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PDBsum entry 1sa3

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
1sa3
Jmol
Contents
Protein chains
262 a.a.
DNA/RNA
Metals
_NA ×2
Waters ×331
PDB id:
1sa3
Name: Hydrolase/DNA
Title: An asymmetric complex of restriction endonuclease mspi on its palindromic DNA recognition site
Structure: 5'-d( Cp Cp Cp Cp Cp Gp Gp Gp Gp G)-3'. Chain: c, d, e, f. Engineered: yes. Type ii restriction enzyme mspi. Chain: a, b. Synonym: endonuclease mspi, r.Mspi. Engineered: yes
Source: Synthetic: yes. Moraxella sp.. Organism_taxid: 479. Gene: mspir. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.95Å     R-factor:   0.223     R-free:   0.252
Authors: Q.S.Xu,R.B.Kucera,R.J.Roberts,H.C.Guo
Key ref:
Q.S.Xu et al. (2004). An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site. Structure, 12, 1741-1747. PubMed id: 15341737 DOI: 10.1016/j.str.2004.07.014
Date:
06-Feb-04     Release date:   07-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P11405  (T2M1_MORSP) -  Type-2 restriction enzyme MspI
Seq:
Struc:
262 a.a.
262 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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.str.2004.07.014 Structure 12:1741-1747 (2004)
PubMed id: 15341737  
 
 
An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site.
Q.S.Xu, R.B.Kucera, R.J.Roberts, H.C.Guo.
 
  ABSTRACT  
 
Most well-known restriction endonucleases recognize palindromic DNA sequences and are classified as Type IIP. Due to the recognition and cleavage symmetry, Type IIP enzymes are usually found to act as homodimers in forming 2-fold symmetric enzyme-DNA complexes. Here we report an asymmetric complex of the Type IIP restriction enzyme MspI in complex with its cognate recognition sequence. Unlike any other Type IIP enzyme reported to date, an MspI monomer and not a dimer binds to a palindromic DNA sequence. The enzyme makes specific contacts with all 4 base pairs in the recognition sequence, by six direct and five water-mediated hydrogen bonds and numerous van der Waal contacts. This MspI-DNA structure represents the first example of asymmetric recognition of a palindromic DNA sequence by two different structural motifs in one polypeptide. A few possible pathways are discussed for MspI to cut both strands of DNA, either as a monomer or dimer.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. MspI-DNA Interactions(A) Stereoview of the tertiary structure of the MspI-DNA complex. The enzyme is represented as ribbons and the DNA as a brown stick model. Secondary structure elements of MspI are labeled and the conserved structural core are colored as in Figure 1. Side chains of the catalytic site residues (Asp99, Asn117, and Lys119) are shown as ball-and-stick representations, with carbons in black, nitrogens in blue, and oxygens in red.(B) Schematic diagram of hydrogen bonding between MspI and DNA. The DNA recognition sequence is shaded in gray, with the scissile phosphate (C4-C5) circled in red. One DNA base pair (G10:C11) is omitted in the final model (see Experimental Procedures). Blue and pink represent amino acids that bind to DNA bases in the major and minor groove, respectively. Amino acids that bind to the phosphate backbone of DNA are colored in black. Solid lines represent direct hydrogen bonds: Ser127-G6 (OG-N7), Thr248-C14 (OG1-N4), Tyr249-C15 (O-N4), Ser251-G16 (OG-N7), Gln259-G6 (NE2-O6), and Lys261-G7 (NZ-O6) in the recognition sequence; and Gly252-C3 (O-N4) outside the recognition sequence. Dotted lines represent water-mediated hydrogen bonds: Glu130-C4 (OE1-N4) through a water that also contacts Gly252 (N), Glu130-C5 (OE1-N4) through another water that also contacts Gln259 (NE2), Ser251-G16 (N-O6), Ser251-G17 (OG-O6), and Lys261-G7 (NZ-N7) in the major groove; and Ser27-C5 (OG-O2) and Asp28-G17 (OD1-N2) in the minor groove.
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1741-1747) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20833632 E.S.Vanamee, H.Viadiu, S.H.Chan, A.Ummat, A.M.Hartline, S.Y.Xu, and A.K.Aggarwal (2011).
Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
  Nucleic Acids Res, 39, 712-719.
PDB code: 3odh
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.  
18400177 A.R.Lambert, D.Sussman, B.Shen, R.Maunus, J.Nix, J.Samuelson, S.Y.Xu, and B.L.Stoddard (2008).
Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding.
  Structure, 16, 558-569.
PDB codes: 3bvq 3c25
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.  
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.  
17407166 J.Kosinski, E.Kubareva, and J.M.Bujnicki (2007).
A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.
  Proteins, 68, 324-336.  
17344322 M.Kaus-Drobek, H.Czapinska, M.Sokołowska, 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
16473850 J.R.Horton, X.Zhang, R.Maunus, Z.Yang, G.G.Wilson, R.J.Roberts, and X.Cheng (2006).
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.
  Nucleic Acids Res, 34, 939-948.
PDB codes: 2fkc 2fkh 2fl3 2flc
16223716 E.Armalyte, J.M.Bujnicki, J.Giedriene, G.Gasiunas, J.Kosiński, and A.Lubys (2005).
Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.
  J Biol Chem, 280, 41584-41594.  
16209953 J.Y.Lee, J.Chang, N.Joseph, R.Ghirlando, D.N.Rao, and W.Yang (2005).
MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage.
  Mol Cell, 20, 155-166.
PDB codes: 2aoq 2aor
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
15888729 S.Nikolajewa, A.Beyer, M.Friedel, J.Hollunder, and T.Wilhelm (2005).
Common patterns in type II restriction enzyme binding sites.
  Nucleic Acids Res, 33, 2726-2733.  
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
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.