9dx4: Difference between revisions

Latest revision as of 13:00, 10 February 2026

EcRuvB T102R mutant

Structural highlights

9dx4 is a 5 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.31Å
Ligands:	ADP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RUVB_ECOLI The RuvABC complex is involved in recombinational repair of UV or chemically damaged DNA (PubMed:6374379). The complex also plays an important role in the rescue of blocked DNA replication forks via replication fork reversal (RFR); RFR and homologous recombination required for UV light survival can be separated (PubMed:16424908, PubMed:18942176, PubMed:9814711). This subunit has a weak ATPase activity that is inhibited by its ADP product; binds ADP better than ATP (PubMed:2529252). Promotes Holliday junction (HJ) branch migration in conjunction with RuvA. Binds to HJ cruciform DNA; in the presence of RuvA, ATP and Mg(2+) the junction is dissociated. Hydrolyzable (d)NTPs can replace ATP but other analogs cannot (PubMed:1608954, PubMed:1617728, PubMed:6374379, PubMed:8393934). The RuvB hexamer acts as a pump, pulling DNA into and through the RuvAB complex (PubMed:9078376). Can bypass UV-induced lesions (PubMed:1617728) and physically cross-linked DNA strands (PubMed:10662672), suggesting RuvB does not unwind large sections of DNA. RuvA gives specificity by binding to cruciform junctions, while the RuvB ATPase provides the motor force for branch migration; excess RuvB can promote branch migration in the absence of RuvA (PubMed:10662672, PubMed:1617728). In vitro the RuvA-RuvB complex has 5'-3' helicase activity that is ATP-dependent and works best on short dsDNA hybrids; 52 and 66-nucleotide (nt) pairs are easily displaced, hybrids greater than 140-nts are not (PubMed:8433990). RuvA stimulates the weak ATPase activity of RuvB in the presence of DNA; HJ DNA stimulates ATPase about 10-fold (PubMed:1435721, PubMed:1833759, PubMed:8393934).[HAMAP-Rule:MF_00016]^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] An in vitro resolvase system that forms and processes HJ has been reconstituted with DNA substrates, RuvA, RuvB and RuvC. RuvA-RuvB increases the rate of strand exchange (branch migration), dissociates the RecA filament and allows RuvC to cleave in both orientations at the cruciform junction (PubMed:10421637, PubMed:9160752). HJ-RuvA-RuvB-RuvC complexes resolve Holliday junctions and also undergo branch migration, providing evidence for a coupled branch migration/HJ resolution reaction (PubMed:10421637).^[14] ^[15]

References

↑ George H, Kuraoka I, Nauman DA, Kobertz WR, Wood RD, West SC. RuvAB-mediated branch migration does not involve extensive DNA opening within the RuvB hexamer. Curr Biol. 2000 Jan 27;10(2):103-6. PMID:10662672 doi:10.1016/s0960-9822(00)00296-7
↑ Tsaneva IR, Illing G, Lloyd RG, West SC. Purification and properties of the RuvA and RuvB proteins of Escherichia coli. Mol Gen Genet. 1992 Oct;235(1):1-10. PMID:1435721 doi:10.1007/BF00286175
↑ Parsons CA, Tsaneva I, Lloyd RG, West SC. Interaction of Escherichia coli RuvA and RuvB proteins with synthetic Holliday junctions. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5452-6. PMID:1608954 doi:10.1073/pnas.89.12.5452
↑ Tsaneva IR, Müller B, West SC. ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E. coli. Cell. 1992 Jun 26;69(7):1171-80. PMID:1617728 doi:10.1016/0092-8674(92)90638-s
↑ Baharoglu Z, Petranovic M, Flores MJ, Michel B. RuvAB is essential for replication forks reversal in certain replication mutants. EMBO J. 2006 Feb 8;25(3):596-604. PMID:16424908 doi:10.1038/sj.emboj.7600941
↑ Shiba T, Iwasaki H, Nakata A, Shinagawa H. SOS-inducible DNA repair proteins, RuvA and RuvB, of Escherichia coli: functional interactions between RuvA and RuvB for ATP hydrolysis and renaturation of the cruciform structure in supercoiled DNA. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8445-9. PMID:1833759 doi:10.1073/pnas.88.19.8445
↑ Le Masson M, Baharoglu Z, Michel B. ruvA and ruvB mutants specifically impaired for replication fork reversal. Mol Microbiol. 2008 Oct;70(2):537-48. PMID:18942176 doi:10.1111/j.1365-2958.2008.06431.x
↑ Iwasaki H, Shiba T, Makino K, Nakata A, Shinagawa H. Overproduction, purification, and ATPase activity of the Escherichia coli RuvB protein involved in DNA repair. J Bacteriol. 1989 Oct;171(10):5276-80. PMID:2529252 doi:10.1128/jb.171.10.5276-5280.1989
↑ Lloyd RG, Benson FE, Shurvinton CE. Effect of ruv mutations on recombination and DNA repair in Escherichia coli K12. Mol Gen Genet. 1984;194(1-2):303-9. PMID:6374379 doi:10.1007/BF00383532
↑ Parsons CA, West SC. Formation of a RuvAB-Holliday junction complex in vitro. J Mol Biol. 1993 Jul 20;232(2):397-405. PMID:8393934 doi:10.1006/jmbi.1993.1399
↑ Tsaneva IR, Muller B, West SC. RuvA and RuvB proteins of Escherichia coli exhibit DNA helicase activity in vitro. Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1315-9. PMID:8433990
↑ Hiom K, Tsaneva IR, West SC. The directionality of RuvAB-mediated branch migration: in vitro studies with three-armed junctions. Genes Cells. 1996 May;1(5):443-51. PMID:9078376 doi:10.1046/j.1365-2443.1996.d01-253.x
↑ Seigneur M, Bidnenko V, Ehrlich SD, Michel B. RuvAB acts at arrested replication forks. Cell. 1998 Oct 30;95(3):419-30. PMID:9814711 doi:10.1016/s0092-8674(00)81772-9
↑ van Gool AJ, Hajibagheri NM, Stasiak A, West SC. Assembly of the Escherichia coli RuvABC resolvasome directs the orientation of holliday junction resolution. Genes Dev. 1999 Jul 15;13(14):1861-70. PMID:10421637 doi:10.1101/gad.13.14.1861
↑ Eggleston AK, Mitchell AH, West SC. In vitro reconstitution of the late steps of genetic recombination in E. coli. Cell. 1997 May 16;89(4):607-17. PMID:9160752 doi:10.1016/s0092-8674(00)80242-1

