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PDBsum entry 2aud

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protein links
Hydrolase PDB id
2aud
Jmol
Contents
Protein chain
242 a.a.
Waters ×448
PDB id:
2aud
Name: Hydrolase
Title: Unliganded hincii
Structure: Type ii restriction enzyme hincii. Chain: a. Fragment: hincii. Synonym: endonuclease hincii, r.Hincii. Engineered: yes
Source: Haemophilus influenzae. Organism_taxid: 727. Gene: hinciir. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.10Å     R-factor:   0.248     R-free:   0.327
Authors: N.C.Horton,E.J.Little
Key ref:
E.J.Little and N.C.Horton (2005). DNA-induced conformational changes in type II restriction endonucleases: the structure of unliganded HincII. J Mol Biol, 351, 76-88. PubMed id: 15993893 DOI: 10.1016/j.jmb.2005.05.063
Date:
27-Aug-05     Release date:   04-Oct-05    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17743  (T2C2_HAEIF) -  Type-2 restriction enzyme HincII
Seq:
Struc:
258 a.a.
242 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 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.2005.05.063 J Mol Biol 351:76-88 (2005)
PubMed id: 15993893  
 
 
DNA-induced conformational changes in type II restriction endonucleases: the structure of unliganded HincII.
E.J.Little, N.C.Horton.
 
  ABSTRACT  
 
The 2.1A crystal structure of the unliganded type II restriction endonuclease, HincII, is described. Although the asymmetric unit contains only a single monomer, crystal lattice contacts bring two monomers together to form a dimer very similar to that found in the DNA bound form. Comparison with the published DNA bound structure reveals that the DNA binding pocket is expanded in the unliganded structure. Comparison of the unliganded and DNA liganded structures reveals a simple rotation of subunits by 11 degrees each, or 22 degrees total, to a more closed structure around the bound DNA. Comparison of this conformational change to that observed in the other type II restriction endonucleases where DNA bound and unliganded forms have both been characterized, shows considerable variation in the types of conformational changes that can occur. The conformational changes in three can be described by a simple rotation of subunits, while in two others both rotation and translation of subunits relative to one another occurs. In addition, the endonucleases having subunits that undergo the greatest amount of rotation upon DNA binding are found to be those that distort the bound DNA the least, suggesting that DNA bending may be less facile in dimers possessing greater flexibility.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Ribbon diagrams colored by temperature factor as indicated for monomers from HincII structures. Left, HincII unliganded; middle and right, HincII bound to DNA. (b) Temperature factors of alpha carbon atoms from residues of a single monomer from HincII structures unliganded (red, dotted) and DNA bound (black, continuous).
Figure 3.
Figure 3. Stereo diagram of the superposition using alpha carbon atoms of chain A 211-233 residues of DNA bound (blue) and unliganded (red) structures of HincII. Notice the deviation of the C terminus of chain A, while that of chain B superimposes well.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 351, 76-88) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20375162 S.K.Menon, B.J.Eilers, M.J.Young, and C.M.Lawrence (2010).
The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily.
  J Virol, 84, 5890-5897.
PDB code: 2w8m
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
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