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Hydrolase/recombination PDB id
1z6a
Jmol
Contents
Protein chain
480 a.a. *
Ligands
PO4 ×8
Metals
_HG ×3
* Residue conservation analysis
PDB id:
1z6a
Name: Hydrolase/recombination
Title: Sulfolobus solfataricus swi2/snf2 atpase core domain
Structure: Helicase of the snf2/rad54 family. Chain: a. Fragment: residue 431-789, 800-906. Engineered: yes
Source: Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Monomer (from PQS)
Resolution:
3.00Å     R-factor:   0.240     R-free:   0.297
Authors: H.Duerr,C.Koerner,M.Mueller,V.Hickmann,K.P.Hopfner
Key ref:
H.Dürr et al. (2005). X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell, 121, 363-373. PubMed id: 15882619 DOI: 10.1016/j.cell.2005.03.026
Date:
22-Mar-05     Release date:   03-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q97XQ5  (Q97XQ5_SULSO) -  Helicase of the snf2/rad54 family (Carboxy end), hypothetical
Seq:
Struc: 		124 a.a.
480 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     4 terms  

 

 
DOI no: 10.1016/j.cell.2005.03.026 Cell 121:363-373 (2005)
PubMed id: 15882619  
 
 
X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA.
H.Dürr, C.Körner, M.Müller, V.Hickmann, K.P.Hopfner.
 
  ABSTRACT  
 
SWI2/SNF2 ATPases remodel chromatin or other DNA:protein complexes by a poorly understood mechanism that involves ATP-dependent DNA translocation and generation of superhelical torsion. Crystal structures of a dsDNA-translocating SWI2/SNF2 ATPase core from Sulfolobus solfataricus reveal two helical SWI2/SNF2 specific subdomains, fused to a DExx box helicase-related ATPase core. Fully base paired duplex DNA binds along a central cleft via both minor groove strands, indicating that SWI2/SNF2 ATPases travel along the dsDNA minor groove without strand separation. A structural switch, linking DNA binding and the active site DExx motif, may account for the stimulation of ATPase activity by dsDNA. Our results suggest that torque in remodeling processes is generated by an ATP-driven screw motion of DNA along the active site cleft. The structures also redefine SWI2/SNF2 functional motifs and uncover unexpected structural correlation of mutations in Cockayne and X-linked mental retardation syndromes.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structure of the SsoRad54cd:DNA Complex 		Figure 3.
Figure 3. DNA Interaction
 
  The above figures are reprinted by permission from Cell Press: Cell (2005, 121, 363-373) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525954 G.Ghosal, J.Yuan, and J.Chen (2011).
The HARP domain dictates the annealing helicase activity of HARP/SMARCAL1.
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21525927 K.Yamada, T.D.Frouws, B.Angst, D.J.Fitzgerald, C.DeLuca, K.Schimmele, D.F.Sargent, and T.J.Richmond (2011).
Structure and mechanism of the chromatin remodelling factor ISW1a.
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21505078 M.Mitson, L.A.Kelley, M.J.Sternberg, D.R.Higgs, and R.J.Gibbons (2011).
Functional significance of mutations in the Snf2 domain of ATRX.
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20089461 A.V.Mazin, O.M.Mazina, D.V.Bugreev, and M.J.Rossi (2010).
Rad54, the motor of homologous recombination.
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20529861 C.Matranga, and A.M.Pyle (2010).
Double-stranded RNA-dependent ATPase DRH-3: insight into its role in RNAsilencing in Caenorhabditis elegans.
  J Biol Chem, 285, 25363-25371.  
20832723 G.Hauk, J.N.McKnight, I.M.Nodelman, and G.D.Bowman (2010).
The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor.
  Mol Cell, 39, 711-723.
PDB code: 3mwy
20111866 M.J.Lathrop, L.Chakrabarti, J.Eng, C.H.Rhodes, T.Lutz, A.Nieto, H.D.Liggitt, S.Warner, J.Fields, R.Stöger, and S.Fiering (2010).
Deletion of the Chd6 exon 12 affects motor coordination.
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20122405 R.J.Lake, A.Geyko, G.Hemashettar, Y.Zhao, and H.Y.Fan (2010).
UV-induced association of the CSB remodeling protein with chromatin requires ATP-dependent relief of N-terminal autorepression.
  Mol Cell, 37, 235-246.  
