spacer
spacer

PDBsum entry 1svo

Go to PDB code: 
protein metals Protein-protein interface(s) links
Viral protein PDB id
1svo
Jmol PyMol
Contents
Protein chains
362 a.a. *
Metals
_ZN ×2
Waters ×188
* Residue conservation analysis
PDB id:
1svo
Name: Viral protein
Title: Structure of sv40 large t antigen helicase domain
Structure: Large t antigen. Chain: a, b. Fragment: helicase domain. Engineered: yes
Source: Simian virus 40. Organism_taxid: 10633. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
2.60Å     R-factor:   0.233     R-free:   0.271
Authors: D.Gai,R.Zhao,C.V.Finkielstein,X.S.Chen
Key ref:
D.Gai et al. (2004). Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Cell, 119, 47-60. PubMed id: 15454080 DOI: 10.1016/j.cell.2004.09.017
Date:
29-Mar-04     Release date:   19-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03070  (LT_SV40) -  Large T antigen
Seq:
Struc:
 
Seq:
Struc:
708 a.a.
362 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   1 term 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1016/j.cell.2004.09.017 Cell 119:47-60 (2004)
PubMed id: 15454080  
 
 
Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen.
D.Gai, R.Zhao, D.Li, C.V.Finkielstein, X.S.Chen.
 
  ABSTRACT  
 
The large tumor antigen (LTag) of simian virus 40, an AAA(+) protein, is a hexameric helicase essential for viral DNA replication in eukaryotic cells. LTag functions as an efficient molecular machine powered by ATP binding and hydrolysis for origin DNA melting and replication fork unwinding. To understand how ATP binding and hydrolysis are coupled to conformational changes, we have determined high-resolution structures ( approximately 1.9 A) of LTag hexamers in distinct nucleotide binding states. The structural differences of LTag in various nucleotide states detail the molecular mechanisms of conformational changes triggered by ATP binding/hydrolysis and reveal a potential mechanism of concerted nucleotide binding and hydrolysis. During these conformational changes, the angles and orientations between domains of a monomer alter, creating an "iris"-like motion in the hexamer. Additionally, six unique beta hairpins on the channel surface move longitudinally along the central channel, possibly serving as a motor for pulling DNA into the LTag double hexamer for unwinding.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. An Overview of the Nt-Free Structure of a LTag Monomer and its Hexamer(A) The LTag domain structure in ribbon diagram. D1 is the N-terminal domain, D2 the AAA+ domain, and D3 the C-terminal α-helical domain. The thin red line shows the border between D2 and D3. The N and C termini are labeled as N and C. ATP binding P loop and the Nt binding pocket (Nt pocket) for binding the base are indicated by arrows.(B) The C-terminal view of a LTag hexamer structure along the hexameric axis, with the D2/D3 on top.
Figure 2.
Figure 2. The Changes of Channel Openings and Hexamerization Interfaces of LTag Hexamers in Three Nt Binding States, Viewing from the C-Terminal EndTo provide a clearer view of the Nt binding cleft at the hexamerization interface, only the D2/D3 parts of the hexamer are shown. Each of the six monomers is in a different color. (A) The ATP bound hexamer structure. The six ATPs at the cleft between two monomers are in pink. (B) The ADP bound hexamer structure, showing ADP (pink) at the cleft. (C) The Nt-free hexamer structure. (D) A close-up view of the cleft between two neighboring monomers (in green and cyan) of the Nt-free structure. (E) The same view of the cleft between two neighbors from two different Nt bound structures: the Nt-free structure (in green and cyan) and the ATP bound structure (in pink and gold), showing a narrowing of the cleft when ATP is bound. The bound ATP and Mg^2+ are in purple.
 
  The above figures are reprinted by permission from Cell Press: Cell (2004, 119, 47-60) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23201686 H.Yardimci, X.Wang, A.B.Loveland, I.Tappin, D.Z.Rudner, J.Hurwitz, A.M.van Oijen, and J.C.Walter (2012).
Bypass of a protein barrier by a replicative DNA helicase.
  Nature, 492, 205-209.  
23201683 M.A.Trakselis, and B.W.Graham (2012).
Biochemistry: Molecular hurdles cleared with ease.
  Nature, 492, 195-197.  
22398446 T.Kon, T.Oyama, R.Shimo-Kon, K.Imamula, T.Shima, K.Sutoh, and G.Kurisu (2012).
The 2.8 Å crystal structure of the dynein motor domain.
