MG_358_359_10MER – Holliday junction DNA helicase

Name
WID	MG_358_359_10MER
Name	Holliday junction DNA helicase
Cross references	PDB: 1HJP

Structure
Biosynthesis	[c]: (4) MG_358_MONOMER + (6) MG_359_MONOMER ⇒ MG_358_359_10MER
No. subunits	10
DNA footprint	Length: 52 (nt), Binding: dsDNA, Region: dsDNA
Empirical formula (pH 7.5)	H₂₂₄₄₄C₁₃₈₀₈N₃₆₃₄O₃₉₃₈S₈₄
Molecular weight (pH 7.5; Da)	305064.50
Extinction coefficient (260 nm, 25C, pH 7.0)	-168820.00
Half life (OD (600 nm) = 0.3, M9 media, 36C; min)	1200.00

Synthesis
Formation process	Process_MacromolecularComplexation
Localization	c

Function
Enzyme	DNA recombination Holliday junction migration [c]: ATP + H2O ⇒ ADP + H + PI
Reaction participant	DNA bound protein release (Holliday junction DNA helicase releases heat-inducible transcription repressor HrcA, putative) MG_205_DIMER[d] + MG_358_359_10MER[c] ⇒ MG_205_DIMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases putative DNA integrity scanning protein) MG_105_OCTAMER[d] + MG_358_359_10MER[c] ⇒ MG_105_OCTAMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases DnaA 5mer-(4)ATP-(1)ADP) MG_358_359_10MER[c] + MG_469_5MER_4ATP_ADP[d] ⇒ MG_358_359_10MER[d] + MG_469_5MER_4ATP_ADP[c] DNA bound protein release (Holliday junction DNA helicase releases adenine-specific DNA modification methylase) MG_184_DIMER[d] + MG_358_359_10MER[c] ⇒ MG_184_DIMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases DnaA-ATP 4mer) MG_358_359_10MER[c] + MG_469_4MER_ATP[d] ⇒ MG_358_359_10MER[d] + MG_469_4MER_ATP[c] ... 30 more DNA bound protein release (Holliday junction DNA helicase releases DNA gyrase) DNA_GYRASE[d] + MG_358_359_10MER[c] ⇒ DNA_GYRASE[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases LuxR bacterial regulatory protein, putative) MG_358_359_10MER[c] + MG_428_DIMER[d] ⇒ MG_358_359_10MER[d] + MG_428_DIMER[c] DNA bound protein release (Holliday junction DNA helicase releases DnaA 3mer-(2)ATP-(1)ADP) MG_358_359_10MER[c] + MG_469_3MER_2ATP_ADP[d] ⇒ MG_358_359_10MER[d] + MG_469_3MER_2ATP_ADP[c] DNA bound protein release (Holliday junction DNA helicase releases DnaA-ATP 2mer) MG_358_359_10MER[c] + MG_469_2MER_ATP[d] ⇒ MG_358_359_10MER[d] + MG_469_2MER_ATP[c] DNA bound protein release (Holliday junction DNA helicase releases DnaA-ATP 7mer) MG_358_359_10MER[c] + MG_469_7MER_ATP[d] ⇒ MG_358_359_10MER[d] + MG_469_7MER_ATP[c] DNA bound protein release (Holliday junction DNA helicase releases DNA-directed RNA polymerase holoenzyme) MG_358_359_10MER[c] + RNA_POLYMERASE_HOLOENZYME[d] ⇒ MG_358_359_10MER[d] + RNA_POLYMERASE_HOLOENZYME[c] DNA bound protein release (Holliday junction DNA helicase releases DNA-directed RNA polymerase) MG_358_359_10MER[c] + RNA_POLYMERASE[d] ⇒ MG_358_359_10MER[d] + RNA_POLYMERASE[c] DNA bound protein release (Holliday junction DNA helicase releases DnaA 4mer-(3)ATP-(1)ADP) MG_358_359_10MER[c] + MG_469_4MER_3ATP_ADP[d] ⇒ MG_358_359_10MER[d] + MG_469_4MER_3ATP_ADP[c] DNA bound protein release (Holliday junction DNA helicase releases Spx subfamily protein) MG_127_MONOMER[d] + MG_358_359_10MER[c] ⇒ MG_127_MONOMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases DnaA-ATP) MG_358_359_10MER[c] + MG_469_1MER_ATP[d] ⇒ MG_358_359_10MER[d] + MG_469_1MER_ATP[c] DNA bound protein release (Holliday junction DNA helicase releases topoisomerase IV) MG_203_204_TETRAMER[d] + MG_358_359_10MER[c] ⇒ MG_203_204_TETRAMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases DNA polymerase III, beta clamp) MG_001_DIMER[d] + MG_358_359_10MER[c] ⇒ MG_001_DIMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases ferric uptake repressor) MG_236_MONOMER[d] + MG_358_359_10MER[c] ⇒ MG_236_MONOMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases DNA topoisomerase I) MG_122_MONOMER[d] + MG_358_359_10MER[c] ⇒ MG_122_MONOMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases DnaA-ATP 6mer) MG_358_359_10MER[c] + MG_469_6MER_ATP[d] ⇒ MG_358_359_10MER[d] + MG_469_6MER_ATP[c] DNA bound protein release (Holliday junction DNA helicase releases DnaA 7mer-(6)ATP-(1)ADP) MG_358_359_10MER[c] + MG_469_7MER_6ATP_ADP[d] ⇒ MG_358_359_10MER[d] + MG_469_7MER_6ATP_ADP[c] DNA bound protein release (Holliday junction DNA helicase releases DNA polymerase core, β-clamp, and γ-complex) DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX[d] + MG_358_359_10MER[c] ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases Uncharacterized HTH-type transcriptional regulator) MG_101_MONOMER[d] + MG_358_359_10MER[c] ⇒ MG_101_MONOMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases replicative DNA helicase) MG_094_HEXAMER[d] + MG_358_359_10MER[c] ⇒ MG_094_HEXAMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases DNA polymerase core, β-clamp, and primase) DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE[d] + MG_358_359_10MER[c] ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases DnaA 6mer-(5)ATP-(1)ADP) MG_358_359_10MER[c] + MG_469_6MER_5ATP_ADP[d] ⇒ MG_358_359_10MER[d] + MG_469_6MER_5ATP_ADP[c] DNA bound protein release (Holliday junction DNA helicase releases DnaA-ADP) MG_358_359_10MER[c] + MG_469_1MER_ADP[d] ⇒ MG_358_359_10MER[d] + MG_469_1MER_ADP[c] DNA bound protein release (Holliday junction DNA helicase releases DnaA-ATP 5mer) MG_358_359_10MER[c] + MG_469_5MER_ATP[d] ⇒ MG_358_359_10MER[d] + MG_469_5MER_ATP[c] DNA bound protein release (Holliday junction DNA helicase releases DNA polymerase (2) core, β-clamp, γ-complex, and primase) DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE[d] + MG_358_359_10MER[c] ⇒ DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases type I restriction modification DNA specificity domain protein) MG_358_359_10MER[c] + MG_438_MONOMER[d] ⇒ MG_358_359_10MER[d] + MG_438_MONOMER[c] DNA bound protein release (Holliday junction DNA helicase releases DnaA 2mer-(1)ATP-(1)ADP) MG_358_359_10MER[c] + MG_469_2MER_1ATP_ADP[d] ⇒ MG_358_359_10MER[d] + MG_469_2MER_1ATP_ADP[c] DNA bound protein release (Holliday junction DNA helicase releases DNA ligase, NAD-dependent) MG_254_MONOMER[d] + MG_358_359_10MER[c] ⇒ MG_254_MONOMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases Chromosome Segregation Protein SMC with SCP Proteins-ADP) MG_213_214_298_6MER_ADP[d] + MG_358_359_10MER[c] ⇒ MG_213_214_298_6MER_ADP[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases single-strand binding protein family, octamer) MG_091_OCTAMER[d] + MG_358_359_10MER[c] ⇒ MG_091_OCTAMER[c] + MG_358_359_10MER[d] DNA bound protein release (Holliday junction DNA helicase releases DnaA-ATP 3mer) MG_358_359_10MER[c] + MG_469_3MER_ATP[d] ⇒ MG_358_359_10MER[d] + MG_469_3MER_ATP[c]
Complex subunit	Holliday junction DNA helicase [c]: (4) MG_358_MONOMER + (6) MG_359_MONOMER ⇒ MG_358_359_10MER

