PDBsum entry 2fkc

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
247 a.a.
_CA ×3
Waters ×44
PDB id:
Name: Hydrolase/DNA
Title: Crystal form i of pre-reactive complex of restriction endonuclease hinp1i with cognate DNA and calcium ion
Structure: 5'-d( Cp Cp Ap Gp Cp Gp Cp Tp Gp G)-3'. Chain: c, d, e, f. Engineered: yes. R.Hinp1i restriction endonuclease. Chain: a, b. Engineered: yes
Source: Synthetic: yes. Other_details: synthesized self-annealing oligonucleotide. Haemophilus influenzae. Organism_taxid: 727. Gene: hinp1ir. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
2.39Å     R-factor:   0.222     R-free:   0.260
Authors: J.R.Horton
Key ref: J.R.Horton et al. (2006). DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion. Nucleic Acids Res, 34, 939-948. PubMed id: 16473850
04-Jan-06     Release date:   21-Feb-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q5I6E6  (Q5I6E6_HAEIF) -  R.HinP1I restriction endonuclease
247 a.a.
247 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   1 term 
  Biochemical function     metal ion binding     2 terms  


Nucleic Acids Res 34:939-948 (2006)
PubMed id: 16473850  
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.
J.R.Horton, X.Zhang, R.Maunus, Z.Yang, G.G.Wilson, R.J.Roberts, X.Cheng.
HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.
  Selected figure(s)  
Figure 2.
HinP1I-DNA interactions. (A) Summary of the protein-DNA contacts of HinP1I (green). Backbone mediated interactions are indicated with main chain amine (N) or carbonyl (O). For simplicity, only single water (w) molecule mediated interactions are shown. The A(3) base can be in either an intrahelical or extrahelical location (see text). (B) HinP1I side chains (green) in the major groove of the DNA duplex with a central GCGC site. The side chain of F91 intercalates DNA immediately outside of the recognition sequence, between the outer base pair of the recognition site (G:C) and the first base pair of the flanking DNA (A:T). (C-F) Detailed interactions with the recognition sequence GCGC. All interactions occur from the major groove side, except for the side chain of F15, which approaches the DNA from the minor groove.
Figure 3.
Base flipping outside of the recognition sequence. (A) Superimposition of the two DNA duplexes, bound with molecule A (colored in grey) or molecule B (colored with yellow for carbon atoms, blue for nitrogen atoms, red for oxygen atoms and magenta for phosphate atoms). Base pairs are numbered from 1 to 10, as shown in Figure 2A. The distances between the stacked bases on strand F are indicated. For comparison, the flipped Ade, A(3) of strand E, and its corresponding A(3) of strand C are enlarged and boxed. (B) The flipped Ade, A(3) of strand E, lies against the HinP1I protein surface of molecule B. The double arrows indicate van der Waals contacts. (C) A view of DNA structure containing a junction between Z-DNA and B-DNA [PDB 2ACJ ([213]17)]. The two bases of a A:T base pair at the junction are extruded. Note the van der Waals interaction (double arrow) between the extruded Thy and an intrahelical base.
  The above figures are reprinted from an Open Access publication published by Oxford University Press: Nucleic Acids Res (2006, 34, 939-948) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21227928 G.Kostiuk, G.Sasnauskas, G.Tamulaitiene, and V.Siksnys (2011).
Degenerate sequence recognition by the monomeric restriction enzyme: single mutation converts BcnI into a strand-specific nicking endonuclease.
  Nucleic Acids Res, 39, 3744-3753.  
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
20693529 I.Stier, and A.Kiss (2010).
The type II restriction endonuclease MvaI has dual specificity.
  Nucleic Acids Res, 38, 8231-8238.  
20587501 T.Raskó, A.Dér, E.Klement, K.Slaska-Kiss, E.Pósfai, K.F.Medzihradszky, D.R.Marshak, R.J.Roberts, and A.Kiss (2010).
BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism.
  Nucleic Acids Res, 38, 7155-7166.  
  19077538 H.Hashimoto, J.R.Horton, X.Zhang, and X.Cheng (2009).
UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
  Epigenetics, 4, 8.
PDB codes: 3f8i 3f8j 3fde
19223323 K.L.Sanders, L.E.Catto, S.R.Bellamy, and S.E.Halford (2009).
Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands.
  Nucleic Acids Res, 37, 2105-2115.  
18086711 G.Gasiunas, G.Sasnauskas, G.Tamulaitis, C.Urbanke, D.Razaniene, and V.Siksnys (2008).
Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family.
  Nucleic Acids Res, 36, 938-949.  
18854319 I.Tessmer, Y.Yang, J.Zhai, C.Du, P.Hsieh, M.M.Hingorani, and D.A.Erie (2008).
Mechanism of MutS searching for DNA mismatches and signaling repair.
  J Biol Chem, 283, 36646-36654.  
18653759 J.L.Lorieau, L.A.Day, and A.E.McDermott (2008).
Conformational dynamics of an intact virus: order parameters for the coat protein of Pf1 bacteriophage.
  Proc Natl Acad Sci U S A, 105, 10366-10371.  
18831563 J.W.Pavlicek, Y.L.Lyubchenko, and Y.Chang (2008).
Quantitative analyses of RAG-RSS interactions and conformations revealed by atomic force microscopy.
  Biochemistry, 47, 11204-11211.  
18515839 M.Gao, and J.Skolnick (2008).
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.
  Nucleic Acids Res, 36, 3978-3992.  
17496048 B.Bouvier, and H.Grubmüller (2007).
A molecular dynamics study of slow base flipping in DNA using conformational flooding.
  Biophys J, 93, 770-786.  
17344322 M.Kaus-Drobek, H.Czapinska, M.SokoĊ‚owska, G.Tamulaitis, R.H.Szczepanowski, C.Urbanke, V.Siksnys, and M.Bochtler (2007).
Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically.
  Nucleic Acids Res, 35, 2035-2046.
PDB codes: 2oa9 2oaa
16962970 G.Tamulaitiene, A.Jakubauskas, C.Urbanke, R.Huber, S.Grazulis, and V.Siksnys (2006).
The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.
  Structure, 14, 1389-1400.
PDB code: 2ixs
16893959 M.Carpenter, P.Divvela, V.Pingoud, J.Bujnicki, and A.S.Bhagwat (2006).
Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI.
  Nucleic Acids Res, 34, 3762-3770.  
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 code is shown on the right.