  Nature, 484, 345-350.
PDB codes: 3vkg 3vkh
21330489 A.P.Carter, C.Cho, L.Jin, and R.D.Vale (2011).
Crystal structure of the dynein motor domain.
  Science, 331, 1159-1165.
PDB code: 3qmz
21282052 A.Y.Lyubimov, M.Strycharska, and J.M.Berger (2011).
The nuts and bolts of ring-translocase structure and mechanism.
  Curr Opin Struct Biol, 21, 240-248.  
20716382 A.S.Brewster, I.M.Slaymaker, S.A.Afif, and X.S.Chen (2010).
Mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and DNA binding.
  BMC Mol Biol, 11, 62.  
20441442 A.S.Brewster, and X.S.Chen (2010).
Insights into the MCM functional mechanism: lessons learned from the archaeal MCM complex.
  Crit Rev Biochem Mol Biol, 45, 243-256.  
20219935 E.A.Niskanen, T.O.Ihalainen, O.Kalliolinna, M.M.Häkkinen, and M.Vihinen-Ranta (2010).
Effect of ATP binding and hydrolysis on dynamics of canine parvovirus NS1.
  J Virol, 84, 5391-5403.  
20379135 E.Crozat, A.Meglio, J.F.Allemand, C.E.Chivers, M.Howarth, C.Vénien-Bryan, I.Grainge, and D.J.Sherratt (2010).
Separating speed and ability to displace roadblocks during DNA translocation by FtsK.
  EMBO J, 29, 1423-1433.  
20219473 I.Cuesta, R.Núñez-Ramírez, S.H.Scheres, D.Gai, X.S.Chen, E.Fanning, and J.M.Carazo (2010).
Conformational rearrangements of SV40 large T antigen during early replication events.
  J Mol Biol, 397, 1276-1286.  
20386832 K.Isozaki, and K.Miki (2010).
Design, synthesis, and complementary recognition of beta-hairpin peptides stabilized by artificial DNA base-pairing amino acids.
  Chem Commun (Camb), 46, 2947-2949.  
20409463 K.Yoshimoto, K.Arora, and C.L.Brooks (2010).
Hexameric helicase deconstructed: interplay of conformational changes and substrate coupling.
  Biophys J, 98, 1449-1457.  
20484375 M.L.Bochman, and A.Schwacha (2010).
The Saccharomyces cerevisiae Mcm6/2 and Mcm5/3 ATPase active sites contribute to the function of the putative Mcm2-7 'gate'.
  Nucleic Acids Res, 38, 6078-6088.  
20357093 S.Bialasiewicz, R.Rockett, D.W.Whiley, Y.Abed, T.Allander, M.Binks, G.Boivin, A.C.Cheng, J.Y.Chung, P.E.Ferguson, N.M.Gilroy, A.J.Leach, C.Lindau, J.W.Rossen, T.C.Sorrell, M.D.Nissen, and T.P.Sloots (2010).
Whole-genome characterization and genotyping of global WU polyomavirus strains.
  J Virol, 84, 6229-6234.  
20507978 T.R.Sweeney, V.Cisnetto, D.Bose, M.Bailey, J.R.Wilson, X.Zhang, G.J.Belsham, and S.Curry (2010).
Foot-and-mouth disease virus 2C is a hexameric AAA+ protein with a coordinated ATP hydrolysis mechanism.
  J Biol Chem, 285, 24347-24359.  
20192763 W.Yang (2010).
Lessons learned from UvrD helicase: mechanism for directional movement.
  Annu Rev Biophys, 39, 367-385.  
20118258 X.Guo, and L.Huang (2010).
A superfamily 3 DNA helicase encoded by plasmid pSSVi from the hyperthermophilic archaeon Sulfolobus solfataricus unwinds DNA as a higher-order oligomer and interacts with host primase.
  J Bacteriol, 192, 1853-1864.  
19939914 X.Liu, and A.Stenlund (2010).
Mutations in Sensor 1 and Walker B in the bovine papillomavirus E1 initiator protein mimic the nucleotide-bound state.
  J Virol, 84, 1912-1919.  
20147403 X.Liu, S.Schuck, and A.Stenlund (2010).
Structure-based mutational analysis of the bovine papillomavirus E1 helicase domain identifies residues involved in the nonspecific DNA binding activity required for double trimer formation.
