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PDBsum entry 1g8y

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protein Protein-protein interface(s) links
Transcription PDB id
1g8y
Jmol
Contents
Protein chains
(+ 6 more) 242 a.a. *
Waters ×480
* Residue conservation analysis
PDB id:
1g8y
Name: Transcription
Title: Crystal structure of the hexameric replicative helicase repa of plasmid rsf1010
Structure: Regulatory protein repa. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Synonym: replication protein a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: repa on plasmid incq rsf1010. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
2.40Å     R-factor:   0.221     R-free:   0.264
Authors: T.Niedenzu,D.Roeleke,G.Bains,E.Scherzinger,W.Saenger
Key ref:
T.Niedenzu et al. (2001). Crystal structure of the hexameric replicative helicase RepA of plasmid RSF1010. J Mol Biol, 306, 479-487. PubMed id: 11178907 DOI: 10.1006/jmbi.2000.4398
Date:
21-Nov-00     Release date:   14-Feb-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P20356  (REPJ_ECOLX) -  Regulatory protein RepA
Seq:
Struc:
279 a.a.
242 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1006/jmbi.2000.4398 J Mol Biol 306:479-487 (2001)
PubMed id: 11178907  
 
 
Crystal structure of the hexameric replicative helicase RepA of plasmid RSF1010.
T.Niedenzu, D.Röleke, G.Bains, E.Scherzinger, W.Saenger.
 
  ABSTRACT  
 
Unwinding of double-stranded DNA into single-stranded intermediates required for various fundamental life processes is catalyzed by helicases, a family of mono-, di- or hexameric motor proteins fueled by nucleoside triphosphate hydrolysis. The three-dimensional crystal structure of the hexameric helicase RepA encoded by plasmid RSF1010 has been determined by X-ray diffraction at 2.4 A resolution. The hexamer shows an annular structure with 6-fold rotational symmetry and a approximately 17 A wide central hole, suggesting that single-stranded DNA may be threaded during unwinding. Homologs of all five conserved sequence motifs of the DnaB-like helicase family are found in RepA, and the topography of the monomer resembles RecA and the helicase domain of the bacteriophage T7 gp4 protein. In a modeled complex, ATP molecules are located at the subunit interfaces and clearly define adenine-binding and ATPase catalytic sites formed by amino acid residues located on adjacent monomers; most remarkable is the "arginine finger" Arg207 contributing to the active site in the adjacent monomer. This arrangement of active-site residues suggests cooperativity between monomers in ATP hydrolysis and helicase activity of RepA. The mechanism of DNA unwinding remains elusive, as RepA is 6-fold symmetric, contrasting the recently published asymmetric structure of the bacteriophage T7 gp4 helicase domain.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Close-up view of the ``embracement'' between RepA monomers in the hexamer. The N termi- nus of one monomer (yellow) is linked by a number of hydrogen bonds (dotted lines) formed by main-chain and side-chain groups to helix aC and the loop b3-aE of the adjacent monomer (green). The hydrogen bonds are supported by van der Waals contacts (not indicated), and there are two additional direct inter-subunit hydro- gen bonds between aF of one monomer and the loop L1 of the adjacent monomer: Glu149 O e2 delta delta delta O g Ser153 and Arg144 N e delta delta delta O e1 Glu164.
Figure 5.
Figure 5. Section of the RepA hexamer showing the position of ATP in the cleft between two RepA monomers (stereo pair). ATP was modeled into the RepA hexamer according to the structurally homologous T7 helicase domain-dTAP complex (see the text). ATP drawn as a wire model (magenta) with adenine sandwiched beween Tyr243 of one RepA monomer (yellow) and Arg86 of the adjacent subunit (green), which also binds the triphosphate moiety in the active site formed by Lys43, Glu77, Asp140, His179. The side-chain of Arg207 (yellow monomer) could act in trans as an arginine finger, contacting the g-phosphate group of ATP bound to the active site of the adjacent (green) monomer. The dotted lines indicate the disordered loops 181-200.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 306, 479-487) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19747005 I.E.Andreeva, A.Roychowdhury, M.R.Szymanski, M.J.Jezewska, and W.Bujalowski (2009).
