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PDBsum entry 1oyy

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protein ligands metals links
Hydrolase PDB id
1oyy
Jmol
Contents
Protein chain
512 a.a. *
Ligands
AGS
Metals
_ZN
_MN ×2
Waters ×43
* Residue conservation analysis
PDB id:
1oyy
Name: Hydrolase
Title: Structure of the recq catalytic core bound to atp-gamma-s
Structure: Atp-dependent DNA helicase. Chain: a. Fragment: 54 kda catalytic domain. Synonym: recq helicase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: recq. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.50Å     R-factor:   0.230     R-free:   0.298
Authors: D.A.Bernstein,M.C.Zittel,J.L.Keck
Key ref: D.A.Bernstein et al. (2003). High-resolution structure of the E.coli RecQ helicase catalytic core. EMBO J, 22, 4910-4921. PubMed id: 14517231
Date:
07-Apr-03     Release date:   07-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15043  (RECQ_ECOLI) -  ATP-dependent DNA helicase RecQ
Seq:
Struc:
 
Seq:
Struc:
609 a.a.
512 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     SOS response   4 terms 
  Biochemical function     nucleic acid binding     5 terms  

 

 
EMBO J 22:4910-4921 (2003)
PubMed id: 14517231  
 
 
High-resolution structure of the E.coli RecQ helicase catalytic core.
D.A.Bernstein, M.C.Zittel, J.L.Keck.
 
  ABSTRACT  
 
RecQ family helicases catalyze critical genome maintenance reactions in bacterial and eukaryotic cells, playing key roles in several DNA metabolic processes. Mutations in recQ genes are linked to genome instability and human disease. To define the physical basis of RecQ enzyme function, we have determined a 1.8 A resolution crystal structure of the catalytic core of Escherichia coli RecQ in its unbound form and a 2.5 A resolution structure of the core bound to the ATP analog ATPgammaS. The RecQ core comprises four conserved subdomains; two of these combine to form its helicase region, while the others form unexpected Zn(2+)-binding and winged-helix motifs. The structures reveal the molecular basis of missense mutations that cause Bloom's syndrome, a human RecQ-associated disease. Finally, based on findings from the structures, we propose a mechanism for RecQ activity that could explain its functional coordination with topoisomerase III.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21059676 B.Lucic, Y.Zhang, O.King, R.Mendoza-Maldonado, M.Berti, F.H.Niesen, N.A.Burgess-Brown, A.C.Pike, C.D.Cooper, O.Gileadi, and A.Vindigni (2011).
A prominent beta-hairpin structure in the winged-helix domain of RECQ1 is required for DNA unwinding and oligomer formation.
  Nucleic Acids Res, 39, 1703-1717.  
20389284 C.F.Chen, and S.J.Brill (2010).
An essential DNA strand-exchange activity is conserved in the divergent N-termini of BLM orthologs.
  EMBO J, 29, 1713-1725.  
20159459 K.A.Hoadley, and J.L.Keck (2010).
Werner helicase wings DNA binding.
  Structure, 18, 149-151.  
20159463 K.Kitano, S.Y.Kim, and T.Hakoshima (2010).
Structural basis for DNA strand separation by the unconventional winged-helix domain of RecQ helicase WRN.
  Structure, 18, 177-187.
PDB code: 3aaf
20211839 M.Gyimesi, K.Sarlós, and M.Kovács (2010).
Processive translocation mechanism of the human Bloom's syndrome helicase along single-stranded DNA.
  Nucleic Acids Res, 38, 4404-4414.  
20048388 N.Li, E.Henry, E.Guiot, P.Rigolet, J.C.Brochon, X.G.Xi, and E.Deprez (2010).
Multiple Escherichia coli RecQ helicase monomers cooperate to unwind long DNA substrates: a fluorescence cross-correlation spectroscopy study.
  J Biol Chem, 285, 6922-6936.  
20086270 P.Cejka, and S.C.Kowalczykowski (2010).
The full-length Saccharomyces cerevisiae Sgs1 protein is a vigorous DNA helicase that preferentially unwinds holliday junctions.
  J Biol Chem, 285, 8290-8301.  
