PDBsum entry 2e52

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protein dna_rna ligands Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
299 a.a. *
GOL ×4
ACT ×3
Waters ×968
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: Crystal structural analysis of hindiii restriction endonucle complex with cognate DNA at 2.0 angstrom resolution
Structure: Type ii restriction enzyme hindiii. Chain: a, c, b, d. Synonym: endonuclease hindiii, r.Hindiii. Engineered: yes. DNA (5'-d( Dgp Dcp Dcp Dap Dap Dgp Dcp Dtp Dtp Dg 3'). Chain: e, f, g, h, i, j. Engineered: yes
Source: Haemophilus influenzae. Organism_taxid: 71421. Strain: rd kw20. Gene: hindiiir. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes
2.00Å     R-factor:   0.177     R-free:   0.217
Authors: N.Watanabe,C.Sato,I.Tanaka
Key ref:
N.Watanabe et al. (2009). Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations. Acta Crystallogr D Biol Crystallogr, 65, 1326-1333. PubMed id: 19966419 DOI: 10.1107/S0907444909041134
18-Dec-06     Release date:   18-Dec-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P43870  (T2D3_HAEIN) -  Type-2 restriction enzyme HindIII
300 a.a.
299 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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     4 terms  


DOI no: 10.1107/S0907444909041134 Acta Crystallogr D Biol Crystallogr 65:1326-1333 (2009)
PubMed id: 19966419  
Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations.
N.Watanabe, Y.Takasaki, C.Sato, S.Ando, I.Tanaka.
The three-dimensional crystal structures of HindIII bound to its cognate DNA with and without divalent cations were solved at 2.17 and 2.00 A resolution, respectively. HindIII forms a dimer. The structures showed that HindIII belongs to the EcoRI-like (alpha-class) subfamily of type II restriction endonucleases. The cognate DNA-complex structures revealed the specific DNA-recognition mechanism of HindIII by which it recognizes the palindromic sequence A/AGCTT. In the Mg(2+) ion-soaked structure the DNA was cleaved and two ions were bound at each active site, corresponding to the two-metal-ion mechanism.
  Selected figure(s)  
Figure 1.
Figure 1 Overall structure of the HindIII monomer. (a) HindIII monomer with labelled helices and -strands. (b) Topology diagram of HindIII. -Sheets are shown in red and helices are shown in cyan.
Figure 2.
Figure 2 The dimer structure of the HindIII-DNA complex. (a) Top view of the complex. (b) View of the complex along the noncrystallographic dyad axis. The two metals observed in the Mg^2+-soaked structure are also shown, with Mg^2+ as blue spheres and Mn^2+ as green spheres.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2009, 65, 1326-1333) copyright 2009.  
  Figures were selected by the author.