PDBsum entry 1in7

Go to PDB code: 
protein ligands links
DNA binding protein PDB id
Protein chain
298 a.a. *
ACT ×2
Waters ×231
* Residue conservation analysis
PDB id:
Name: DNA binding protein
Title: Thermotoga maritima ruvb r170a
Structure: Holliday junction DNA helicase ruvb. Chain: a. Synonym: ruvb. Engineered: yes. Mutation: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: ruvb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.90Å     R-factor:   0.216     R-free:   0.250
Authors: C.D.Putnam,S.B.Clancy,H.Tsuruta,J.G.Wetmur,J.A.Tainer
Key ref:
C.D.Putnam et al. (2001). Structure and mechanism of the RuvB Holliday junction branch migration motor. J Mol Biol, 311, 297-310. PubMed id: 11478862 DOI: 10.1006/jmbi.2001.4852
12-May-01     Release date:   08-Aug-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q56313  (RUVB_THEMA) -  Holliday junction ATP-dependent DNA helicase RuvB
334 a.a.
298 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
+ H(2)O
Bound ligand (Het Group name = ADP)
corresponds exactly
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to DNA damage stimulus   5 terms 
  Biochemical function     nucleotide binding     7 terms  


DOI no: 10.1006/jmbi.2001.4852 J Mol Biol 311:297-310 (2001)
PubMed id: 11478862  
Structure and mechanism of the RuvB Holliday junction branch migration motor.
C.D.Putnam, S.B.Clancy, H.Tsuruta, S.Gonzalez, J.G.Wetmur, J.A.Tainer.
The RuvB hexamer is the chemomechanical motor of the RuvAB complex that migrates Holliday junction branch-points in DNA recombination and the rescue of stalled DNA replication forks. The 1.6 A crystal structure of Thermotoga maritima RuvB together with five mutant structures reveal that RuvB is an ATPase-associated with diverse cellular activities (AAA+-class ATPase) with a winged-helix DNA-binding domain. The RuvB-ADP complex structure and mutagenesis suggest how AAA+-class ATPases couple nucleotide binding and hydrolysis to interdomain conformational changes and asymmetry within the RuvB hexamer implied by the crystallographic packing and small-angle X-ray scattering in solution. ATP-driven domain motion is positioned to move double-stranded DNA through the hexamer and drive conformational changes between subunits by altering the complementary hydrophilic protein- protein interfaces. Structural and biochemical analysis of five motifs in the protein suggest that ATP binding is a strained conformation recognized both by sensors and the Walker motifs and that intersubunit activation occurs by an arginine finger motif reminiscent of the GTPase-activating proteins. Taken together, these results provide insights into how RuvB functions as a motor for branch migration of Holliday junctions.
  Selected figure(s)  
Figure 2.
Figure 2. RuvB nucleotide recognition and an implied strained ATP-bound conformation. (a) Details of the nucleotide-binding site reveal that the phosphate groups are coordinated by the Walker A motif (including Lys64 and Thr65) with the ADP moiety contacted by residues of the sensor 2 motif (Pro216 and Arg217). Sensor 1 (Thr158) and Walker B (Asp109 and Glu110) motifs are located near the position of the g-phosphate group. The isosurface of the simulated annealing omit difference density is shown for ADP, contoured at 3s (green). (b) Structure-based mutational analysis reveals the importance of ATP hydrolysis in branch migration and the key roles played by sensor 1, sensor 2, and arginine finger in RuvB. Biochemical characterization of the DNA-dependent ATPase activity of RuvB mutants[21] and branch migration of an in vitro reconstituted RuvAB-Holliday junction complex.[51 and 52] Proteins scored as inactive, "-", in branch migration activity are either wholly or substantially compromised, as they showed less than 3 % of wild-type activity after an incubation of 60 minutes. (c) Overlay of the wild-type RuvB protein (blue) with structures of the sensor 1 mutations Ala156Ser (yellow), Thr158Val (light blue), and the Walker A mutation Lys64Arg (light brown). (d) Overlay of the sensor 2 mutation Pro216Gly (yellow) with wild-type RuvB, illustrating some of the structural rearrangements required to accommodate the misregistered ATP (Figure 2(c) in the nucleotide-binding site. (e) Details of ATP binding from the Pro216Gly structure (red) and ADP binding from the wild-type structure (blue) demonstrating the reorientation of the both adenine and ribose moieties and the phosphate misregistration, where the ATP g-phosphate group binds at the b position and the ATP b-phosphate group binds at the a position. This structure suggests that binding ATP in the appropriate conformation channels binding energy into a strained RuvB conformation. (f) Overlay of the arginine finger mutation Arg170Ala (yellow) with wild-type RuvB, suggesting the dramatic loss of ATPase and branch migration assay are due to loss of the guanidium functionality, as structural perturbations are small.