  J Virol, 84, 4264-4276.  
19217392 B.Bae, Y.H.Chen, A.Costa, S.Onesti, J.S.Brunzelle, Y.Lin, I.K.Cann, and S.K.Nair (2009).
Insights into the architecture of the replicative helicase from the structure of an archaeal MCM homolog.
  Structure, 17, 211-222.
PDB code: 3f8t
19446588 B.Ramaswami, I.Popescu, C.Macedo, D.Metes, M.Bueno, A.Zeevi, R.Shapiro, R.Viscidi, and P.S.Randhawa (2009).
HLA-A01-, -A03-, and -A024-binding nanomeric epitopes in polyomavirus BK large T antigen.
  Hum Immunol, 70, 722-728.  
19109389 C.Luo, M.Bueno, J.Kant, J.Martinson, and P.Randhawa (2009).
Genotyping schemes for polyomavirus BK, using gene-specific phylogenetic trees and single nucleotide polymorphism analysis.
  J Virol, 83, 2285-2297.  
19158782 E.A.Abbondanzieri, and X.Zhuang (2009).
Molecular biology: Concealed enzyme coordination.
  Nature, 457, 392-393.  
19101707 E.Fanning, and K.Zhao (2009).
SV40 DNA replication: from the A gene to a nanomachine.
  Virology, 384, 352-359.  
19164574 E.R.Barry, J.E.Lovett, A.Costa, S.M.Lea, and S.D.Bell (2009).
Intersubunit allosteric communication mediated by a conserved loop in the MCM helicase.
  Proc Natl Acad Sci U S A, 106, 1051-1056.  
19084558 G.Zeng, M.Bueno, C.J.Camachos, B.Ramaswami, C.Luo, and P.Randhawa (2009).
Validation of BKV large T-antigen ATP-binding site as a target for drug discovery.
  Antiviral Res, 81, 184-187.  
19383795 H.Liu, Y.Shi, X.S.Chen, and A.Warshel (2009).
Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases.
  Proc Natl Acad Sci U S A, 106, 7449-7454.  
19129763 J.R.Moffitt, Y.R.Chemla, K.Aathavan, S.Grimes, P.J.Jardine, D.L.Anderson, and C.Bustamante (2009).
Intersubunit coordination in a homomeric ring ATPase.
  Nature, 457, 446-450.  
19801685 J.W.Lee, E.Park, M.S.Jeong, Y.J.Jeon, S.H.Eom, J.H.Seol, and C.H.Chung (2009).
HslVU ATP-dependent protease utilizes maximally six among twelve threonine active sites during proteolysis.
  J Biol Chem, 284, 33475-33484.  
19401329 K.Fujimitsu, T.Senriuchi, and T.Katayama (2009).
Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA.
  Genes Dev, 23, 1221-1233.  
19946136 M.L.Bochman, and A.Schwacha (2009).
The Mcm complex: unwinding the mechanism of a replicative helicase.
  Microbiol Mol Biol Rev, 73, 652-683.  
19762479 M.Sanchez, M.Drechsler, H.Stark, and G.Lipps (2009).
DNA translocation activity of the multifunctional replication protein ORF904 from the archaeal plasmid pRN1.
  Nucleic Acids Res, 37, 6831-6848.  
19415794 N.Sakakibara, L.M.Kelman, and Z.Kelman (2009).
Unwinding the structure and function of the archaeal MCM helicase.
  Mol Microbiol, 72, 286-296.  
19520852 P.Adams, E.Kandiah, G.Effantin, A.C.Steven, and E.Ehrenfeld (2009).
Poliovirus 2C protein forms homo-oligomeric structures required for ATPase activity.
  J Biol Chem, 284, 22012-22021.  
19486295 P.C.Burrows, J.Schumacher, S.Amartey, T.Ghosh, T.A.Burgis, X.Zhang, B.T.Nixon, and M.Buck (2009).
Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein.
  Mol Microbiol, 73, 519-533.  
19362537 P.Wendler, J.Shorter, D.Snead, C.Plisson, D.K.Clare, S.Lindquist, and H.R.Saibil (2009).
Motor mechanism for protein threading through Hsp104.
  Mol Cell, 34, 81-92.  
19914167 S.E.Glynn, A.Martin, A.R.Nager, T.A.Baker, and R.T.Sauer (2009).
Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine.
  Cell, 139, 744-756.