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] George H, Kuraoka I, Nauman DA, Kobertz WR, Wood RD, West SC. RuvAB-mediated branch migration does not involve extensive DNA opening within the RuvB hexamer. Curr Biol. 2000 Jan 27;10(2):103-6. PMID:10662672 doi:10.1016/s0960-9822(00)00296-7

[2] Tsaneva IR, Illing G, Lloyd RG, West SC. Purification and properties of the RuvA and RuvB proteins of Escherichia coli. Mol Gen Genet. 1992 Oct;235(1):1-10. PMID:1435721 doi:10.1007/BF00286175

[3] Parsons CA, Tsaneva I, Lloyd RG, West SC. Interaction of Escherichia coli RuvA and RuvB proteins with synthetic Holliday junctions. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5452-6. PMID:1608954 doi:10.1073/pnas.89.12.5452

[4] Tsaneva IR, Müller B, West SC. ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E. coli. Cell. 1992 Jun 26;69(7):1171-80. PMID:1617728 doi:10.1016/0092-8674(92)90638-s

[5] Baharoglu Z, Petranovic M, Flores MJ, Michel B. RuvAB is essential for replication forks reversal in certain replication mutants. EMBO J. 2006 Feb 8;25(3):596-604. PMID:16424908 doi:10.1038/sj.emboj.7600941

[6] Shiba T, Iwasaki H, Nakata A, Shinagawa H. SOS-inducible DNA repair proteins, RuvA and RuvB, of Escherichia coli: functional interactions between RuvA and RuvB for ATP hydrolysis and renaturation of the cruciform structure in supercoiled DNA. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8445-9. PMID:1833759 doi:10.1073/pnas.88.19.8445

[7] Le Masson M, Baharoglu Z, Michel B. ruvA and ruvB mutants specifically impaired for replication fork reversal. Mol Microbiol. 2008 Oct;70(2):537-48. PMID:18942176 doi:10.1111/j.1365-2958.2008.06431.x

[8] Iwasaki H, Shiba T, Makino K, Nakata A, Shinagawa H. Overproduction, purification, and ATPase activity of the Escherichia coli RuvB protein involved in DNA repair. J Bacteriol. 1989 Oct;171(10):5276-80. PMID:2529252 doi:10.1128/jb.171.10.5276-5280.1989

[9] Lloyd RG, Benson FE, Shurvinton CE. Effect of ruv mutations on recombination and DNA repair in Escherichia coli K12. Mol Gen Genet. 1984;194(1-2):303-9. PMID:6374379 doi:10.1007/BF00383532

[10] Parsons CA, West SC. Formation of a RuvAB-Holliday junction complex in vitro. J Mol Biol. 1993 Jul 20;232(2):397-405. PMID:8393934 doi:10.1006/jmbi.1993.1399

[11] Tsaneva IR, Muller B, West SC. RuvA and RuvB proteins of Escherichia coli exhibit DNA helicase activity in vitro. Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1315-9. PMID:8433990