Figure 6.
Figure 6. Structurally implied mechanism for branch migration. Illustration of a mechanism for RuvB branch migration involving a rotation of the RuvB hexamer (green, cyan, and blue subunits) relative to the RuvA tetramer (yellow bar). Stepwise migration of the DNA is indicated by motion of the circled numbers through the center of the hexamer, although the fundamental translocation step size is unknown. The 2-fold symmetry of the loading of the nucleotide binding sites is based on pre-steady state kinetics of RuvB, which hydrolyzes two ATP molecules per hexamer.[38 and 45] The starting state (a) with two ATP and two ADP molecules is inferred from the optimal nucleotide ratio (2 ATPgS:1 ATP) for forming topologically underwound DNA, [21, 38 and 49] equivalent to step (b), and the productive arginine finger geometry observed in the AMP-PNP bound NSF-D2. [41] ATP hydrolysis in step (b) may drive rotation of the RuvB hexamer (c) by opening of the ADP-bound state along DNA as well as through interactions with RuvA. ATP serves as an allosteric effector for ADP release, [45] which may be driven by interface changes between subunits that may be released after rotation (d) or during rotation. Hydrolysis of ATP by RuvB is kinetically rapid and ADP release is slow. [45]
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 311, 297-310) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20412048 A.Niewiarowski, A.S.Bradley, J.Gor, A.R.McKay, S.J.Perkins, and I.R.Tsaneva (2010).
Oligomeric assembly and interactions within the human RuvB-like RuvBL1 and RuvBL2 complexes.
  Biochem J, 429, 113-125.  
19887446 C.Zhao, E.A.Matveeva, Q.Ren, and S.W.Whiteheart (2010).
Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains.
  J Biol Chem, 285, 761-772.  
20122942 D.Das, D.Moiani, H.L.Axelrod, M.D.Miller, D.McMullan, K.K.Jin, P.Abdubek, T.Astakhova, P.Burra, D.Carlton, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, D.Ernst, J.Feuerhelm, J.C.Grant, A.Grzechnik, S.K.Grzechnik, G.W.Han, L.Jaroszewski, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, D.Marciano, A.T.Morse, E.Nigoghossian, L.Okach, J.Paulsen, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, J.A.Tainer, and I.A.Wilson (2010).
Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair.
  J Mol Biol, 397, 647-663.
PDB code: 2q8u
20130681 K.L.Cheung, J.Huen, W.A.Houry, and J.Ortega (2010).
Comparison of the multiple oligomeric structures observed for the Rvb1 and Rvb2 proteins.
  Biochem Cell Biol, 88, 77-88.  
19919849 S.Park, and A.Terzic (2010).
Quaternary structure of KATP channel SUR2A nucleotide binding domains resolved by synchrotron radiation X-ray scattering.
  J Struct Biol, 169, 243-251.  
18834951 A.Gospodinov, I.Tsaneva, and B.Anachkova (2009).
RAD51 foci formation in response to DNA damage is modulated by TIP49.
  Int J Biochem Cell Biol, 41, 925-933.  
19095618 M.E.Stroupe, C.Xu, B.L.Goode, and N.Grigorieff (2009).
Actin filament labels for localizing protein components in large complexes viewed by electron microscopy.
