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Hydrolase/DNA PDB id
1pt3
Jmol
Contents
Protein chains
128 a.a. *
DNA/RNA
Waters ×232
* Residue conservation analysis
PDB id:
1pt3
Name: Hydrolase/DNA
Title: Crystal structures of nuclease-cole7 complexed with octamer
Structure: 5'-gcgatcgc-3'. Chain: c, d, g, h, e, f. Engineered: yes. Colicin e7. Chain: a, b. Fragment: residues 449-576. Engineered: yes
Source: Synthetic: yes. Other_details: this sequence occurs naturally in e. Coli.. Escherichia coli str. K12 substr.. Organism_taxid: 316407. Strain: w3110. Gene: cole7. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PQS)
Resolution:
2.50Å     R-factor:   0.216     R-free:   0.289
Authors: K.C.Hsia,K.F.Chak,Y.S.Cheng,W.Y.Ku,H.S.Yuan
Key ref:
K.C.Hsia et al. (2004). DNA binding and degradation by the HNH protein ColE7. Structure, 12, 205-214. PubMed id: 14962381 DOI: 10.1016/S0969-2126(04)00006-1
Date:
22-Jun-03     Release date:   30-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q47112  (CEA7_ECOLX) -  Colicin-E7
Seq:
Struc: 		 
Seq:
Struc: 		576 a.a.
128 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cytolysis   3 terms 
  Biochemical function     nucleic acid binding     3 terms  

 

 
DOI no: 10.1016/S0969-2126(04)00006-1 Structure 12:205-214 (2004)
PubMed id: 14962381  
 
 
DNA binding and degradation by the HNH protein ColE7.
K.C.Hsia, K.F.Chak, P.H.Liang, Y.S.Cheng, W.Y.Ku, H.S.Yuan.
 
  ABSTRACT  
 
The bacterial toxin ColE7 bears an HNH motif which has been identified in hundreds of prokaryotic and eukaryotic endonucleases, involved in DNA homing, restriction, repair, or chromosome degradation. The crystal structure of the nuclease domain of ColE7 in complex with a duplex DNA has been determined at 2.5 A resolution. The HNH motif is bound at the minor groove primarily to DNA phosphate groups at and beyond the 3' side of the scissile phosphate, with little interaction with ribose groups and bases. This result provides a structural basis for sugar- and sequence-independent DNA recognition and the inhibition mechanism by inhibitor Im7, which blocks the substrate binding site but not the active site. Structural comparison shows that two families of endonucleases bind and bend DNA in a similar way to that of the HNH ColE7, indicating that endonucleases containing a "betabetaalpha-metal" fold of active site possess a universal mode for protein-DNA interactions.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. The Molecular Surface of Nuclease-ColE7, Color Coded to Represent Electrostatic Potential(A) One of the DNA strands is bound at the central cleft region and DNA is cleaved at the P4 phosphate group, indicated by an arrow. The most basic surface (displayed in blue) of the protein contacts P5, P6, and P7 phosphate groups located at the 3' side of the scissile phosphate.(B) The inhibitor Im7 protein is bound to this basic region, based on the structure of nuclease-ColE7/Im7 complex (PDB entry: 7CEI) (Ko et al., 1999). Therefore, Im7 blocks the major substrate binding site but not the endonuclease active site.
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 205-214) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21214869 Z.T.Wen, A.H.Nguyen, J.P.Bitoun, J.Abranches, H.V.Baker, and R.A.Burne (2011).
Transcriptome analysis of LuxS-deficient Streptococcus mutans grown in biofilms.
  Mol Oral Microbiol, 26, 2.  
19053714 C.Chen, K.Krause, and B.M.Pettitt (2009).
Advantage of being a dimer for Serratia marcescens endonuclease.
  J Phys Chem B, 113, 511-521.  
  20333208 J.A.Vriezen, M.Valliere, and M.A.Riley (2009).
The evolution of reduced microbial killing.
  Genome Biol Evol, 1, 400-408.  
19380375 M.Sokolowska, H.Czapinska, and M.Bochtler (2009).
Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
  Nucleic Acids Res, 37, 3799-3810.
PDB codes: 3fc3 3gox
18953336 W.Yang (2008).
An equivalent metal ion in one- and two-metal-ion catalysis.
  Nat Struct Mol Biol, 15, 1228-1231.  
17347522 E.Cascales, S.K.Buchanan, D.Duché, C.Kleanthous, R.Lloubès, K.Postle, M.Riley, S.Slatin, and D.Cavard (2007).
Colicin biology.
  Microbiol Mol Biol Rev, 71, 158-229.  
17138564 M.Ghosh, G.Meiss, A.M.Pingoud, R.E.London, and L.C.Pedersen (2007).
The nuclease a-inhibitor complex is characterized by a novel metal ion bridge.
  J Biol Chem, 282, 5682-5690.
PDB code: 2o3b
17175542 Y.T.Wang, W.J.Yang, C.L.Li, L.G.Doudeva, and H.S.Yuan (2007).
Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.
  Nucleic Acids Res, 35, 584-594.
PDB codes: 2ivh 2ivk
16738128 A.Flaus, D.M.Martin, G.J.Barton, and T.Owen-Hughes (2006).
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs.
  Nucleic Acids Res, 34, 2887-2905.  
16470805 C.H.Lu, Y.S.Lin, Y.C.Chen, C.S.Yu, S.Y.Chang, and J.K.Hwang (2006).
The fragment transformation method to detect the protein structural motifs.
  Proteins, 63, 636-643.  
16434744 L.G.Doudeva, H.Huang, K.C.Hsia, Z.Shi, C.L.Li, Y.Shen, Y.S.Cheng, and H.S.Yuan (2006).
Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+.
  Protein Sci, 15, 269-280.
PDB codes: 1zns 1znv
15572351 C.Korn, S.R.Scholz, O.Gimadutdinow, R.Lurz, A.Pingoud, and G.Meiss (2005).
Interaction of DNA fragmentation factor (DFF) with DNA reveals an unprecedented mechanism for nuclease inhibition and suggests that DFF can be activated in a DNA-bound state.
  J Biol Chem, 280, 6005-6015.  
15574519 F.J.Blocker, G.Mohr, L.H.Conlan, L.Qi, M.Belfort, and A.M.Lambowitz (2005).
Domain structure and three-dimensional model of a group II intron-encoded reverse transcriptase.
  RNA, 11, 14-28.  
16103871 K.Samejima, and W.C.Earnshaw (2005).
Trashing the genome: the role of nucleases during apoptosis.
  Nat Rev Mol Cell Biol, 6, 677-688.  
15897201 M.Ghosh, G.Meiss, A.Pingoud, R.E.London, and L.C.Pedersen (2005).
Structural insights into the mechanism of nuclease A, a betabeta alpha metal nuclease from Anabaena.
  J Biol Chem, 280, 27990-27997.
PDB code: 1zm8
16236713 S.Reh, C.Korn, O.Gimadutdinow, and G.Meiss (2005).
Structural basis for stable DNA complex formation by the caspase-activated DNase.
  J Biol Chem, 280, 41707-41715.  
15190054 M.J.Maté, and C.Kleanthous (2004).
Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases.
  J Biol Chem, 279, 34763-34769.
PDB codes: 1v13 1v14 1v15
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.