PDBsum entry 1eop

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protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
238 a.a.
Waters ×70
PDB id:
Name: Hydrolase/DNA
Title: Ecorv bound to cognate DNA
Structure: DNA (5'-d( Gp Ap Ap Gp Ap Tp Ap Tp Cp Tp Tp C)- 3'). Chain: c, d. Engineered: yes. Type ii restriction enzyme ecorv. Chain: a, b. Synonym: endonuclease ecorv, r.Ecorv. Engineered: yes
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
2.60Å     R-factor:   0.181     R-free:   0.302
Authors: N.C.Horton,J.J.Perona
Key ref:
N.C.Horton and J.J.Perona (2000). Crystallographic snapshots along a protein-induced DNA-bending pathway. Proc Natl Acad Sci U S A, 97, 5729-5734. PubMed id: 10801972 DOI: 10.1073/pnas.090370797
23-Mar-00     Release date:   04-Apr-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P04390  (T2E5_ECOLX) -  Type-2 restriction enzyme EcoRV
245 a.a.
238 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Type Ii site-specific deoxyribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
      Cofactor: Mg(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   3 terms 
  Biochemical function     hydrolase activity     6 terms  


DOI no: 10.1073/pnas.090370797 Proc Natl Acad Sci U S A 97:5729-5734 (2000)
PubMed id: 10801972  
Crystallographic snapshots along a protein-induced DNA-bending pathway.
N.C.Horton, J.J.Perona.
Two new high-resolution cocrystal structures of EcoRV endonuclease bound to DNA show that a large variation in DNA-bending angles is sampled in the ground state binary complex. Together with previous structures, these data reveal a contiguous series of protein conformational states delineating a specific trajectory for the induced-fit pathway. Rotation of the DNA-binding domains, together with movements of two symmetry-related helices binding in the minor groove, causes base unstacking at a key base-pair step and propagates structural changes that assemble the active sites. These structures suggest a complex mechanism for DNA bending that depends on forces generated by interacting protein segments, and on selective neutralization of phosphate charges along the inner face of the bent double helix.
  Selected figure(s)  
Figure 2.
Fig. 2. (A) Cross-correlation matrix plot of the distances between -carbons i and j of each DNA-bound structure, and roll angle of the DNA at the center TA step. Shown is the upper right quadrant of the full matrix. Residues 1-245 of subunit I are on the horizontal axis, and residues 1-245 of subunit II are on the vertical axis. A gray point is placed for -carbon atom pairs having |r| > 0.90 (i.e., the distance between these atoms is significantly correlated with roll angle for the five structures I-IV and NS). Shading of points from gray to black indicates values of |r| ranging from 0.9 to 1.0. Colored segments 1 through 5 (Upper and Left) are assigned by inspection of this plot. Residues 184-187 in segment 4 and 221-228 in segment 5 are not included in the calculation because they are disordered in the nonspecific complex; these residues appear as stripes with discrete borders. Similar plots were calculated with each of the other two measures of DNA-bending angle (Table 3) as well as with random values for the bend angle. The total number of points (i, j) having |r| > 0.90 are: using center-step bend of the DNA, 28,251; using roll angle at the center step, 34,681; using overall bend of the DNA, 10,465; using random values for bend angles, 1,893. Segments 1 through 5 appear in the three plots using experimental DNA-bending angles but not in the plot using random bend angles. Inspection of other quadrants of the matrix plot shows no significant correlations for interatomic distances within either subunit. Analysis of cross-correlation coefficients has also been used to assess correlated atomic displacements in molecular dynamics simulations of proteins (32). (B) Ribbon diagram of the specific complex in crystal form IV color coded by segments defined by the plot in A. (C) Schematic drawing of the protein conformational changes occurring with DNA bending. The white and black models represent complexes containing DNA which is bent to a lesser and greater degree, respectively. As the DNA bends, the B helices translate apart and rotate up into the DNA-binding site, and the DNA-binding domains rotate about the axes indicated.
Figure 3.
