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PDBsum entry 1bgb

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protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
1bgb
Jmol
Contents
Protein chains
237 a.a.
DNA/RNA
Waters ×236
PDB id:
1bgb
Name: Hydrolase/DNA
Title: Ecorv endonuclease complex with 5'-cgggatatccc DNA
Structure: DNA (5'-d( Cp Gp Gp Gp Ap Tp Ap Tp Cp Cp C)-3'). Chain: c, d. Engineered: yes. Ecorv endonuclease. Chain: a, b. Engineered: yes
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.184     R-free:   0.246
Authors: J.Perona,N.C.Horton
Key ref:
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. PubMed id: 9705308 DOI: 10.1074/jbc.273.34.21721
Date:
28-May-98     Release date:   28-Oct-98    
PROCHECK
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 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.3.1.21.4  - 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: 10.1074/jbc.273.34.21721 J Biol Chem 273:21721-21729 (1998)
PubMed id: 9705308  
 
 
Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.
N.C.Horton, J.J.Perona.
 
  ABSTRACT  
 
The 2.1-A cocrystal structure of EcoRV endonuclease bound to 5'-CGGGATATCCC, in a crystal lattice isomorphous with the cocrystallized undecamer 5'-AAAGATATCTT previously determined, shows novel base recognition in the major groove of the DNA flanking the GATATC target site. Lys104 of the enzyme interacts through water molecules with the exocyclic N-4 amino groups of flanking cytosines. Steric exclusion of water molecule-binding sites by the 5-methyl group of thymine drives the adoption of alternative water-mediated contacts with AT versus GC flanks. This structure provides a rare example of structural adaptability in the recognition of different DNA sequences by a protein and suggests preferred strategies for the expansion of target site specificity by EcoRV.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Superposition of the interactions of Arg221 in subunit I of the dAT and dGC structures. Hydrogen bonds of Arg221 to a DNA phosphate within the target site in the dAT structure (5), and through water molecules to Arg115 in the dGC structure, are shown by dotted lines. The DNA target half-site GAT is shown at top.
Figure 4.
Fig. 4. Superposition of subunits I and II of the dGC structure, based on polypeptide backbone atoms within the core region of the DNA-binding domain (see Fig. 1 and Ref. 6). The DNA flank interacting with subunit I is in red and that interacting with subunit II is in gray. The shift in position of C-11 of the outer flanking pair in subunit II is evident. Interactions of water molecules 1-7 of subunit I and 1'-3' of subunit II are delineated in Table II, and their hydrogen-bonding contacts are shown in Fig. 3, A and B. Protein atoms of Lys104 and Ala^181-Gly184 are shown in green for subunit I and in yellow for subunit II.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 21721-21729) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19587036 C.Zhao, Z.Lou, Y.Guo, M.Ma, Y.Chen, S.Liang, L.Zhang, S.Chen, X.Li, Y.Liu, M.Bartlam, and Z.Rao (2009).
Nucleoside monophosphate complex structures of the endonuclease domain from the influenza virus polymerase PA subunit reveal the substrate binding site inside the catalytic center.
  J Virol, 83, 9024-9030.
PDB codes: 3hw3 3hw4 3hw5 3hw6
  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.  
19625490 N.T.Uyen, S.Y.Park, J.W.Choi, H.J.Lee, K.Nishi, and J.S.Kim (2009).
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.
  Nucleic Acids Res, 37, 6960-6969.
PDB code: 3h1t
17308914 G.A.Papadakos, H.Nastri, P.Riggs, and C.M.Dupureur (2007).
Uncoupling metallonuclease metal ion binding sites via nudge mutagenesis.
  J Biol Inorg Chem, 12, 557-569.  
15893669 S.A.Townson, J.C.Samuelson, S.Y.Xu, and A.K.Aggarwal (2005).
Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.
  Structure, 13, 791-801.
PDB codes: 1vrr 1yuv
12583893 V.Tosato, K.Gjuracic, K.Vlahovicek, S.Pongor, A.Danchin, and C.V.Bruschi (2003).
The DNA secondary structure of the Bacillus subtilis genome.
  FEMS Microbiol Lett, 218, 23-30.  
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.  
11847127 T.K.Chiu, C.Sohn, R.E.Dickerson, and R.C.Johnson (2002).
Testing water-mediated DNA recognition by the Hin recombinase.
  EMBO J, 21, 801-814.
PDB codes: 1ijw 1jj6 1jj8 1jko 1jkp 1jkq 1jkr
11327870 S.L.Reid, D.Parry, H.H.Liu, and B.A.Connolly (2001).
Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization.
  Biochemistry, 40, 2484-2494.  
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.  
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.  
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.