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PDBsum entry 1d02

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protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
1d02
Jmol
Contents
Protein chains
197 a.a.
DNA/RNA
Waters ×646
PDB id:
1d02
Name: Hydrolase/DNA
Title: Crystal structure of muni restriction endonuclease in comple cognate DNA
Structure: DNA (5'-d( Gp Cp Cp Ap Ap Tp Tp Gp Gp C)-3'). Chain: c, d. Engineered: yes. Type ii restriction enzyme muni. Chain: a, b. Synonym: endonuclease muni. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Other_details: decameric oligonucleotide 5'-ds(gpcpcpapaptp was synthesized with standard procedures. Mycoplasma. Organism_taxid: 2093. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.70Å     R-factor:   0.180     R-free:   0.213
Authors: M.Deibert,S.Grazulis,A.Janulaitis,V.Siksnys,R.Huber
Key ref:
M.Deibert et al. (1999). Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution. EMBO J, 18, 5805-5816. PubMed id: 10545092 DOI: 10.1093/emboj/18.21.5805
Date:
08-Sep-99     Release date:   08-Mar-00    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P43642  (T2MU_MYCSP) -  Type-2 restriction enzyme MunI
Seq:
Struc:
202 a.a.
197 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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: 10.1093/emboj/18.21.5805 EMBO J 18:5805-5816 (1999)
PubMed id: 10545092  
 
 
Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution.
M.Deibert, S.Grazulis, A.Janulaitis, V.Siksnys, R.Huber.
 