19894250 V.Laugel, C.Dalloz, M.Durand, F.Sauvanaud, U.Kristensen, M.C.Vincent, L.Pasquier, S.Odent, V.Cormier-Daire, B.Gener, E.S.Tobias, J.L.Tolmie, D.Martin-Coignard, V.Drouin-Garraud, D.Heron, H.Journel, E.Raffo, J.Vigneron, S.Lyonnet, V.Murday, D.Gubser-Mercati, B.Funalot, L.Brueton, J.Sanchez Del Pozo, E.Muñoz, A.R.Gennery, M.Salih, M.Noruzinia, K.Prescott, L.Ramos, Z.Stark, K.Fieggen, B.Chabrol, P.Sarda, P.Edery, A.Bloch-Zupan, H.Fawcett, D.Pham, J.M.Egly, A.R.Lehmann, A.Sarasin, and H.Dollfus (2010).
Mutation update for the CSB/ERCC6 and CSA/ERCC8 genes involved in Cockayne syndrome.
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20142505 Y.Lorch, B.Maier-Davis, and R.D.Kornberg (2010).
Mechanism of chromatin remodeling.
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20179009 Z.Yue, S.Xiong, L.Sun, W.Huang, Y.Mo, L.Huang, X.Jiang, S.Chen, B.Hu, and Y.Wang (2010).
Novel compound mutations of SMARCAL1 associated with severe Schimke immuno-osseous dysplasia in a Chinese patient.
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19956593 A.Neves-Costa, W.R.Will, A.T.Vetter, J.R.Miller, and P.Varga-Weisz (2009).
The SNF2-family member Fun30 promotes gene silencing in heterochromatic loci.
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19464317 B.Illi, C.Colussi, A.Grasselli, A.Farsetti, M.C.Capogrossi, and C.Gaetano (2009).
NO sparks off chromatin: tales of a multifaceted epigenetic regulator.
  Pharmacol Ther, 123, 344-352.  
19580815 B.R.Berquist, and D.M.Wilson (2009).
Nucleic acid binding activity of human Cockayne syndrome B protein and identification of Ca(2+) as a novel metal cofactor.
  J Mol Biol, 391, 820-832.  
19282450 C.A.Haseltine, and S.C.Kowalczykowski (2009).
An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA.
  Nucleic Acids Res, 37, 2757-2770.  
20033039 L.R.Racki, J.G.Yang, N.Naber, P.D.Partensky, A.Acevedo, T.J.Purcell, R.Cooke, Y.Cheng, and G.J.Narlikar (2009).
The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes.
  Nature, 462, 1016-1021.  
19079266 M.Lapkouski, S.Panjikar, P.Janscak, I.K.Smatanova, J.Carey, R.Ettrich, and E.Csefalvay (2009).
Structure of the motor subunit of type I restriction-modification complex EcoR124I.
  Nat Struct Mol Biol, 16, 94-95.
PDB code: 2w00
19324887 M.Nongkhlaw, P.Dutta, J.W.Hockensmith, S.S.Komath, and R.Muthuswami (2009).
Elucidating the mechanism of DNA-dependent ATP hydrolysis mediated by DNA-dependent ATPase A, a member of the SWI2/SNF2 protein family.
  Nucleic Acids Res, 37, 3332-3341.  
19625490 N.T.Uyen, S.Y.Park, J.W.Choi, H.J.Lee, K.Nishi, and J.S.Kim (2009).
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.
  Nucleic Acids Res, 37, 6960-6969.
PDB code: 3h1t
19119185 S.Myong, S.Cui, P.V.Cornish, A.Kirchhofer, M.U.Gack, J.U.Jung, K.P.Hopfner, and T.Ha (2009).
Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA.
  Science, 323, 1070-1074.  
19713942 V.Oksenych, B.B.de Jesus, A.Zhovmer, J.M.Egly, and F.Coin (2009).
Molecular insights into the recruitment of TFIIH to sites of DNA damage.
  EMBO J, 28, 2971-2980.  
19074197 X.Li, and W.D.Heyer (2009).
RAD54 controls access to the invading 3'-OH end after RAD51-mediated DNA strand invasion in homologous recombination in Saccharomyces cerevisiae.
  Nucleic Acids Res, 37, 638-646.  
19139279 Z.Wang, and G.Prelich (2009).
Quality control of a transcriptional regulator by SUMO-targeted degradation.
  Mol Cell Biol, 29, 1694-1706.  
18786404 G.Shaw, J.Gan, Y.N.Zhou, H.Zhi, P.Subburaman, R.Zhang, A.Joachimiak, D.J.Jin, and X.Ji (2008).
Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription.