20383562 P.Umate, R.Tuteja, and N.Tuteja (2010).
Genome-wide analysis of helicase gene family from rice and Arabidopsis: a comparison with yeast and human.
  Plant Mol Biol, 73, 449-465.  
20639533 Y.M.Kim, and B.S.Choi (2010).
Structure and function of the regulatory HRDC domain from human Bloom syndrome protein.
  Nucleic Acids Res, 38, 7764-7777.
PDB code: 2kv2
20061189 Y.Wu, and R.M.Brosh (2010).
Distinct roles of RECQ1 in the maintenance of genomic stability.
  DNA Repair (Amst), 9, 315-324.  
19151156 A.C.Pike, B.Shrestha, V.Popuri, N.Burgess-Brown, L.Muzzolini, S.Costantini, A.Vindigni, and O.Gileadi (2009).
Structure of the human RECQ1 helicase reveals a putative strand-separation pin.
  Proc Natl Acad Sci U S A, 106, 1039-1044.
PDB code: 2v1x
19949442 A.Vindigni, and I.D.Hickson (2009).
RecQ helicases: multiple structures for multiple functions?
  HFSP J, 3, 153-164.  
19165145 J.G.Yodh, B.C.Stevens, R.Kanagaraj, P.Janscak, and T.Ha (2009).
BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation.
  EMBO J, 28, 405-416.  
19017267 M.P.Killoran, P.L.Kohler, J.P.Dillard, and J.L.Keck (2009).
RecQ DNA helicase HRDC domains are critical determinants in Neisseria gonorrhoeae pilin antigenic variation and DNA repair.
  Mol Microbiol, 71, 158-171.  
19150358 R.D.Shereda, N.J.Reiter, S.E.Butcher, and J.L.Keck (2009).
Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus.
  J Mol Biol, 386, 612-625.  
19159486 T.Oyama, H.Oka, K.Mayanagi, T.Shirai, K.Matoba, R.Fujikane, Y.Ishino, and K.Morikawa (2009).
Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm.
  BMC Struct Biol, 9, 2.
PDB codes: 2zj2 2zj5 2zj8 2zja
19657341 W.K.Chu, and I.D.Hickson (2009).
RecQ helicases: multifunctional genome caretakers.
  Nat Rev Cancer, 9, 644-654.  
19099189 Y.Wu, A.N.Suhasini, and R.M.Brosh (2009).
Welcome the family of FANCJ-like helicases to the block of genome stability maintenance proteins.
  Cell Mol Life Sci, 66, 1209-1222.  
18591666 D.Lu, and J.L.Keck (2008).
Structural basis of Escherichia coli single-stranded DNA-binding protein stimulation of exonuclease I.
  Proc Natl Acad Sci U S A, 105, 9169-9174.
PDB codes: 3c94 3c95
18329872 E.J.Enemark, and L.Joshua-Tor (2008).
On helicases and other motor proteins.
  Curr Opin Struct Biol, 18, 243-257.  
18702526 K.M.Sinha, N.C.Stephanou, M.C.Unciuleac, M.S.Glickman, and S.Shuman (2008).
Domain requirements for DNA unwinding by mycobacterial UvrD2, an essential DNA helicase.
  Biochemistry, 47, 9355-9364.  
18411208 M.P.Killoran, and J.L.Keck (2008).
Structure and function of the regulatory C-terminal HRDC domain from Deinococcus radiodurans RecQ.
  Nucleic Acids Res, 36, 3139-3149.
PDB code: 2rhf
18491386 N.Cicmil, and R.H.Huang (2008).
Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis.
  Proteins, 72, 1084-1088.
PDB code: 3bl5
  18473724 R.Gupta, and R.M.Brosh (2008).
Helicases as prospective targets for anti-cancer therapy.
  Anticancer Agents Med Chem, 8, 390-401.  
18414490 T.M.Lohman, E.J.Tomko, and C.G.Wu (2008).
Non-hexameric DNA helicases and translocases: mechanisms and regulation.
  Nat Rev Mol Cell Biol, 9, 391-401.  