PDB codes: 3hte 3hws
19144705 W.Wang, and D.T.Simmons (2009).
Simian virus 40 large T antigen can specifically unwind the central palindrome at the origin of DNA replication.
  J Virol, 83, 3312-3322.  
19779548 Y.Shi, H.Liu, D.Gai, J.Ma, and X.S.Chen (2009).
A computational analysis of ATP binding of SV40 large tumor antigen helicase motor.
  PLoS Comput Biol, 5, e1000514.  
18579587 A.Kumar, W.S.Joo, G.Meinke, S.Moine, E.N.Naumova, and P.A.Bullock (2008).
Evidence for a structural relationship between BRCT domains and the helicase domains of the replication initiators encoded by the Polyomaviridae and Papillomaviridae families of DNA tumor viruses.
  J Virol, 82, 8849-8862.  
19073923 A.S.Brewster, G.Wang, X.Yu, W.B.Greenleaf, J.M.Carazo, M.Tjajadia, M.G.Klein, and X.S.Chen (2008).
Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase.
  Proc Natl Acad Sci U S A, 105, 20191-20196.
PDB code: 3f9v
18057007 D.E.Kainov, E.J.Mancini, J.Telenius, J.Lísal, J.M.Grimes, D.H.Bamford, D.I.Stuart, and R.Tuma (2008).
Structural basis of mechanochemical coupling in a hexameric molecular motor.
  J Biol Chem, 283, 3607-3617.
PDB codes: 2vhc 2vhj 2vhq 2vht 2vhu
18801730 D.M.Kanter, I.Bruck, and D.L.Kaplan (2008).
Mcm subunits can assemble into two different active unwinding complexes.
  J Biol Chem, 283, 31172-31182.  
18329872 E.J.Enemark, and L.Joshua-Tor (2008).
On helicases and other motor proteins.
  Curr Opin Struct Biol, 18, 243-257.  
18157148 G.Wang, M.G.Klein, E.Tokonzaba, Y.Zhang, L.G.Holden, and X.S.Chen (2008).
The structure of a DnaB-family replicative helicase and its interactions with primase.
  Nat Struct Mol Biol, 15, 94.
PDB codes: 3bgw 3bh0
18582897 J.A.Yakamavich, T.A.Baker, and R.T.Sauer (2008).
Asymmetric nucleotide transactions of the HslUV protease.
  J Mol Biol, 380, 946-957.  
18462676 J.M.Davies, A.T.Brunger, and W.I.Weis (2008).
Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.
  Structure, 16, 715-726.
PDB codes: 3cf0 3cf1 3cf2 3cf3
18662997 M.L.Bochman, S.P.Bell, and A.Schwacha (2008).
Subunit organization of Mcm2-7 and the unequal role of active sites in ATP hydrolysis and viability.
  Mol Cell Biol, 28, 5865-5873.  
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.  
18754676 R.J.Fletcher, J.Shen, L.G.Holden, and X.S.Chen (2008).
Identification of amino acids important for the biochemical activity of Methanothermobacter thermautotrophicus MCM.
  Biochemistry, 47, 9981-9986.  
18660534 R.P.Leon, M.Tecklenburg, and R.A.Sclafani (2008).
Functional conservation of beta-hairpin DNA binding domains in the Mcm protein of Methanobacterium thermoautotrophicum and the Mcm5 protein of Saccharomyces cerevisiae.
  Genetics, 179, 1757-1768.  
18003733 S.Khopde, and D.T.Simmons (2008).
Simian virus 40 DNA replication is dependent on an interaction between topoisomerase I and the C-terminal end of T antigen.
  J Virol, 82, 1136-1145.  
18400864 W.B.Greenleaf, J.Shen, D.Gai, and X.S.Chen (2008).
Systematic study of the functions for the residues around the nucleotide pocket in simian virus 40 AAA+ hexameric helicase.
  J Virol, 82, 6017-6023.  
18849995 X.Zhang, and D.B.Wigley (2008).
The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins.
  Nat Struct Mol Biol, 15, 1223-1227.  
18353955 X.Zhao, R.J.Madden-Fuentes, B.X.Lou, J.M.Pipas, J.Gerhardt, C.J.Rigell, and E.Fanning (2008).
Ataxia telangiectasia-mutated damage-signaling kinase- and proteasome-dependent destruction of Mre11-Rad50-Nbs1 subunits in Simian virus 40-infected primate cells.