  Structure, 16, 1417-1427.
PDB code: 3dmq
18339542 L.R.Racki, and G.J.Narlikar (2008).
ATP-dependent chromatin remodeling enzymes: two heads are not better, just different.
  Curr Opin Genet Dev, 18, 137-144.  
18814851 M.Hu, Y.B.Zhang, L.Qian, R.P.Briñas, L.Kuznetsova, and J.F.Hainfeld (2008).
Three-dimensional structure of human chromatin accessibility complex hCHRAC by electron microscopy.
  J Struct Biol, 164, 263-269.  
18647240 N.D.Thomsen, and J.M.Berger (2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
  Mol Microbiol, 69, 1071-1090.  
18267970 R.Lewis, H.Dürr, K.P.Hopfner, and J.Michaelis (2008).
Conformational changes of a Swi2/Snf2 ATPase during its mechano-chemical cycle.
  Nucleic Acids Res, 36, 1881-1890.  
18606810 R.O.Sprouse, I.Shcherbakova, H.Cheng, E.Jamison, M.Brenowitz, and D.T.Auble (2008).
Function and structural organization of mot1 bound to a natural target promoter.
  J Biol Chem, 283, 24935-24948.  
19029894 Y.Chaban, C.Ezeokonkwo, W.H.Chung, F.Zhang, R.D.Kornberg, B.Maier-Davis, Y.Lorch, and F.J.Asturias (2008).
Structure of a RSC-nucleosome complex and insights into chromatin remodeling.
  Nat Struct Mol Biol, 15, 1272-1277.  
17239578 A.M.Deaconescu, N.Savery, and S.A.Darst (2007).
The bacterial transcription repair coupling factor.
  Curr Opin Struct Biol, 17, 96.  
17704061 A.V.Nimonkar, I.Amitani, R.J.Baskin, and S.C.Kowalczykowski (2007).
Single molecule imaging of Tid1/Rdh54, a Rad54 homolog that translocates on duplex DNA and can disrupt joint molecules.
  J Biol Chem, 282, 30776-30784.  
17913745 B.A.McKinley, and M.V.Sukhodolets (2007).
Escherichia coli RNA polymerase-associated SWI/SNF protein RapA: evidence for RNA-directed binding and remodeling activity.
  Nucleic Acids Res, 35, 7044-7060.  
17984961 B.R.Cairns (2007).
Chromatin remodeling: insights and intrigue from single-molecule studies.
  Nat Struct Mol Biol, 14, 989-996.  
17508131 G.Bernal, and E.Maldonado (2007).
Isolation of a novel complex of the SWI/SNF family from Schizosaccharomyces pombe and its effects on in vitro transcription in nucleosome arrays.
  Mol Cell Biochem, 303, 131-139.  
17949749 H.Ferreira, A.Flaus, and T.Owen-Hughes (2007).
Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms.
  J Mol Biol, 374, 563-579.  
17878153 I.D.Kerr, S.Sivakolundu, Z.Li, J.C.Buchsbaum, L.A.Knox, R.Kriwacki, and S.W.White (2007).
Crystallographic and NMR analyses of UvsW and UvsW.1 from bacteriophage T4.
  J Biol Chem, 282, 34392-34400.
PDB codes: 2jpn 2oca
17558417 K.Büttner, S.Nehring, and K.P.Hopfner (2007).
Structural basis for DNA duplex separation by a superfamily-2 helicase.
  Nat Struct Mol Biol, 14, 647-652.
PDB codes: 2p6r 2p6u
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.  
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.  
17572090 N.J.Savery (2007).
The molecular mechanism of transcription-coupled DNA repair.
  Trends Microbiol, 15, 326-333.  
17545145 O.M.Mazina, M.J.Rossi, N.H.Thomaä, and A.V.Mazin (2007).
Interactions of human rad54 protein with branched DNA molecules.
  J Biol Chem, 282, 21068-21080.  
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
17306844 V.K.Gangaraju, and B.Bartholomew (2007).
Mechanisms of ATP dependent chromatin remodeling.
  Mutat Res, 618, 3.  
17908792 W.Dang, and B.Bartholomew (2007).
Domain architecture of the catalytic subunit in the ISW2-nucleosome complex.
  Mol Cell Biol, 27, 8306-8317.  
16738128 A.Flaus, D.M.Martin, G.J.Barton, and T.Owen-Hughes (2006).
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs.
  Nucleic Acids Res, 34, 2887-2905.  