Mechanisms of interactions of the nucleotide cofactor with the RepA protein of plasmid RSF1010. Binding dynamics studied using the fluorescence stopped-flow method.
  Biochemistry, 48, 10620-10636.  
19289128 I.E.Andreeva, M.R.Szymanski, M.J.Jezewska, R.Galletto, and W.Bujalowski (2009).
Dynamics of the ssDNA recognition by the RepA hexameric helicase of plasmid RSF1010: analyses using fluorescence stopped-flow intensity and anisotropy methods.
  J Mol Biol, 388, 751-775.  
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.  
19465049 R.Meyer (2009).
Replication and conjugative mobilization of broad host-range IncQ plasmids.
  Plasmid, 62, 57-70.  
19495981 T.J.Lee, C.Schwartz, and P.Guo (2009).
Construction of bacteriophage phi29 DNA packaging motor and its applications in nanotechnology and therapy.
  Ann Biomed Eng, 37, 2064-2081.  
18022636 A.Marcinowicz, M.J.Jezewska, and W.Bujalowski (2008).
Multiple global conformational states of the hexameric RepA helicase of plasmid RSF1010 with different ssDNA-binding capabilities are induced by different numbers of bound nucleotides. Analytical ultracentrifugation and dynamic light scattering studies.
  J Mol Biol, 375, 386-408.  
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
17965162 D.Schwudke, A.Ergin, K.Michael, S.Volkmar, B.Appel, D.Knabner, A.Konietzny, and E.Strauch (2008).
Broad-host-range Yersinia phage PY100: genome sequence, proteome analysis of virions, and DNA packaging strategy.
  J Bacteriol, 190, 332-342.  
18940870 F.Xiao, H.Zhang, and P.Guo (2008).
Novel mechanism of hexamer ring assembly in protein/RNA interactions revealed by single molecule imaging.
  Nucleic Acids Res, 36, 6620-6632.  
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.  
18593709 Y.Matsushima, C.L.Farr, L.Fan, and L.S.Kaguni (2008).
Physiological and Biochemical Defects in Carboxyl-terminal Mutants of Mitochondrial DNA Helicase.
  J Biol Chem, 283, 23964-23971.  
17372655 A.Vindigni (2007).
Biochemical, biophysical, and proteomic approaches to study DNA helicases.
  Mol Biosyst, 3, 266-274.  
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.  
17501915 P.Guo, and T.J.Lee (2007).
Viral nanomotors for packaging of dsDNA and dsRNA.
  Mol Microbiol, 64, 886-903.  
17324440 T.D.Ziebarth, C.L.Farr, and L.S.Kaguni (2007).
Modular architecture of the hexameric human mitochondrial DNA helicase.
  J Mol Biol, 367, 1382-1391.  
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
16916635 T.H.Massey, C.P.Mercogliano, J.Yates, D.J.Sherratt, and J.Löwe (2006).
Double-stranded DNA translocation: structure and mechanism of hexameric FtsK.
  Mol Cell, 23, 457-469.
PDB codes: 2ius 2iut 2iuu
16148308 C.Neylon, A.V.Kralicek, T.M.Hill, and N.E.Dixon (2005).
Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex.
  Microbiol Mol Biol Rev, 69, 501-526.  
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
15235592 A.B.Conway, T.W.Lynch, Y.Zhang, G.S.Fortin, C.W.Fung, L.S.Symington, and P.A.Rice (2004).
Crystal structure of a Rad51 filament.
  Nat Struct Mol Biol, 11, 791-796.
PDB code: 1szp
15369673 E.J.Mancini, D.E.Kainov, J.M.Grimes, R.Tuma, D.H.Bamford, and D.I.Stuart (2004).
Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation.
  Cell, 118, 743-755.
PDB codes: 1w44 1w46 1w47 1w48 1w49 1w4a 1w4b 1w4c
15173380 J.Thirlway, I.J.Turner, C.T.Gibson, L.Gardiner, K.Brady, S.Allen, C.J.Roberts, and P.Soultanas (2004).
DnaG interacts with a linker region that joins the N- and C-domains of DnaB and induces the formation of 3-fold symmetric rings.
  Nucleic Acids Res, 32, 2977-2986.  