  J Virol, 82, 5316-5328.  
17596312 A.Fradet-Turcotte, C.Vincent, S.Joubert, P.A.Bullock, and J.Archambault (2007).
Quantitative analysis of the binding of simian virus 40 large T antigen to DNA.
  J Virol, 81, 9162-9174.  
17287270 A.Kumar, G.Meinke, D.K.Reese, S.Moine, P.J.Phelan, A.Fradet-Turcotte, J.Archambault, A.Bohm, and P.A.Bullock (2007).
Model for T-antigen-dependent melting of the simian virus 40 core origin based on studies of the interaction of the beta-hairpin with DNA.
  J Virol, 81, 4808-4818.  
17372655 A.Vindigni (2007).
Biochemical, biophysical, and proteomic approaches to study DNA helicases.
  Mol Biosyst, 3, 266-274.  
17881379 C.M.Sanders, O.V.Kovalevskiy, D.Sizov, A.A.Lebedev, M.N.Isupov, and A.A.Antson (2007).
Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors.
  Nucleic Acids Res, 35, 6451-6457.
PDB code: 2v9p
17253903 G.Meinke, P.Phelan, S.Moine, E.Bochkareva, A.Bochkarev, P.A.Bullock, and A.Bohm (2007).
The crystal structure of the SV40 T-antigen origin binding domain in complex with DNA.
  PLoS Biol, 5, e23.
PDB codes: 2if9 2ntc
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.  
17242399 J.Schumacher, N.Joly, M.Rappas, D.Bradley, S.R.Wigneshweraraj, X.Zhang, and M.Buck (2007).
Sensor I threonine of the AAA+ ATPase transcriptional activator PspF is involved in coupling nucleotide triphosphate hydrolysis to the restructuring of sigma 54-RNA polymerase.
  J Biol Chem, 282, 9825-9833.  
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.  
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.  
17964268 M.J.Moreau, A.T.McGeoch, A.R.Lowe, L.S.Itzhaki, and S.D.Bell (2007).
ATPase site architecture and helicase mechanism of an archaeal MCM.
  Mol Cell, 28, 304-314.  
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.  
18160044 P.Wendler, J.Shorter, C.Plisson, A.G.Cashikar, S.Lindquist, and H.R.Saibil (2007).
Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104.
  Cell, 131, 1366-1377.  
17630848 R.A.Sclafani, and T.M.Holzen (2007).
Cell cycle regulation of DNA replication.
  Annu Rev Genet, 41, 237-280.  
17202221 S.Schuck, and A.Stenlund (2007).
ATP-dependent minor groove recognition of TA base pairs is required for template melting by the E1 initiator protein.
  J Virol, 81, 3293-3302.  
17301125 W.Wang, D.Manna, and D.T.Simmons (2007).
Role of the hydrophilic channels of simian virus 40 T-antigen helicase in DNA replication.
  J Virol, 81, 4510-4519.  
17386260 X.Liu, S.Schuck, and A.Stenlund (2007).
Adjacent residues in the E1 initiator beta-hairpin define different roles of the beta-hairpin in Ori melting, helicase loading, and helicase activity.
  Mol Cell, 25, 825-837.  
17062628 A.Costa, T.Pape, M.van Heel, P.Brick, A.Patwardhan, and S.Onesti (2006).
Structural basis of the Methanothermobacter thermautotrophicus MCM helicase activity.
  Nucleic Acids Res, 34, 5829-5838.  
16678092 B.Bukau, J.Weissman, and A.Horwich (2006).
Molecular chaperones and protein quality control.
  Cell, 125, 443-451.  
17005644 D.K.Reese, G.Meinke, A.Kumar, S.Moine, K.Chen, J.L.Sudmeier, W.Bachovchin, A.Bohm, and P.A.Bullock (2006).
Analyses of the interaction between the origin binding domain from simian virus 40 T antigen and single-stranded DNA provide insights into DNA unwinding and initiation of DNA replication.
  J Virol, 80, 12248-12259.  
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.  
17139255 E.Bochkareva, D.Martynowski, A.Seitova, and A.Bochkarev (2006).
Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA.
  EMBO J, 25, 5961-5969.
PDB codes: 2ipr 2itj 2itl 2nl8
16855583 E.J.Enemark, and L.Joshua-Tor (2006).
Mechanism of DNA translocation in a replicative hexameric helicase.
