PDBsum entry: 1z6a

Hydrolase/recombination

PDB-id

1z6a

	Biological unit* = asymmetric unit, as shown (as deduced by PQS*)


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Description

Header details

Protein chain

Ligands

PO4 ×8

Metal ions

_HG ×3

* Residue conservation analysis

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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 p2. Organism_taxid: 273057. Strain: p2. Expressed in: escherichia coli. Expression_system_taxid: 562

Biological unit:

Monomer (from PQS)

UniProt:

Q97XQ5 (Q97XQ5_SULSO)

Seq:

Struc:

Seq:

124 a.a.

Struc:

480 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

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

Related entries:

1z5z
1z63

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Key reference

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.