Fig. 3. (A) Superposition (based on the R-loop residues 184-187) of the least-bent form IV (red) and the most-bent form I (blue), showing interdigitation of Leu-46, Thr-42, and Val-39 at the B-helix interface. Arrows indicate the antiparallel movements of the helices during the 11° bending of the DNA in progressing from form IV to form I. Distances between C T42 (blue) and C Thr-42 (red) are 3.4 Å in subunit A and 2.2 Å in subunit B. (B) Propagation of the B-helix conformational changes to DNA bending, with structures superimposed as in A. The B-helices and DNA from crystal form I (blue) and crystal form IV (red) are shown, with coupling between the Thr-37-Thy-8 ribose contact and the B-helix translation also illustrated. Thr-37 and the ribose sugar in form I are shown in green in thicker bonds for clarity. These groups in form IV are shown in gold. (C) Plot of the center-step DNA-bending angle as a function of distance between Thr-37C and Thy-8-C4'. Error bars for crystal forms II and IV reported here indicate coordinate error as calculated with the program SIGMAA. The error bars for crystal forms I and III (9, 10) were estimated from the resolutions of the data sets, based on calculations from truncated penicillopepsin data, and may represent underestimates (33). The points represent the average Thr-37(C )-ribose(C4') distance for the two monomer subunits of each dimer. Roman numerals adjacent to the data points indicate the crystal form (Tables 1 and 3). (D) Propagation of the B-helix conformational change into the adjacent Q-loops. Residues in the active sites Glu-45, Glu-65, and Asp-74 are shown, as is the Thr-37-Gln-69 contact in crystal form I (blue) and crystal form IV (red). The superposition was done as in A.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19413964 A.Vologodskii (2009).
Determining protein-induced DNA bending in force-extension experiments: theoretical analysis.
  Biophys J, 96, 3591-3599.  
19089001 C.Liu, and L.Wang (2009).
DNA hydrolytic cleavage catalyzed by synthetic multinuclear metallonucleases.
  Dalton Trans, (), 227-239.  
19343221 M.Gao, and J.Skolnick (2009).
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions.
  PLoS Comput Biol, 5, e1000341.  
19217852 X.Zheng, and A.Vologodskii (2009).
Theoretical analysis of disruptions in DNA minicircles.
  Biophys J, 96, 1341-1349.  
19081059 E.J.Little, A.C.Babic, and N.C.Horton (2008).
Early interrogation and recognition of DNA sequence by indirect readout.
  Structure, 16, 1828-1837.
PDB code: 3ebc
18549246 F.Wang, F.Li, M.Ganguly, L.A.Marky, B.Gold, M.Egli, and M.P.Stone (2008).
A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards.
  Biochemistry, 47, 7147-7157.
PDB codes: 2qef 2qeg
16981705 D.A.Hiller, and J.J.Perona (2006).
Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage.
  Biochemistry, 45, 11453-11463.
PDB code: 2ge5
15886396 B.van den Broek, M.C.Noom, and G.J.Wuite (2005).
DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway.
  Nucleic Acids Res, 33, 2676-2684.  
15130133 P.A.Pribil, S.J.Wardle, and D.B.Haniford (2004).
Enhancement and rescue of target capture in Tn10 transposition by site-specific modifications in target DNA.
  Mol Microbiol, 52, 1173-1186.  
15341737 Q.S.Xu, R.B.Kucera, R.J.Roberts, and H.C.Guo (2004).
An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site.
  Structure, 12, 1741-1747.
PDB code: 1sa3
14661948 D.A.Hiller, J.M.Fogg, A.M.Martin, J.M.Beechem, N.O.Reich, and J.J.Perona (2003).
Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence.
  Biochemistry, 42, 14375-14385.  
12142452 M.Fuxreiter, and I.Simon (2002).
Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
  Protein Sci, 11, 1978-1983.  
11742344 N.C.Horton, L.F.Dorner, and J.J.Perona (2002).
Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation.
  Nat Struct Biol, 9, 42-47.
PDB code: 1kc6
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
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.