMed:10778854, PubMed:11459957). Also rewinds unwound dsDNA in an ATP-dependent manner (PubMed:24013402). Has double-stranded (ds)DNA unwinding activity characteristic of a DNA helicase with 3'-5' polarity in vitro on linear dsDNA; branched duplex DNA (Y-DNA) substrates adopt different conformations that influence which of the two arms are unwound (PubMed:7957087). Binds and unwinds HJ and Y-DNA but not linear duplex DNA; binds no more than 10 nucleotides of ssDNA at a fork (PubMed:8428576, PubMed:7957087, PubMed:8127666, PubMed:10871364, PubMed:11459957, PubMed:15533834). Has a role in constitutive stable DNA replication (cSDR, DNA replication in the absence of protein synthesis) and R-loop (RNA annealed with dsDNA) formation (PubMed:7774596). Unwinds R-loops but not RNA:DNA hybrids (PubMed:8980680, PubMed:15533834). Is genetically synergistic to RadA and RuvABC (PubMed:12446634, PubMed:25484163).<ref>PMID:10778854</ref> <ref>PMID:10871364</ref> <ref>PMID:11459957</ref> <ref>PMID:12446634</ref> <ref>PMID:15533834</ref> <ref>PMID:24013402</ref> <ref>PMID:25484163</ref> <ref>PMID:32644157</ref> <ref>PMID:7774596</ref> <ref>PMID:7957087</ref> <ref>PMID:8127666</ref> <ref>PMID:8428576</ref> <ref>PMID:9265736</ref>   Uup probably acts upstream of RecG; they are important in repair of stalled replication forks and postreplication gaps (PubMed:32644157). Lethal double radD-recG deletions are suppressed by a reduction in recA expression, by point mutations in priA helicase, by deletions in recF, recO or uup, suggesting all these proteins create branched DNA intermediates requiring RadD or RecG for resolution (PubMed:32644157).<ref>PMID:32644157</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Chemical production metagenome]]
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Cheng K]]

9wm2: Difference between revisions

Latest revision as of 08:07, 9 September 2026

Crystal structure of Escherichia coli RecG in complex with a partial replication fork and ADPAlF4

Structural highlights

Function

References

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