  RNA, 15, 244-248.  
19089981 Q.Xu, C.L.Rife, D.Carlton, M.D.Miller, S.S.Krishna, M.A.Elsliger, P.Abdubek, T.Astakhova, H.J.Chiu, T.Clayton, L.Duan, J.Feuerhelm, S.K.Grzechnik, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, R.Reyes, H.van den Bedem, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus.
  Proteins, 74, 1041-1049.
PDB code: 2fna
19000695 Q.Xu, D.McMullan, P.Abdubek, T.Astakhova, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, M.A.Elsliger, J.Feuerhelm, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.Sri Krishna, A.Kumar, D.Marciano, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, C.Trame, H.van den Bedem, D.Weekes, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
A structural basis for the regulatory inactivation of DnaA.
  J Mol Biol, 385, 368-380.
PDB code: 3bos
18332143 L.C.Briggs, G.S.Baldwin, N.Miyata, H.Kondo, X.Zhang, and P.S.Freemont (2008).
Analysis of nucleotide binding to P97 reveals the properties of a tandem AAA hexameric ATPase.
  J Biol Chem, 283, 13745-13752.  
18942176 M.Le Masson, Z.Baharoglu, and B.Michel (2008).
ruvA and ruvB mutants specifically impaired for replication fork reversal.
  Mol Microbiol, 70, 537-548.  
  18765919 S.Gorynia, P.M.Matias, T.M.Bandeiras, P.Donner, and M.A.Carrondo (2008).
Cloning, expression, purification, crystallization and preliminary X-ray analysis of the human RuvBL1-RuvBL2 complex.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 840-846.  
17255937 A.Yamagata, and J.A.Tainer (2007).
Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism.
  EMBO J, 26, 878-890.
PDB codes: 2oap 2oaq
18078545 C.D.Putnam, M.Hammel, G.L.Hura, and J.A.Tainer (2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
  Q Rev Biophys, 40, 191-285.  
17720918 D.L.Updike, and S.E.Mango (2007).
Genetic suppressors of Caenorhabditis elegans pha-4/FoxA identify the predicted AAA helicase ruvb-1/RuvB.
  Genetics, 177, 819-833.  
17393462 I.Aksentijevich, C.D Putnam, E.F.Remmers, J.L.Mueller, J.Le, R.D.Kolodner, Z.Moak, M.Chuang, F.Austin, R.Goldbach-Mansky, H.M.Hoffman, and D.L.Kastner (2007).
The clinical continuum of cryopyrinopathies: novel CIAS1 mutations in North American patients and a new cryopyrin model.
  Arthritis Rheum, 56, 1273-1285.  
17157498 K.P.Hopfner, and J.Michaelis (2007).
Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics.
  Curr Opin Struct Biol, 17, 87-95.  
17716973 K.Siddiqui, and B.Stillman (2007).
ATP-dependent assembly of the human origin recognition complex.
  J Biol Chem, 282, 32370-32383.  
17506634 M.R.Singleton, M.S.Dillingham, and D.B.Wigley (2007).
Structure and mechanism of helicases and nucleic acid translocases.
  Annu Rev Biochem, 76, 23-50.  
17373706 W.Zheng, J.C.Liao, B.R.Brooks, and S.Doniach (2007).
Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model.
  Proteins, 67, 886-896.  
16527806 J.M.Cox, S.N.Abbott, S.Chitteni-Pattu, R.B.Inman, and M.M.Cox (2006).
Complementation of one RecA protein point mutation by another. Evidence for trans catalysis of ATP hydrolysis.
  J Biol Chem, 281, 12968-12975.  
16689629 J.P.Erzberger, and J.M.Berger (2006).
Evolutionary relationships and structural mechanisms of AAA+ proteins.
  Annu Rev Biophys Biomol Struct, 35, 93.  
17060327 P.M.Matias, S.Gorynia, P.Donner, and M.A.Carrondo (2006).
Crystal structure of the human AAA+ protein RuvBL1.
  J Biol Chem, 281, 38918-38929.