Parameters
Parameters	Parameter_0053: HR_RuvAB_JunctionMigrationHop = 2.2 b

Comments
Comments	RuvAB is responsible for Holliday junction migration in an ATP-dependent manner [PUB_0532]. RuvAB is composed of 1-2 RuvA tetramers and 1-2 RuvB hexameric rings [PUB_0532]. RuvA tetramers unfold the junction in a square planar conformation, energetically favorable to branch-point migration [PUB_0532]. RuvB possesses DNA-dependent ATPase activity, but this activity is extremely weak (kcat < 1/min) [PUB_0536]. RuvA stimulates RuvB ATPase activity 10X [PUB_0536]. 1 ATP binding site per RuvB monomer, but 2 ATPs bind per RuvB hexamer [PUB_0537]. Several groups have examined the kinetics of RuvAB-directed strand migration: Dawid observed 43 bp/sec under zero load [PUB_0532], Tsaneva et al observed 10-20 bp/sec in bulk [PUB_0533], Dennis et observed 50 bp/s [PUB_0534], Grigoriev and Hsieh observed 10 bp/s [PUB_0535], and Karymov et al observed 10 steps/s [PUB_0538]. Spontaneous junction migration occurs at rate 1/300 ms in presence of Mg2+, and 1/12 μs in presence of Na+ [PUB_0531]. Junction migration can be slowed by DNA mismatches [PUB_0531]. In presence of RecA migration occurs at 3 bp/s [PUB_0531]. Migration occurs in discrete hops of 1-5 bp with a mean of 2.2 bp [PUB_0538]. RuvAB is highly processive, >4431 bp [PUB_0532, PUB_0534]. Dennis et al describe a mathematical model of RuvAB-directed strand migration [PUB_0534]. DNA-binding RuvAB junction migration hop is 2.2 bp [PUB_0538]. RuvA footprint extends 13 nt on xsDNA side of crossover point [PUB_0716]. RuvAB footprint spans 50-54 nt along all four strands [PUB_0716]. Composition [PUB_0083].
References	Dawid A, Croquette V, Grigoriev M, Heslot F. Single-molecule study of RuvAB-mediated Holliday-junction migration. Proc Natl Acad Sci U S A 101, 11611-6 (2004). WholeCell: PUB_0532, PubMed: 15292508 Dennis C, Fedorov A, Käs E, Salomé L, Grigoriev M. RuvAB-directed branch migration of individual Holliday junctions is impeded by sequence heterology. EMBO J 23, 2413-22 (2004). WholeCell: PUB_0534, PubMed: 15167893 Grigoriev M, Hsieh P. Migration of a Holliday junction through a nucleosome directed by the E. coli RuvAB motor protein. Mol Cell 2, 373-81 (1998). WholeCell: PUB_0535, PubMed: 9774975 Hiom K, West SC. Branch migration during homologous recombination: assembly of a RuvAB-Holliday junction complex in vitro. Cell 80, 787-93 (1995). WholeCell: PUB_0716, PubMed: 7889572 Karymov MA, Chinnaraj M, Bogdanov A, Srinivasan AR, Zheng G, Olson WK, Lyubchenko YL. Structure, dynamics, and branch migration of a DNA Holliday junction: a single-molecule fluorescence and modeling study. Biophys J 95, 4372-83 (2008). WholeCell: PUB_0538, PubMed: 18658216 ... 5 more Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 58, 401-65 (1994). WholeCell: PUB_0536, PubMed: 7968921 Panyutin IG, Hsieh P. The kinetics of spontaneous DNA branch migration. Proc Natl Acad Sci U S A 91, 2021-5 (1994). WholeCell: PUB_0531, PubMed: 8134343 Sharples GJ, Ingleston SM, Lloyd RG. Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA. J Bacteriol 181, 5543-50 (1999). WholeCell: PUB_0083, PubMed: 10482492 Tsaneva IR, Müller B, West SC. ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E. coli. Cell 69, 1171-80 (1992). WholeCell: PUB_0533, PubMed: 1617728 West SC. Processing of recombination intermediates by the RuvABC proteins. Annu Rev Genet 31, 213-44 (1997). WholeCell: PUB_0537, PubMed: 9442895

Metadata
Created	2012-10-01 15:07:41
Last updated	2012-10-01 15:14:14