18448429 V.Popuri, C.Z.Bachrati, L.Muzzolini, G.Mosedale, S.Costantini, E.Giacomini, I.D.Hickson, and A.Vindigni (2008).
The Human RecQ helicases, BLM and RECQ1, display distinct DNA substrate specificities.
  J Biol Chem, 283, 17766-17776.  
18042682 X.Zhang, T.Nakashima, Y.Kakuta, M.Yao, I.Tanaka, and M.Kimura (2008).
Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.
  Protein Sci, 17, 136-145.
PDB code: 2z41
18276648 Y.Yang, S.X.Dou, H.Ren, P.Y.Wang, X.D.Zhang, M.Qian, B.Y.Pan, and X.G.Xi (2008).
Evidence for a functional dimeric form of the PcrA helicase in DNA unwinding.
  Nucleic Acids Res, 36, 1976-1989.  
17631491 A.Niedziela-Majka, M.A.Chesnik, E.J.Tomko, and T.M.Lohman (2007).
Bacillus stearothermophilus PcrA monomer is a single-stranded DNA translocase but not a processive helicase in vitro.
  J Biol Chem, 282, 27076-27085.  
17084859 D.N.Frick, S.Banik, and R.S.Rypma (2007).
Role of divalent metal cations in ATP hydrolysis catalyzed by the hepatitis C virus NS3 helicase: magnesium provides a bridge for ATP to fuel unwinding.
  J Mol Biol, 365, 1017-1032.  
17766252 H.Ren, S.X.Dou, P.Rigolet, Y.Yang, P.Y.Wang, M.Amor-Gueret, and X.G.Xi (2007).
The arginine finger of the Bloom syndrome protein: its structural organization and its role in energy coupling.
  Nucleic Acids Res, 35, 6029-6041.  
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
17911100 J.A.Harrigan, J.Piotrowski, L.Di Noto, R.L.Levine, and V.A.Bohr (2007).
Metal-catalyzed oxidation of the Werner syndrome protein causes loss of catalytic activities and impaired protein-protein interactions.
  J Biol Chem, 282, 36403-36411.  
17174478 J.J.Perry, L.Fan, and J.A.Tainer (2007).
Developing master keys to brain pathology, cancer and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair.
  Neuroscience, 145, 1280-1299.  
17148451 K.Kitano, N.Yoshihara, and T.Hakoshima (2007).
Crystal structure of the HRDC domain of human Werner syndrome protein, WRN.
  J Biol Chem, 282, 2717-2728.
PDB codes: 2e1e 2e1f
17227144 L.Muzzolini, F.Beuron, A.Patwardhan, V.Popuri, S.Cui, B.Niccolini, M.Rappas, P.S.Freemont, and A.Vindigni (2007).
Different quaternary structures of human RECQ1 are associated with its dual enzymatic activity.
  PLoS Biol, 5, e20.  
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.  
17878217 R.B.Guo, P.Rigolet, H.Ren, B.Zhang, X.D.Zhang, S.X.Dou, P.Y.Wang, M.Amor-Gueret, and X.G.Xi (2007).
Structural and functional analyses of disease-causing missense mutations in Bloom syndrome protein.
  Nucleic Acids Res, 35, 6297-6310.  
17483090 R.D.Shereda, D.A.Bernstein, and J.L.Keck (2007).
A central role for SSB in Escherichia coli RecQ DNA helicase function.
  J Biol Chem, 282, 19247-19258.  
16766518 C.Ralf, I.D.Hickson, and L.Wu (2006).
The Bloom's syndrome helicase can promote the regression of a model replication fork.
  J Biol Chem, 281, 22839-22846.  
16783375 D.Keramisanou, N.Biris, I.Gelis, G.Sianidis, S.Karamanou, A.Economou, and C.G.Kalodimos (2006).
Disorder-order folding transitions underlie catalysis in the helicase motor of SecA.
  Nat Struct Mol Biol, 13, 594-602.  
16950766 J.D.Bartos, W.Wang, J.E.Pike, and R.A.Bambara (2006).
Mechanisms by which Bloom protein can disrupt recombination intermediates of Okazaki fragment maturation.
  J Biol Chem, 281, 32227-32239.  