PDB code: 2c9o
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
16864792 Y.W.Han, T.Tani, M.Hayashi, T.Hishida, H.Iwasaki, H.Shinagawa, and Y.Harada (2006).
Direct observation of DNA rotation during branch migration of Holliday junction DNA by Escherichia coli RuvA-RuvB protein complex.
  Proc Natl Acad Sci U S A, 103, 11544-11548.  
15556943 C.V.Privezentzev, A.Keeley, B.Sigala, and I.R.Tsaneva (2005).
The role of RuvA octamerization for RuvAB function in vitro and in vivo.
  J Biol Chem, 280, 3365-3375.  
15989952 G.L.Hersch, R.E.Burton, D.N.Bolon, T.A.Baker, and R.T.Sauer (2005).
Asymmetric interactions of ATP with the AAA+ ClpX6 unfoldase: allosteric control of a protein machine.
  Cell, 121, 1017-1027.  
15612912 L.A.Fernández (2005).
Exploring prokaryotic diversity: there are other molecular worlds.
  Mol Microbiol, 55, 5.  
15611053 M.Su'etsugu, T.R.Shimuta, T.Ishida, H.Kawakami, and T.Katayama (2005).
Protein associations in DnaA-ATP hydrolysis mediated by the Hda-replicase clamp complex.
  J Biol Chem, 280, 6528-6536.  
15642269 T.Nishino, K.Komori, D.Tsuchiya, Y.Ishino, and K.Morikawa (2005).
Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing.
  Structure, 13, 143-153.
PDB code: 1wp9
15972826 T.Ohnishi, T.Hishida, Y.Harada, H.Iwasaki, and H.Shinagawa (2005).
Structure-function analysis of the three domains of RuvB DNA motor protein.
  J Biol Chem, 280, 30504-30510.  
15371413 B.Pucci, M.De Felice, M.Rossi, S.Onesti, and F.M.Pisani (2004).
Amino acids of the Sulfolobus solfataricus mini-chromosome maintenance-like DNA helicase involved in DNA binding/remodeling.
  J Biol Chem, 279, 49222-49228.  
15070725 D.J.Crampton, S.Guo, D.E.Johnson, and C.C.Richardson (2004).
The arginine finger of bacteriophage T7 gene 4 helicase: role in energy coupling.
  Proc Natl Acad Sci U S A, 101, 4373-4378.  
15289463 E.A.Abbate, J.M.Berger, and M.R.Botchan (2004).
The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2.
  Genes Dev, 18, 1981-1996.
PDB code: 1tue
14990749 F.Constantinesco, P.Forterre, E.V.Koonin, L.Aravind, and C.Elie (2004).
A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea.
  Nucleic Acids Res, 32, 1439-1447.  
15093826 K.Yamada, M.Ariyoshi, and K.Morikawa (2004).
Three-dimensional structural views of branch migration and resolution in DNA homologous recombination.
  Curr Opin Struct Biol, 14, 130-137.  
15466593 L.M.Iyer, K.S.Makarova, E.V.Koonin, and L.Aravind (2004).
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging.
  Nucleic Acids Res, 32, 5260-5279.  
15292509 R.Amit, O.Gileadi, and J.Stavans (2004).
Direct observation of RuvAB-catalyzed branch migration of single Holliday junctions.
  Proc Natl Acad Sci U S A, 101, 11605-11610.  
15210950 T.Hishida, Y.W.Han, S.Fujimoto, H.Iwasaki, and H.Shinagawa (2004).
Direct evidence that a conserved arginine in RuvB AAA+ ATPase acts as an allosteric effector for the ATPase activity of the adjacent subunit in a hexamer.
  Proc Natl Acad Sci U S A, 101, 9573-9577.  
14747526 Y.M.Loo, and T.Melendy (2004).
Recruitment of replication protein A by the papillomavirus E1 protein and modulation by single-stranded DNA.
  J Virol, 78, 1605-1615.  
12582167 A.Johnson, and M.O'Donnell (2003).
Ordered ATP hydrolysis in the gamma complex clamp loader AAA+ machine.
