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PDBsum entry 1xhv

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
1xhv
Jmol
Contents
Protein chains
254 a.a.
DNA/RNA
Metals
_MN ×22
Waters ×1027
PDB id:
1xhv
Name: Hydrolase/DNA
Title: Hincii bound to cleaved cognate DNA gtcgac and mn2+
Structure: 5'-d( Gp Cp Cp Gp Gp Tp C)-3'. Chain: e, g, i, k. Engineered: yes. 5'-d(p Gp Ap Cp Cp Gp G)-3'. Chain: f, h, j, l. Engineered: yes. Type ii restriction enzyme hincii. Chain: a, b, c, d. Synonym: endonuclease hincii, r.Hincii.
Source: Synthetic: yes. Other_details: phosphoramidite synthetic chemistry. Haemophilus influenzae. Organism_taxid: 727. Gene: hinciir. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PQS)
Resolution:
2.50Å     R-factor:   0.199     R-free:   0.274
Authors: C.Etzkorn,N.C.Horton
Key ref:
C.Etzkorn and N.C.Horton (2004). Mechanistic insights from the structures of HincII bound to cognate DNA cleaved from addition of Mg2+ and Mn2+. J Mol Biol, 343, 833-849. PubMed id: 15476804 DOI: 10.1016/j.jmb.2004.08.082
Date:
20-Sep-04     Release date:   28-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P17743  (T2C2_HAEIF) -  Type-2 restriction enzyme HincII
Seq:
Struc:
258 a.a.
254 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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     5 terms  

 

 
DOI no: 10.1016/j.jmb.2004.08.082 J Mol Biol 343:833-849 (2004)
PubMed id: 15476804  
 
 
Mechanistic insights from the structures of HincII bound to cognate DNA cleaved from addition of Mg2+ and Mn2+.
C.Etzkorn, N.C.Horton.
 
  ABSTRACT  
 
The three-dimensional X-ray crystal structures of HincII bound to cognate DNA containing GTCGAC and Mn(2+) or Mg(2+), at 2.50A and 2.95A resolution, respectively, are presented. In both structures, the DNA is found cleaved, and the positions of the active-site groups, cleaved phosphate group, and 3' oxygen atom of the leaving group are in very similar positions. Two highly occupied Mn(2+) positions are found in each active site of the four crystallographically independent subunit copies in the HincII/DNA/Mn(2+) structure. The manganese ion closest to the previously identified single Ca(2+) position of HincII is shifted 1.7A and has lost direct ligation to the active-site aspartate residue, Asp127. A Mn(2+)-ligated water molecule in a position analogous to that seen in the HincII/DNA/Ca(2+) structure, and proposed to be the attacking nucleophile, is beyond hydrogen bonding distance from the active-site lysine residue, Lys129, but remains within hydrogen bonding distance from the proRp oxygen atom of the phosphate group 3' to the scissile phosphate group. In addition, the position of the cleaved phosphate group is on the opposite side of the axis connecting the two metal ions relative to that found in the BamHI/product DNA/Mn(2+) structure. Mechanistic implications are discussed, and a model for the two-metal-ion mechanism of DNA cleavage by HincII is proposed.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. (a) Geometry around the two main manganese ions. (b) Simulated annealing omit map at the 3s level of the HincII/DNA/Mn 2C structure subunit A where the nucleotides around the scissile bond, Cyt7 and Gua8, have been excluded. The manganese ions are shown as green spheres. (c) Simulated annealing omit map at the 3s level of the HincII/DNA/Mg 2C structure subunit A where the nucleotides around the scissile bond, Cyt7 and Gua8, have been excluded. Water molecules are shown as small red spheres. (d) Superposition of subunit A of HincII/cleaved DNA/Mn 2C (red) and HincII/cleaved DNA/Mg 2C (green) showing an equivalent position of the phosphate resulting from cleavage. Although both of the two main Mn 2C positions (large red sphere) were present in the Figure, only one is visible, as the view is down the Mn 2C --Mn 2C axis. Water molecules are indicated by small spheres.
 
  The above figure is reprinted by permission from Elsevier: J Mol Biol (2004, 343, 833-849) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18762194 A.C.Babic, E.J.Little, V.M.Manohar, J.Bitinaite, and N.C.Horton (2008).
DNA distortion and specificity in a sequence-specific endonuclease.
  J Mol Biol, 383, 186-204.
PDB codes: 3e3y 3e40 3e41 3e42 3e43 3e44 3e45
18974222 M.J.Marcaida, J.Prieto, P.Redondo, A.D.Nadra, A.Alibés, L.Serrano, S.Grizot, P.Duchateau, F.Pâques, F.J.Blanco, and G.Montoya (2008).
Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.
  Proc Natl Acad Sci U S A, 105, 16888-16893.
PDB codes: 2vs7 2vs8
18701646 P.W.Dunten, E.J.Little, M.T.Gregory, V.M.Manohar, M.Dalton, D.Hough, J.Bitinaite, and N.C.Horton (2008).
The structure of SgrAI bound to DNA; recognition of an 8 base pair target.
  Nucleic Acids Res, 36, 5405-5416.
PDB codes: 3dpg 3dvo 3dw9
17214552 L.Mones, I.Simon, and M.Fuxreiter (2007).
Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.
  Biol Chem, 388, 73-78.  
17427952 N.Oezguen, C.H.Schein, S.R.Peddi, T.D.Power, T.Izumi, and W.Braun (2007).
A "moving metal mechanism" for substrate cleavage by the DNA repair endonuclease APE-1.
  Proteins, 68, 313-323.  
16675462 H.K.Joshi, C.Etzkorn, L.Chatwell, J.Bitinaite, and N.C.Horton (2006).
Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.
  J Biol Chem, 281, 23852-23869.
PDB codes: 2gie 2gig 2gih 2gii 2gij
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.