  Nature, 442, 270-275.
PDB code: 2gxa
17158702 E.R.Barry, and S.D.Bell (2006).
DNA replication in the archaea.
  Microbiol Mol Biol Rev, 70, 876-887.  
16679413 E.R.Jenkinson, and J.P.Chong (2006).
Minichromosome maintenance helicase activity is controlled by N- and C-terminal motifs and requires the ATPase domain helix-2 insert.
  Proc Natl Acad Sci U S A, 103, 7613-7618.  
17081977 E.Skordalakes, and J.M.Berger (2006).
Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor.
  Cell, 127, 553-564.
PDB code: 2ht1
16611889 G.Meinke, P.A.Bullock, and A.Bohm (2006).
Crystal structure of the simian virus 40 large T-antigen origin-binding domain.
  J Virol, 80, 4304-4312.
PDB code: 2fuf
16467299 I.G.Duggin, and S.D.Bell (2006).
The chromosome replication machinery of the archaeon Sulfolobus solfataricus.
  J Biol Chem, 281, 15029-15032.  
16525504 J.Kirstein, T.Schlothauer, D.A.Dougan, H.Lilie, G.Tischendorf, A.Mogk, B.Bukau, and K.Turgay (2006).
Adaptor protein controlled oligomerization activates the AAA+ protein ClpC.
  EMBO J, 25, 1481-1491.  
16762834 J.L.Adelman, Y.J.Jeong, J.C.Liao, G.Patel, D.E.Kim, G.Oster, and S.S.Patel (2006).
Mechanochemistry of transcription termination factor Rho.
  Mol Cell, 22, 611-621.  
16689629 J.P.Erzberger, and J.M.Berger (2006).
Evolutionary relationships and structural mechanisms of AAA+ proteins.
  Annu Rev Biophys Biomol Struct, 35, 93.  
16829961 J.P.Erzberger, M.L.Mott, and J.M.Berger (2006).
Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling.
  Nat Struct Mol Biol, 13, 676-683.
PDB code: 2hcb
16886007 K.D.Raney (2006).
A helicase staircase.
  Nat Struct Mol Biol, 13, 671-672.  
16430918 M.Rappas, J.Schumacher, H.Niwa, M.Buck, and X.Zhang (2006).
Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF.
  J Mol Biol, 357, 481-492.
PDB codes: 2c96 2c98 2c99 2c9c
17027480 M.S.Dillingham (2006).
Replicative helicases: a staircase with a twist.
  Curr Biol, 16, R844-R847.  
16973614 N.Joly, J.Schumacher, and M.Buck (2006).
Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator.
  J Biol Chem, 281, 34997-35007.  
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
16893956 S.Castella, D.Burgin, and C.M.Sanders (2006).
Role of ATP hydrolysis in the DNA translocase activity of the bovine papillomavirus (BPV-1) E1 helicase.
  Nucleic Acids Res, 34, 3731-3741.  
16738139 S.Castella, G.Bingham, and C.M.Sanders (2006).
Common determinants in DNA melting and helicase-catalysed DNA unwinding by papillomavirus replication protein E1.
  Nucleic Acids Res, 34, 3008-3019.  
16431356 S.E.Ades (2006).
AAA+ molecular machines: firing on all cylinders.
  Curr Biol, 16, R46-R48.  
16670085 S.S.Patel, and I.Donmez (2006).
Mechanisms of helicases.
  J Biol Chem, 281, 18265-18268.  
17082766 V.Kabaleeswaran, N.Puri, J.E.Walker, A.G.Leslie, and D.M.Mueller (2006).
Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1 ATPase.
  EMBO J, 25, 5433-5442.
PDB code: 2hld
16951253 W.Lilyestrom, M.G.Klein, R.Zhang, A.Joachimiak, and X.S.Chen (2006).
Crystal structure of SV40 large T-antigen bound to p53: interplay between a viral oncoprotein and a cellular tumor suppressor.
  Genes Dev, 20, 2373-2382.
PDB code: 2h1l
17110927 X.Jiang, V.Klimovich, A.I.Arunkumar, E.B.Hysinger, Y.Wang, R.D.Ott, G.D.Guler, B.Weiner, W.J.Chazin, and E.Fanning (2006).
Structural mechanism of RPA loading on DNA during activation of a simple pre-replication complex.
  EMBO J, 25, 5516-5526.  