  J Biol Chem, 278, 14406-14413.  
12774115 D.Li, R.Zhao, W.Lilyestrom, D.Gai, R.Zhang, J.A.DeCaprio, E.Fanning, A.Jochimiak, G.Szakonyi, and X.S.Chen (2003).
Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen.
  Nature, 423, 512-518.
PDB code: 1n25
12441335 H.Yokoyama, H.Kurumizaka, S.Ikawa, S.Yokoyama, and T.Shibata (2003).
Holliday junction binding activity of the human Rad51B protein.
  J Biol Chem, 278, 2767-2772.  
12906833 J.A.James, C.R.Escalante, M.Yoon-Robarts, T.A.Edwards, R.M.Linden, and A.K.Aggarwal (2003).
Crystal structure of the SF3 helicase from adeno-associated virus type 2.
  Structure, 11, 1025-1035.
PDB code: 1s9h
12480933 M.J.Davey, C.Indiani, and M.O'Donnell (2003).
Reconstitution of the Mcm2-7p heterohexamer, subunit arrangement, and ATP site architecture.
  J Biol Chem, 278, 4491-4499.  
12586394 R.Giraldo (2003).
Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives.
  FEMS Microbiol Rev, 26, 533-554.  
12940820 T.Hishida, H.Iwasaki, Y.W.Han, T.Ohnishi, and H.Shinagawa (2003).
Uncoupling of the ATPase activity from the branch migration activity of RuvAB protein complexes containing both wild-type and ATPase-defective RuvB proteins.
  Genes Cells, 8, 721-730.  
14566326 T.Pape, H.Meka, S.Chen, G.Vicentini, M.van Heel, and S.Onesti (2003).
Hexameric ring structure of the full-length archaeal MCM protein complex.
  EMBO Rep, 4, 1079-1083.  
14526036 Y.K.Wang, S.Park, B.T.Nixon, and T.R.Hoover (2003).
Nucleotide-dependent conformational changes in the sigma54-dependent activator DctD.
  J Bacteriol, 185, 6215-6219.  
11782421 D.A.Hattendorf, and S.L.Lindquist (2002).
Cooperative kinetics of both Hsp104 ATPase domains and interdomain communication revealed by AAA sensor-1 mutants.
  EMBO J, 21, 12-21.  
11867765 D.A.Hattendorf, and S.L.Lindquist (2002).
Analysis of the AAA sensor-2 motif in the C-terminal ATPase domain of Hsp104 with a site-specific fluorescent probe of nucleotide binding.
  Proc Natl Acad Sci U S A, 99, 2732-2737.  
12205096 F.Guo, M.R.Maurizi, L.Esser, and D.Xia (2002).
Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease.
  J Biol Chem, 277, 46743-46752.
PDB codes: 1k6k 1ksf
12434150 I.Rouiller, B.DeLaBarre, A.P.May, W.I.Weis, A.T.Brunger, R.A.Milligan, and E.M.Wilson-Kubalek (2002).
Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle.
  Nat Struct Biol, 9, 950-957.  
11839499 J.M.Caruthers, and D.B.McKay (2002).
Helicase structure and mechanism.
  Curr Opin Struct Biol, 12, 123-133.  
12234917 J.P.Erzberger, M.M.Pirruccello, and J.M.Berger (2002).
The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation.
  EMBO J, 21, 4763-4773.
PDB code: 1l8q
12415300 M.J.Davey, D.Jeruzalmi, J.Kuriyan, and M.O'Donnell (2002).
Motors and switches: AAA+ machines within the replisome.
  Nat Rev Mol Cell Biol, 3, 826-835.  
12209147 P.Chène (2002).
ATPases as drug targets: learning from their structure.
  Nat Rev Drug Discov, 1, 665-673.  
11595187 M.R.Singleton, S.Scaife, and D.B.Wigley (2001).
Structural analysis of DNA replication fork reversal by RecG.
  Cell, 107, 79-89.
PDB code: 1gm5
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.