[12] Hiom K, Tsaneva IR, West SC. The directionality of RuvAB-mediated branch migration: in vitro studies with three-armed junctions. Genes Cells. 1996 May;1(5):443-51. PMID:9078376 doi:10.1046/j.1365-2443.1996.d01-253.x

[13] Seigneur M, Bidnenko V, Ehrlich SD, Michel B. RuvAB acts at arrested replication forks. Cell. 1998 Oct 30;95(3):419-30. PMID:9814711 doi:10.1016/s0092-8674(00)81772-9

[14] van Gool AJ, Hajibagheri NM, Stasiak A, West SC. Assembly of the Escherichia coli RuvABC resolvasome directs the orientation of holliday junction resolution. Genes Dev. 1999 Jul 15;13(14):1861-70. PMID:10421637 doi:10.1101/gad.13.14.1861

[15] Eggleston AK, Mitchell AH, West SC. In vitro reconstitution of the late steps of genetic recombination in E. coli. Cell. 1997 May 16;89(4):607-17. PMID:9160752 doi:10.1016/s0092-8674(00)80242-1

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9dx4 is ON HOLD
+==EcRuvB T102R mutant==
+<StructureSection load='9dx4' size='340' side='right'caption='[[9dx4]], [[Resolution|resolution]] 3.31&Aring;' scene=''>
-Authors: Rish, A.D., Fu, T.M.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9dx4]] is a 5 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=9DX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9DX4 FirstGlance]. <br>
-Description: EcRuvB T102R mutant
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.31&#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></td></tr>
-[[Category: Rish, A.D]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9dx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9dx4 OCA], [https://pdbe.org/9dx4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9dx4 RCSB], [https://www.ebi.ac.uk/pdbsum/9dx4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9dx4 ProSAT]</span></td></tr>
-[[Category: Fu, T.M]]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RUVB_ECOLI RUVB_ECOLI] The RuvABC complex is involved in recombinational repair of UV or chemically damaged DNA (PubMed:6374379). The complex also plays an important role in the rescue of blocked DNA replication forks via replication fork reversal (RFR); RFR and homologous recombination required for UV light survival can be separated (PubMed:16424908, PubMed:18942176, PubMed:9814711). This subunit has a weak ATPase activity that is inhibited by its ADP product; binds ADP better than ATP (PubMed:2529252). Promotes Holliday junction (HJ) branch migration in conjunction with RuvA. Binds to HJ cruciform DNA; in the presence of RuvA, ATP and Mg(2+) the junction is dissociated. Hydrolyzable (d)NTPs can replace ATP but other analogs cannot (PubMed:1608954, PubMed:1617728, PubMed:6374379, PubMed:8393934). The RuvB hexamer acts as a pump, pulling DNA into and through the RuvAB complex (PubMed:9078376). Can bypass UV-induced lesions (PubMed:1617728) and physically cross-linked DNA strands (PubMed:10662672), suggesting RuvB does not unwind large sections of DNA. RuvA gives specificity by binding to cruciform junctions, while the RuvB ATPase provides the motor force for branch migration; excess RuvB can promote branch migration in the absence of RuvA (PubMed:10662672, PubMed:1617728). In vitro the RuvA-RuvB complex has 5'-3' helicase activity that is ATP-dependent and works best on short dsDNA hybrids; 52 and 66-nucleotide (nt) pairs are easily displaced, hybrids greater than 140-nts are not (PubMed:8433990). RuvA stimulates the weak ATPase activity of RuvB in the presence of DNA; HJ DNA stimulates ATPase about 10-fold (PubMed:1435721, PubMed:1833759, PubMed:8393934).[HAMAP-Rule:MF_00016]<ref>PMID:10662672</ref> <ref>PMID:1435721</ref> <ref>PMID:1608954</ref> <ref>PMID:1617728</ref> <ref>PMID:16424908</ref> <ref>PMID:1833759</ref> <ref>PMID:18942176</ref> <ref>PMID:2529252</ref> <ref>PMID:6374379</ref> <ref>PMID:8393934</ref> <ref>PMID:8433990</ref> <ref>PMID:9078376</ref> <ref>PMID:9814711</ref>   An in vitro resolvase system that forms and processes HJ has been reconstituted with DNA substrates, RuvA, RuvB and RuvC. RuvA-RuvB increases the rate of strand exchange (branch migration), dissociates the RecA filament and allows RuvC to cleave in both orientations at the cruciform junction (PubMed:10421637, PubMed:9160752). HJ-RuvA-RuvB-RuvC complexes resolve Holliday junctions and also undergo branch migration, providing evidence for a coupled branch migration/HJ resolution reaction (PubMed:10421637).<ref>PMID:10421637</ref> <ref>PMID:9160752</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Fu TM]]
+[[Category: Rish AD]]

9dx4: Difference between revisions

Latest revision as of 13:00, 10 February 2026

EcRuvB T102R mutant

Structural highlights

Function

References

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