  ABSTRACT  
 
The MunI restriction enzyme recognizes the palindromic hexanucleotide sequence C/AATTG (the '/' indicates the cleavage site). The crystal structure of its active site mutant D83A bound to cognate DNA has been determined at 1.7 A resolution. Base-specific contacts between MunI and DNA occur exclusively in the major groove. While DNA-binding sites of most other restriction enzymes are comprised of discontinuous sequence segments, MunI combines all residues involved in the base-specific contacts within one short stretch (residues R115-R121) located at the N-terminal region of the 3(10)4 helix. The outer CG base pair of the recognition sequence is recognized solely by R115 through hydrogen bonds made by backbone and side chain atoms to both bases. The mechanism of recognition of the central AATT nucleotides by MunI is similar to that of EcoRI, which recognizes the G/AATTC sequence. The local conformation of AATT deviates from the typical B-DNA form and is remarkably similar to EcoRI-DNA. It appears to be essential for specific hydrogen bonding and recognition by MunI and EcoRI.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 DNA sequence of the decameric oligonucleotide used in the MunI D83A -DNA complex. The recognition sequence is boxed. The cleavage sites are indicated by arrows. The position of the crystallographic 2-fold axis is shown.
Figure 6.
Figure 6 Stereo view of MunI active site arrangement. Active site residues are labelled. Water molecules are depicted as blue spheres, with hydrogen bonds shown as dashed black lines. One DNA strand is shown in stick representation, with the scissile phosphate shown as purple and O1P and O2P as red spheres.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 5805-5816) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20541511 B.W.Shen, D.F.Heiter, S.H.Chan, H.Wang, S.Y.Xu, R.D.Morgan, G.G.Wilson, and B.L.Stoddard (2010).
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.
  Structure, 18, 734-743.
PDB codes: 3ldy 3m7k
18456708 J.Orlowski, and J.M.Bujnicki (2008).
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
  Nucleic Acids Res, 36, 3552-3569.  
17308914 G.A.Papadakos, H.Nastri, P.Riggs, and C.M.Dupureur (2007).
Uncoupling metallonuclease metal ion binding sites via nudge mutagenesis.
  J Biol Inorg Chem, 12, 557-569.  
17332011 K.Miyazono, M.Watanabe, J.Kosinski, K.Ishikawa, M.Kamo, T.Sawasaki, K.Nagata, J.M.Bujnicki, Y.Endo, M.Tanokura, and I.Kobayashi (2007).
Novel protein fold discovered in the PabI family of restriction enzymes.
  Nucleic Acids Res, 35, 1908-1918.
PDB code: 2dvy
16308566 E.S.Vanamee, H.Viadiu, R.Kucera, L.Dorner, S.Picone, I.Schildkraut, and A.K.Aggarwal (2005).
A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
  EMBO J, 24, 4198-4208.
PDB codes: 2ezv 2f03
16195548 Q.S.Xu, R.J.Roberts, and H.C.Guo (2005).
Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.
  Protein Sci, 14, 2590-2600.
PDB code: 1yfi
15805123 Z.Yang, J.R.Horton, R.Maunus, G.G.Wilson, R.J.Roberts, and X.Cheng (2005).
Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.
  Nucleic Acids Res, 33, 1892-1901.
PDB code: 1ynm
14654694 S.Jones, H.P.Shanahan, H.M.Berman, and J.M.Thornton (2003).
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
  Nucleic Acids Res, 31, 7189-7198.  
12777809 X.E.Zhou, Y.Wang, M.Reuter, P.Mackeldanz, D.H.Krüger, E.J.Meehan, and L.Chen (2003).
A single mutation of restriction endonuclease EcoRII led to a new crystal form that diffracts to 2.1 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 910-912.  
11917015 G.Vilkaitis, A.Lubys, E.Merkiene, A.Timinskas, A.Janulaitis, and S.Klimasauskas (2002).
Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation.
  Nucleic Acids Res, 30, 1547-1557.  
12081482 J.Huang, J.Lu, F.Barany, and W.Cao (2002).
Mutational analysis of endonuclease V from Thermotoga maritima.
  Biochemistry, 41, 8342-8350.  
12142452 M.Fuxreiter, and I.Simon (2002).
Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
  Protein Sci, 11, 1978-1983.  
11842098 S.Grazulis, M.Deibert, R.Rimseliene, R.Skirgaila, G.Sasnauskas, A.Lagunavicius, V.Repin, C.Urbanke, R.Huber, and V.Siksnys (2002).
Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.
  Nucleic Acids Res, 30, 876-885.
PDB code: 1knv
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
11179886 C.M.Lukacs, and A.K.Aggarwal (2001).
BglII and MunI: what a difference a base makes.
  Curr Opin Struct Biol, 11, 14-18.  
11331763 C.S.Bond, M.Kvaratskhelia, D.Richard, M.F.White, and W.N.Hunter (2001).
Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus.
  Proc Natl Acad Sci U S A, 98, 5509-5514.
PDB code: 1hh1
11250198 M.J.van der Woerd, J.J.Pelletier, S.Xu, and A.M.Friedman (2001).
Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.
  Structure, 9, 133-144.
PDB code: 1dc1
11327870 S.L.Reid, D.Parry, H.H.Liu, and B.A.Connolly (2001).
Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization.
  Biochemistry, 40, 2484-2494.  
11257528 W.Cao, and J.Lu (2001).
Exploring the catalytic center of TaqI endonuclease: rescuing catalytic activity by double mutations and Mn2+.
  Biochim Biophys Acta, 1546, 253-260.  
10666447 E.A.Kubareva, H.Thole, A.S.Karyagina, T.S.Oretskaya, A.Pingoud, and V.Pingoud (2000).
Identification of a base-specific contact between the restriction endonuclease SsoII and its recognition sequence by photocross-linking.
  Nucleic Acids Res, 28, 1085-1091.  
10982859 L.Aravind, K.S.Makarova, and E.V.Koonin (2000).
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
  Nucleic Acids Res, 28, 3417-3432.  
10856254 Q.Huai, J.D.Colandene, Y.Chen, F.Luo, Y.Zhao, M.D.Topal, and H.Ke (2000).
Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase.
  EMBO J, 19, 3110-3118.
PDB code: 1ev7
12760025 S.D.Bruner, D.P.Norman, J.C.Fromme, and G.L.Verdine (2000).
Structural and mechanistic studies on repair of 8-oxoguanine in mammalian cells.
  Cold Spring Harb Symp Quant Biol, 65, 103-111.  
11092936 T.J.O'Loughlin, Q.Xu, R.B.Kucera, L.F.Dorner, S.Sweeney, I.Schildkraut, and H.C.Guo (2000).
Crystallization and preliminary X-ray diffraction analysis of MspI restriction endonuclease in complex with its cognate DNA.
  Acta Crystallogr D Biol Crystallogr, 56, 1652-1655.  
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.