PDBsum entry 1rv5

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protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
240 a.a.
227 a.a.
Waters ×492
PDB id:
Name: Hydrolase/DNA
Title: Complex of ecorv endonuclease with d(aaagat)/d(atctt)
Structure: 5'-d( Ap Ap Ap Gp Ap T Ap Tp Cp Tp T)-3'. Chain: c, d. Synonym: cognate sequence. Engineered: yes. Ecorv endonuclease. Chain: a, b. Ec:
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562
Biol. unit: Tetramer (from PQS)
2.10Å     R-factor:   0.193     R-free:   0.272
Authors: N.C.Horton,J.J.Perona
Key ref:
N.C.Horton and J.J.Perona (1998). Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT). J Mol Biol, 277, 779-787. PubMed id: 9545372 DOI: 10.1006/jmbi.1998.1655
01-Jun-98     Release date:   11-Nov-98    
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Protein chain
Pfam   ArchSchema ?
P04390  (T2E5_ECOLX) -  Type-2 restriction enzyme EcoRV
245 a.a.
240 a.a.
Protein chain
Pfam   ArchSchema ?
P04390  (T2E5_ECOLX) -  Type-2 restriction enzyme EcoRV
245 a.a.
227 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: 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: 10.1006/jmbi.1998.1655 J Mol Biol 277:779-787 (1998)
PubMed id: 9545372  
Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT).
N.C.Horton, J.J.Perona.
The crystal structure of EcoRV endonuclease has been determined at 2. 1 A resolution complexed to two five-base-pair DNA duplexes each containing the cognate recognition half-site. The highly localized 50 degrees bend into the major groove seen at the center TA-step of the continuous GATATC site is preserved in this discontinuous DNA complex lacking the scissile phosphates. Thus, this crystal structure provides evidence that covalent constraints associated with a continuous target site are not essential to enzyme-induced DNA bending, even when these constraints are removed directly at the locus of the bend. The scissile phosphates are also absent in the crystal structure of EcoRV bound to the non-specific site TCGCGA, which shows a straight B-like conformation. We conclude that DNA bending by EcoRV is governed only by the sequence and is not influenced by the continuity of the phosphodiester backbone. Together with other data showing that cleavable non-cognate sites are bent, these results indicate that EcoRV bends non-cognate sites differing by one or two base-pairs from GATATC, but does not bend non-specific sites that are less similar. Structural and thermodynamic considerations suggest that the sequence-dependent energy cost of DNA bending is likely to play an important role in determining the specificity of EcoRV. This differential cost is manifested at the binding step for bent non-cognate sequences and at the catalytic step for unbent non-specific sequences.
  Selected figure(s)  
Figure 1.
Figure 1. A, Crystal structure of EcoRV bound to the specific DNA undecamer 5′-AAAGATATCTT [Kostrewa and Winkler 1995]. B, Crystal structure of EcoRV bound to two non-specific DNA octamers CGAGCTCG [Winkler et al 1993], in which the two octamers are stacked end-to-end with phosphates in the scissile position missing. C, Crystal structure of EcoRV complexed with the two duplexes d(AAAGAT) + d(ATCTT), also with the scissile phosphates missing (Table 1). The helical axes of the DNA are indicated by the continuous black lines in each case.
Figure 3.
Figure 3. Stereo view of the EcoRV-DNA specific DNA complex (blue), the product complex (green) and the discontinuous specific co-crystal structure lacking the scissile phosphates (red), at the center TA step of the recognition site. Cross-strand stacking of A7 of GATATC from each strand of the DNA duplex in the product complex (green) can be seen at center.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 277, 779-787) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
20859960 J.I.Yeh, E.Pohl, D.Truan, W.He, G.M.Sheldrick, S.Du, and C.Achim (2010).
The crystal structure of non-modified and bipyridine-modified PNA duplexes.
  Chemistry, 16, 11867-11875.
PDB codes: 3mbs 3mbu
  18541926 M.T.Langhans, and M.J.Palladino (2009).
Cleavage of mispaired heteroduplex DNA substrates by numerous restriction enzymes.
  Curr Issues Mol Biol, 11, 1.  
18477633 D.Svozil, J.Kalina, M.Omelka, and B.Schneider (2008).
DNA conformations and their sequence preferences.
  Nucleic Acids Res, 36, 3690-3706.  
17524420 E.S.Vanamee, J.Berriman, and A.K.Aggarwal (2007).
An EM view of the FokI synaptic complex by single particle analysis.
  J Mol Biol, 370, 207-212.  
11842098 S.Grazulis, M.Deibert, R.Rimseliene, R.Skirgaila, G.Sasnauskas, A.Lagunavicius, V.Repin, C.Urbanke, R.Huber, and V.Siksnys (2002).
Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.
  Nucleic Acids Res, 30, 876-885.
PDB code: 1knv
11180561 A.P.Demchenko (2001).
Recognition between flexible protein molecules: induced and assisted folding.
  J Mol Recognit, 14, 42-61.  
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
10801972 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.
PDB codes: 1eoo 1eop
10387089 A.M.Martin, N.C.Horton, S.Lusetti, N.O.Reich, and J.J.Perona (1999).
Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease.
  Biochemistry, 38, 8430-8439.  
10097110 L.I.Pietrasanta, D.Thrower, W.Hsieh, S.Rao, O.Stemmann, J.Lechner, J.Carbon, and H.Hansma (1999).
Probing the Saccharomyces cerevisiae centromeric DNA (CEN DNA)-binding factor 3 (CBF3) kinetochore complex by using atomic force microscopy.
  Proc Natl Acad Sci U S A, 96, 3757-3762.  
10350476 M.D.Sam, and J.J.Perona (1999).
Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease.
  Biochemistry, 38, 6576-6586.  
9705308 N.C.Horton, and J.J.Perona (1998).
Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.
  J Biol Chem, 273, 21721-21729.
PDB code: 1bgb
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