16237435 A.Martin, T.A.Baker, and R.T.Sauer (2005).
Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines.
  Nature, 437, 1115-1120.  
16193069 A.Scott, H.Y.Chung, M.Gonciarz-Swiatek, G.C.Hill, F.G.Whitby, J.Gaspar, J.M.Holton, R.Viswanathan, S.Ghaffarian, C.P.Hill, and W.I.Sundquist (2005).
Structural and mechanistic studies of VPS4 proteins.
  EMBO J, 24, 3658-3669.
PDB code: 1xwi
16116441 A.T.McGeoch, M.A.Trakselis, R.A.Laskey, and S.D.Bell (2005).
Organization of the archaeal MCM complex on DNA and implications for the helicase mechanism.
  Nat Struct Mol Biol, 12, 756-762.  
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.  
15870080 G.Ondrovicová, T.Liu, K.Singh, B.Tian, H.Li, O.Gakh, D.Perecko, J.Janata, Z.Granot, J.Orly, E.Kutejová, and C.K.Suzuki (2005).
Cleavage site selection within a folded substrate by the ATP-dependent lon protease.
  J Biol Chem, 280, 25103-25110.  
15901724 H.Kawakami, K.Keyamura, and T.Katayama (2005).
Formation of an ATP-DnaA-specific initiation complex requires DnaA Arginine 285, a conserved motif in the AAA+ protein family.
  J Biol Chem, 280, 27420-27430.  
15989953 J.Hinnerwisch, W.A.Fenton, K.J.Furtak, G.W.Farr, and A.L.Horwich (2005).
Loops in the central channel of ClpA chaperone mediate protein binding, unfolding, and translocation.
  Cell, 121, 1029-1041.  
15840563 J.Lísal, and R.Tuma (2005).
Cooperative mechanism of RNA packaging motor.
  J Biol Chem, 280, 23157-23164.  
15834422 J.Lísal, T.T.Lam, D.E.Kainov, M.R.Emmett, A.G.Marshall, and R.Tuma (2005).
Functional visualization of viral molecular motor by hydrogen-deuterium exchange reveals transient states.
  Nat Struct Mol Biol, 12, 460-466.  
16142223 J.P.Chong (2005).
Learning to unwind.
  Nat Struct Mol Biol, 12, 734-736.  
16061814 J.Shen, D.Gai, A.Patrick, W.B.Greenleaf, and X.S.Chen (2005).
The roles of the residues on the channel beta-hairpin and loop structures of simian virus 40 hexameric helicase.
  Proc Natl Acad Sci U S A, 102, 11248-11253.  
16304143 P.W.White, A.M.Faucher, M.J.Massariol, E.Welchner, J.Rancourt, M.Cartier, and J.Archambault (2005).
Biphenylsulfonacetic acid inhibitors of the human papillomavirus type 6 E1 helicase inhibit ATP hydrolysis by an allosteric mechanism involving tyrosine 486.
  Antimicrob Agents Chemother, 49, 4834-4842.  
16221679 R.J.Fletcher, J.Shen, Y.Gómez-Llorente, C.S.Martín, J.M.Carazo, and X.S.Chen (2005).
Double hexamer disruption and biochemical activities of Methanobacterium thermoautotrophicum MCM.
  J Biol Chem, 280, 42405-42410.  
15829969 S.J.Riedl, W.Li, Y.Chao, R.Schwarzenbacher, and Y.Shi (2005).
Structure of the apoptotic protease-activating factor 1 bound to ADP.
  Nature, 434, 926-933.
PDB code: 1z6t
16285920 S.Schuck, and A.Stenlund (2005).
Assembly of a double hexameric helicase.
  Mol Cell, 20, 377-389.  
16002295 T.S.Takahashi, D.B.Wigley, and J.C.Walter (2005).
Pumps, paradoxes and ploughshares: mechanism of the MCM2-7 DNA helicase.
  Trends Biochem Sci, 30, 437-444.  
16306270 Z.Bu, R.Biehl, M.Monkenbusch, D.Richter, and D.J.Callaway (2005).
Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy.
  Proc Natl Acad Sci U S A, 102, 17646-17651.  
15454074 B.F.Eichman, and E.Fanning (2004).
The power of pumping together; deconstructing the engine of a DNA replication machine.
  Cell, 119, 3-4.  
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 codes are shown on the right.

 

spacer

spacer