16469698 A.M.Deaconescu, A.L.Chambers, A.J.Smith, B.E.Nickels, A.Hochschild, N.J.Savery, and S.A.Darst (2006).
Structural basis for bacterial transcription-coupled DNA repair.
  Cell, 124, 507-520.
PDB code: 2eyq
16723979 A.Saha, J.Wittmeyer, and B.R.Cairns (2006).
Chromatin remodelling: the industrial revolution of DNA around histones.
  Nat Rev Mol Cell Biol, 7, 437-447.  
16317791 D.W.Heinz, M.S.Weiss, and K.U.Wendt (2006).
Biomacromolecular interactions, assemblies and machines: a structural view.
  Chembiochem, 7, 203-208.  
16935875 H.Dürr, A.Flaus, T.Owen-Hughes, and K.P.Hopfner (2006).
Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures.
  Nucleic Acids Res, 34, 4160-4167.  
16487697 H.Wurtele, and A.Verreault (2006).
Histone post-translational modifications and the response to DNA double-strand breaks.
  Curr Opin Cell Biol, 18, 137-144.  
16818238 I.Amitani, R.J.Baskin, and S.C.Kowalczykowski (2006).
Visualization of Rad54, a chromatin remodeling protein, translocating on single DNA molecules.
  Mol Cell, 23, 143-148.  
17190599 J.Y.Lee, and W.Yang (2006).
UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke.
  Cell, 127, 1349-1360.
PDB codes: 2is1 2is2 2is4 2is6
16821138 K.Bouazoune, and A.Brehm (2006).
ATP-dependent chromatin remodeling complexes in Drosophila.
  Chromosome Res, 14, 433-449.  
16785421 K.Kiianitsa, J.A.Solinger, and W.D.Heyer (2006).
Terminal association of Rad54 protein with the Rad51-dsDNA filament.
  Proc Natl Acad Sci U S A, 103, 9767-9772.  
16679012 L.Aravind, L.M.Iyer, and E.V.Koonin (2006).
Comparative genomics and structural biology of the molecular innovations of eukaryotes.
  Curr Opin Struct Biol, 16, 409-419.  
16642041 L.K.Stanley, R.Seidel, C.van der Scheer, N.H.Dekker, M.D.Szczelkun, and C.Dekker (2006).
When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I.
  EMBO J, 25, 2230-2239.  
16831867 P.Chi, Y.Kwon, C.Seong, A.Epshtein, I.Lam, P.Sung, and H.L.Klein (2006).
Yeast recombination factor Rdh54 functionally interacts with the Rad51 recombinase and catalyzes Rad51 removal from DNA.
  J Biol Chem, 281, 26268-26279.  
16503135 P.D.Varga-Weisz, and P.B.Becker (2006).
Regulation of higher-order chromatin structures by nucleosome-remodelling factors.
  Curr Opin Genet Dev, 16, 151-156.  
16541100 R.O.Sprouse, M.Brenowitz, and D.T.Auble (2006).
Snf2/Swi2-related ATPase Mot1 drives displacement of TATA-binding protein by gripping DNA.
  EMBO J, 25, 1492-1504.  
16935872 W.D.Heyer, X.Li, M.Rolfsmeier, and X.P.Zhang (2006).
Rad54: the Swiss Army knife of homologous recombination?
  Nucleic Acids Res, 34, 4115-4125.  
16086025 A.Saha, J.Wittmeyer, and B.R.Cairns (2005).
Chromatin remodeling through directional DNA translocation from an internal nucleosomal site.
  Nat Struct Mol Biol, 12, 747-755.  
16287714 S.J.Bultman, T.C.Gebuhr, and T.Magnuson (2005).
A Brg1 mutation that uncouples ATPase activity from chromatin remodeling reveals an essential role for SWI/SNF-related complexes in beta-globin expression and erythroid development.
  Genes Dev, 19, 2849-2861.  
16301801 T.S.Peat, J.A.Christopher, and J.Newman (2005).
Tapping the Protein Data Bank for crystallization information.
  Acta Crystallogr D Biol Crystallogr, 61, 1662-1669.  
16107709 T.Thorslund, C.von Kobbe, J.A.Harrigan, F.E.Indig, M.Christiansen, T.Stevnsner, and V.A.Bohr (2005).
Cooperation of the Cockayne syndrome group B protein and poly(ADP-ribose) polymerase 1 in the response to oxidative stress.
  Mol Cell Biol, 25, 7625-7636.  
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.