15371437 M.Yoon-Robarts, A.G.Blouin, S.Bleker, J.A.Kleinschmidt, A.K.Aggarwal, C.R.Escalante, and R.M.Linden (2004).
Residues within the B' motif are critical for DNA binding by the superfamily 3 helicase Rep40 of adeno-associated virus type 2.
  J Biol Chem, 279, 50472-50481.  
15128295 N.Tuteja, and R.Tuteja (2004).
Unraveling DNA helicases. Motif, structure, mechanism and function.
  Eur J Biochem, 271, 1849-1863.  
12923524 E.H.Egelman (2003).
A tale of two polymers: new insights into helical filaments.
  Nat Rev Mol Cell Biol, 4, 621-630.  
14646113 E.J.Mancini, J.M.Grimes, R.Malby, G.C.Sutton, D.E.Kainov, J.T.Juuti, E.V.Makeyev, R.Tuma, D.H.Bamford, and D.I.Stuart (2003).
Order and disorder in crystals of hexameric NTPases from dsRNA bacteriophages.
  Acta Crystallogr D Biol Crystallogr, 59, 2337-2341.  
14530440 G.Ziegelin, T.Niedenzu, R.Lurz, W.Saenger, and E.Lanka (2003).
Hexameric RSF1010 helicase RepA: the structural and functional importance of single amino acid residues.
  Nucleic Acids Res, 31, 5917-5929.
PDB code: 1olo
12777796 H.Xu, N.Sträter, W.Schröder, C.Böttcher, K.Ludwig, and W.Saenger (2003).
Structure of DNA helicase RepA in complex with sulfate at 1.95 A resolution implicates structural changes to an "open" form.
  Acta Crystallogr D Biol Crystallogr, 59, 815-822.
PDB code: 1nlf
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
12554674 M.H.Lamers, H.H.Winterwerp, and T.K.Sixma (2003).
The alternating ATPase domains of MutS control DNA mismatch repair.
  EMBO J, 22, 746-756.
PDB code: 1ng9
11823434 A.C.Rodríguez, and D.Stock (2002).
Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA.
  EMBO J, 21, 418-426.
PDB codes: 1gku 1gl9
12244108 A.I.Alexandrov, M.R.Botchan, and N.R.Cozzarelli (2002).
Characterization of simian virus 40 T-antigen double hexamers bound to a replication fork. The active form of the helicase.
  J Biol Chem, 277, 44886-44897.  
11748238 F.X.Gomis-Rüth, G.Moncalían, F.de la Cruz, and M.Coll (2002).
Conjugative plasmid protein TrwB, an integral membrane type IV secretion system coupling protein. Detailed structural features and mapping of the active site cleft.
  J Biol Chem, 277, 7556-7566.  
11839740 G.Tombline, K.S.Shim, and R.Fishel (2002).
Biochemical characterization of the human RAD51 protein. II. Adenosine nucleotide binding and competition.
  J Biol Chem, 277, 14426-14433.  
11839499 J.M.Caruthers, and D.B.McKay (2002).
Helicase structure and mechanism.
  Curr Opin Struct Biol, 12, 123-133.  
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.  
11889086 M.R.Singleton, and D.B.Wigley (2002).
Modularity and specialization in superfamily 1 and 2 helicases.
  J Bacteriol, 184, 1819-1826.  
12235389 P.Soultanas, and D.B.Wigley (2002).
Site-directed mutagenesis reveals roles for conserved amino acid residues in the hexameric DNA helicase DnaB from Bacillus stearothermophilus.
  Nucleic Acids Res, 30, 4051-4060.  
12151340 X.Yu, M.S.VanLoock, A.Poplawski, Z.Kelman, T.Xiang, B.K.Tye, and E.H.Egelman (2002).
The Methanobacterium thermoautotrophicum MCM protein can form heptameric rings.
  EMBO Rep, 3, 792-797.  
11812837 H.Xu, G.Ziegelin, W.Schröder, J.Frank, S.Ayora, J.C.Alonso, E.Lanka, and W.Saenger (2001).
Flavones inhibit the hexameric replicative helicase RepA.
  Nucleic Acids Res, 29, 5058-5066.  
11473577 T.Ogura, and A.J.Wilkinson (2001).
AAA+ superfamily ATPases: common structure--diverse function.
  Genes Cells, 6, 575-597.  
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.