16622405 J.J.Perry, S.M.Yannone, L.G.Holden, C.Hitomi, A.Asaithamby, S.Han, P.K.Cooper, D.J.Chen, and J.A.Tainer (2006).
WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing.
  Nat Struct Mol Biol, 13, 414-422.
PDB codes: 2fbt 2fbv 2fbx 2fby 2fc0
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
16856806 L.Wu, and I.D.Hickson (2006).
DNA helicases required for homologous recombination and repair of damaged replication forks.
  Annu Rev Genet, 40, 279-306.  
16990798 M.D.Allen, C.G.Grummitt, C.Hilcenko, S.Y.Min, L.M.Tonkin, C.M.Johnson, S.M.Freund, M.Bycroft, and A.J.Warren (2006).
Solution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase.
  EMBO J, 25, 4503-4512.
PDB code: 2j2s
16935877 M.P.Killoran, and J.L.Keck (2006).
Sit down, relax and unwind: structural insights into RecQ helicase mechanisms.
  Nucleic Acids Res, 34, 4098-4105.  
16531400 M.P.Killoran, and J.L.Keck (2006).
Three HRDC domains differentially modulate Deinococcus radiodurans RecQ DNA helicase biochemical activity.
  J Biol Chem, 281, 12849-12857.  
16507576 X.D.Zhang, S.X.Dou, P.Xie, J.S.Hu, P.Y.Wang, and X.G.Xi (2006).
Escherichia coli RecQ is a rapid, efficient, and monomeric helicase.
  J Biol Chem, 281, 12655-12663.  
15845538 A.Machwe, L.Xiao, J.Groden, S.W.Matson, and D.K.Orren (2005).
RecQ family members combine strand pairing and unwinding activities to catalyze strand exchange.
  J Biol Chem, 280, 23397-23407.  
16024743 C.F.Cheok, L.Wu, P.L.Garcia, P.Janscak, and I.D.Hickson (2005).
The Bloom's syndrome helicase promotes the annealing of complementary single-stranded DNA.
  Nucleic Acids Res, 33, 3932-3941.  
15994460 C.P.Guy, and E.L.Bolt (2005).
Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands.
  Nucleic Acids Res, 33, 3678-3690.  
16084389 D.A.Bernstein, and J.L.Keck (2005).
Conferring substrate specificity to DNA helicases: role of the RecQ HRDC domain.
  Structure, 13, 1173-1182.
PDB code: 1wud
15719017 I.Leiros, J.Timmins, D.R.Hall, and S.McSweeney (2005).
Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans.
  EMBO J, 24, 906-918.
PDB code: 1w3s
16339893 J.S.Hu, H.Feng, W.Zeng, G.X.Lin, and X.G.Xi (2005).
Solution structure of a multifunctional DNA- and protein-binding motif of human Werner syndrome protein.
  Proc Natl Acad Sci U S A, 102, 18379-18384.
PDB code: 2axl
16150736 J.W.Lee, R.Kusumoto, K.M.Doherty, G.X.Lin, W.Zeng, W.H.Cheng, C.von Kobbe, R.M.Brosh, J.S.Hu, and V.A.Bohr (2005).
Modulation of Werner syndrome protein function by a single mutation in the conserved RecQ domain.
  J Biol Chem, 280, 39627-39636.  
16051820 J.Wu, A.K.Bera, R.J.Kuhn, and J.L.Smith (2005).
Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing.
  J Virol, 79, 10268-10277.
PDB codes: 1yks 1ymf
15990871 L.Wu, K.L.Chan, C.Ralf, D.A.Bernstein, P.L.Garcia, V.A.Bohr, A.Vindigni, P.Janscak, J.L.Keck, and I.D.Hickson (2005).
The HRDC domain of BLM is required for the dissolution of double Holliday junctions.
  EMBO J, 24, 2679-2687.  
16340008 M.C.Zittel, and J.L.Keck (2005).
Coupling DNA-binding and ATP hydrolysis in Escherichia coli RecQ: role of a highly conserved aromatic-rich sequence.
  Nucleic Acids Res, 33, 6982-6991.  
