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Hydrolase/protein binding PDB id
1znv
Jmol
Contents
Protein chains
87 a.a. *
119 a.a. *
Ligands
PO4 ×2
Metals
_NI ×2
Waters ×423
* Residue conservation analysis
PDB id:
1znv
Name: Hydrolase/protein binding
Title: How a his-metal finger endonuclease cole7 binds and cleaves transition metal ion cofactor
Structure: Colicin e7 immunity protein. Chain: a, c. Synonym: imme7, microcin e7 immunity protein. Engineered: yes. Colicin e7. Chain: b, d. Fragment: nuclease domain. Engineered: yes. Mutation: yes
Source: Escherichia coli str. K12 substr.. Organism_taxid: 316407. Strain: w3110. Gene: cei7. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.188     R-free:   0.235
Authors: L.G.Doudeva,H.Huang,K.C.Hsia,Z.Shi,C.L.Li,Y.Shen,H.S.Yuan
Key ref:
L.G.Doudeva et al. (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. PubMed id: 16434744 DOI: 10.1110/ps.051903406
Date:
12-May-05     Release date:   14-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q03708  (IMM7_ECOLX) -  Colicin-E7 immunity protein
Seq:
Struc: 		87 a.a.
87 a.a.
Protein chains
Pfam   ArchSchema ?
Q47112  (CEA7_ECOLX) -  Colicin-E7
Seq:
Struc: 		 
Seq:
Struc: 		576 a.a.
119 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cytolysis   4 terms 
  Biochemical function     protein binding     4 terms  

 

 
DOI no: 10.1110/ps.051903406 Protein Sci 15:269-280 (2006)
PubMed id: 16434744  
 
 
Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+.
L.G.Doudeva, H.Huang, K.C.Hsia, Z.Shi, C.L.Li, Y.Shen, Y.S.Cheng, H.S.Yuan.
 
  ABSTRACT  
 
The nuclease domain of ColE7 (N-ColE7) contains an H-N-H motif that folds in a beta beta alpha-metal topology. Here we report the crystal structures of a Zn2+-bound N-ColE7 (H545E mutant) in complex with a 12-bp duplex DNA and a Ni2+-bound N-ColE7 in complex with the inhibitor Im7 at a resolution of 2.5 A and 2.0 A, respectively. Metal-dependent cleavage assays showed that N-ColE7 cleaves double-stranded DNA with a single metal ion cofactor, Ni2+, Mg2+, Mn2+, and Zn2+. ColE7 purified from Escherichia coli contains an endogenous zinc ion that was not replaced by Mg2+ at concentrations of <25 mM, indicating that zinc is the physiologically relevant metal ion in N-ColE7 in host E. coli. In the crystal structure of N-ColE7/DNA complex, the zinc ion is directly coordinated to three histidines and the DNA scissile phosphate in a tetrahedral geometry. In contrast, Ni2+ is bound in N-ColE7 in two different modes, to four ligands (three histidines and one phosphate ion), or to five ligands with an additional water molecule. These data suggest that the divalent metal ion in the His-metal finger motif can be coordinated to six ligands, such as Mg2+ in I-PpoI, Serratia nuclease and Vvn, five ligands or four ligands, such as Ni2+ or Zn2+ in ColE7. Universally, the metal ion in the His-metal finger motif is bound to the DNA scissile phosphate and serves three roles during hydrolysis: polarization of the P-O bond for nucleophilic attack, stabilization of the phosphoanion transition state and stabilization of the cleaved product.
 
  Selected figure(s)  
 
Figure 4.
The omit electron density maps of Zn-bound and Ni-bound endonuclease active sites in H545E/DNA/Zn^2+ and N- ColE7/Im7/Ni^2+ complexes, respectively. (A) Stereo view of the omit difference maps (F[o] [minus sign] F[c]) contoured at 2.5 [sigma] (blue) and 12.0 [sigma] (red) shows that the DNA scissile phosphate (P5) is bound directly to the zinc ion. The tetrahedral geometry and bond distances around the Zn atom are schematically shown in the right panel. (B) Stereo views of the omit difference maps contoured at 2.5 [sigma] (blue) and 18.0 [sigma] (red) around the Ni-binding site in the two noncrystallographic-symmetry related molecules in N-ColE7/Im7/Ni^2+ complex structure. In molecule A, Ni^2+ is bound to three histidines and a phosphate in a tetrahedral geometry. In molecule B, Ni^2+ is bound to three histidines, a phosphate, and a water molecule in a distorted trigonal bi-pyramidal geometry. 		Figure 6.
Schematic presentations of the interactions between N-ColE7 and DNA. (A) The solid blue lines indicate hydrogen bonds or salt bridges (<3.50 A) and the red arrows show van der Waals contacts (<3.35 A) between N-ColE7 and DNA. Most of the interactions are between proteins side chains and DNA phosphate backbones. (B) DNA groove widths were plotted for each base step in H545E/12-mer DNA complex (this study), N-ColE7/8-mer DNA complex (PDB entry 1PT3), Vvn/DNA (PDB entry 1OUP), and I-PpoI/DNA (PDB entry 1A74). The DNA cleavage sites are aligned and marked by a solid arrow, shown at the bottom of the figure. The minor groove widths are widened to ~9 A at the region bound to [beta][beta][alpha]-metal motif in all complexes. DNA is cleaved right at the 3[prime prime or minute]-side of the widened minor groove.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2006, 15, 269-280) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19651876 L.E.Corina, W.Qiu, A.Desai, and D.L.Herrin (2009).
Biochemical and mutagenic analysis of I-CreII reveals distinct but important roles for both the H-N-H and GIY-YIG motifs.
  Nucleic Acids Res, 37, 5810-5821.  
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
18261473 C.M.Dupureur (2008).
Roles of metal ions in nucleases.
  Curr Opin Chem Biol, 12, 250-255.  
19032786 D.Zhang, H.Xiong, J.Shan, X.Xia, and V.L.Trudeau (2008).
Functional insight into Maelstrom in the germline piRNA pathway: a unique domain homologous to the DnaQ-H 3'-5' exonuclease, its lineage-specific expansion/loss and evolutionarily active site switch.
  Biol Direct, 3, 48.  
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.  
17289754 J.B.Robbins, M.Stapleton, M.J.Stanger, D.Smith, J.T.Dansereau, V.Derbyshire, and M.Belfort (2007).
Homing endonuclease I-TevIII: dimerization as a means to a double-strand break.
  Nucleic Acids Res, 35, 1589-1600.  
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
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.