15806108 N.H.Thomä, B.K.Czyzewski, A.A.Alexeev, A.V.Mazin, S.C.Kowalczykowski, and N.P.Pavletich (2005).
Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54.
  Nat Struct Mol Biol, 12, 350-356.
PDB code: 1z3i
15930159 R.B.Guo, P.Rigolet, L.Zargarian, S.Fermandjian, and X.G.Xi (2005).
Structural and functional characterizations reveal the importance of a zinc binding domain in Bloom's syndrome helicase.
  Nucleic Acids Res, 33, 3109-3124.  
16326861 S.Sharma, J.A.Sommers, R.K.Gary, E.Friedrich-Heineken, U.Hübscher, and R.M.Brosh (2005).
The interaction site of Flap Endonuclease-1 with WRN helicase suggests a coordination of WRN and PCNA.
  Nucleic Acids Res, 33, 6769-6781.  
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
15753311 V.Guallar, and K.W.Borrelli (2005).
A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding.
  Proc Natl Acad Sci U S A, 102, 3954-3959.  
15489508 A.S.Kamath-Loeb, P.Welcsh, M.Waite, E.T.Adman, and L.A.Loeb (2004).
The enzymatic activities of the Werner syndrome protein are disabled by the amino acid polymorphism R834C.
  J Biol Chem, 279, 55499-55505.  
15221026 D.S.Daniels, T.T.Woo, K.X.Luu, D.M.Noll, N.D.Clarke, A.E.Pegg, and J.A.Tainer (2004).
DNA binding and nucleotide flipping by the human DNA repair protein AGT.
  Nat Struct Mol Biol, 11, 714-720.
PDB codes: 1t38 1t39
15292213 J.L.Liu, P.Rigolet, S.X.Dou, P.Y.Wang, and X.G.Xi (2004).
The zinc finger motif of Escherichia coli RecQ is implicated in both DNA binding and protein folding.
  J Biol Chem, 279, 42794-42802.  
15090549 M.E.Stauffer, and W.J.Chazin (2004).
Structural mechanisms of DNA replication, repair, and recombination.
  J Biol Chem, 279, 30915-30918.  
15128295 N.Tuteja, and R.Tuteja (2004).
Unraveling DNA helicases. Motif, structure, mechanism and function.
  Eur J Biochem, 271, 1849-1863.  
15256542 P.L.Garcia, G.Bradley, C.J.Hayes, S.Krintel, P.Soultanas, and P.Janscak (2004).
RPA alleviates the inhibitory effect of vinylphosphonate internucleotide linkages on DNA unwinding by BLM and WRN helicases.
  Nucleic Acids Res, 32, 3771-3778.  
15241474 P.L.Garcia, Y.Liu, J.Jiricny, S.C.West, and P.Janscak (2004).
Human RECQ5beta, a protein with DNA helicase and strand-annealing activities in a single polypeptide.
  EMBO J, 23, 2882-2891.  
15023996 P.L.Opresko, W.H.Cheng, and V.A.Bohr (2004).
Junction of RecQ helicase biochemistry and human disease.
  J Biol Chem, 279, 18099-18102.  
15187093 S.Choudhary, J.A.Sommers, and R.M.Brosh (2004).
Biochemical and kinetic characterization of the DNA helicase and exonuclease activities of werner syndrome protein.
  J Biol Chem, 279, 34603-34613.  
15096578 S.Cui, D.Arosio, K.M.Doherty, R.M.Brosh, A.Falaschi, and A.Vindigni (2004).
Analysis of the unwinding activity of the dimeric RECQ1 helicase in the presence of human replication protein A.
  Nucleic Acids Res, 32, 2158-2170.  
14665634 S.X.Dou, P.Y.Wang, H.Q.Xu, and X.G.Xi (2004).
The DNA binding properties of the Escherichia coli RecQ helicase.
  J Biol Chem, 279, 6354-6363.  
14534320 C.von Kobbe, N.H.Thomä, B.K.Czyzewski, N.P.Pavletich, and V.A.Bohr (2003).
Werner syndrome protein contains three structure-specific DNA binding domains.
  J Biol Chem, 278, 52997-53006.  
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.