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PDBsum entry 1cw0

Go to PDB code: 
protein dna_rna metals links
Hydrolase/DNA PDB id
1cw0
Jmol PyMol
Contents
Protein chain
155 a.a. *
DNA/RNA
Metals
_MG ×2
_ZN
Waters ×206
* Residue conservation analysis
PDB id:
1cw0
Name: Hydrolase/DNA
Title: Crystal structure analysis of very short patch repair (vsr) endonuclease in complex with a duplex DNA
Structure: DNA (5'-d( Ap Cp Gp Tp Ap Cp Cp Tp Gp Gp Cp T)- 3'). Chain: m. Engineered: yes. DNA (5'-d( Ap Gp C)-3'). Chain: n. Engineered: yes. DNA (5'-d(p Tp Ap Gp Gp Tp Ap Cp Gp T)-3'). Chain: o.
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.30Å     R-factor:   0.204     R-free:   0.230
Authors: S.E.Tsutakawa,H.Jingami,K.Morikawa
Key ref:
S.E.Tsutakawa et al. (1999). Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Cell, 99, 615-623. PubMed id: 10612397 DOI: 10.1016/S0092-8674(00)81550-0
Date:
25-Aug-99     Release date:   12-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09184  (VSR_ECOLI) -  Very short patch repair protein
Seq:
Struc:
156 a.a.
155 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   4 terms 
  Biochemical function     protein binding     7 terms  

 

 
DOI no: 10.1016/S0092-8674(00)81550-0 Cell 99:615-623 (1999)
PubMed id: 10612397  
 
 
Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex.
S.E.Tsutakawa, H.Jingami, K.Morikawa.
 
  ABSTRACT  
 
The crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution. In E. coli, the enzyme recognizes a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine. Extensive interactions between the DNA and the protein characterize a novel recognition mechanism, where three aromatic residues intercalate from the major groove into the DNA to strikingly deform the base pair stacking. With the presence of a cleaved DNA intermediate in the active center, the structure of the Vsr/DNA complex provides detailed insights into the catalytic mechanism for endonuclease activity.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Schematic Diagram of Polar Interactions between Protein and DNABases that are part of the substrate recognition sequence are colored in red, and residues within hydrogen-bonding distances (black) or involved in water-mediated interactions (blue) are denoted, with main chain contacts distinguished by (O) or (N). Intercalating residues (green) are placed according to their relative position to the bases. The diagram excludes interactions with the cleaved 5′ and 3′ termini (see Figure 5). The minor groove contacts are all contributed by N-terminal residues 5, 10, 13, 14, 15, or 17.
Figure 5.
Figure 5. Magnesium–Water Clusters in Vsr(A) Stereo F[o] − F[c] simulated annealed omit map (at 2.3 Å ) where the metal–water clusters have been omitted and that has been contoured at 5 (blue) and 11 (magenta) σ. Mg^2+ atoms are represented by white spheres, and all directly metal-coordinating water molecules or residues are depicted and colored as in Figure 4A.[14] Figure 4A(B) Schematic view of the metal–water clusters and distances (Å) between Mg^2+ atoms and coordinating atoms. An asterisk indicates the probable oxygen that was involved in attacking the phosphodiester bond.
 
  The above figures are reprinted by permission from Cell Press: Cell (1999, 99, 615-623) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
20961958 M.Laganeckas, M.Margelevicius, and C.Venclovas (2011).
Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.
  Nucleic Acids Res, 39, 1187-1196.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20890269 A.B.Hickman, J.A.James, O.Barabas, C.Pasternak, B.Ton-Hoang, M.Chandler, S.Sommer, and F.Dyda (2010).
DNA recognition and the precleavage state during single-stranded DNA transposition in D. radiodurans.
  EMBO J, 29, 3840-3852.
PDB codes: 2xm3 2xma 2xo6 2xqc
20511499 A.Kwiatek, M.Luczkiewicz, K.Bandyra, D.C.Stein, and A.Piekarowicz (2010).
Neisseria gonorrhoeae FA1090 carries genes encoding two classes of Vsr endonucleases.
  J Bacteriol, 192, 3951-3960.  
  20725617 K.Fukui (2010).
DNA mismatch repair in eukaryotes and bacteria.
  J Nucleic Acids, 2010, 0.  
19264795 B.Dassa, N.London, B.L.Stoddard, O.Schueler-Furman, and S.Pietrokovski (2009).
Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family.
  Nucleic Acids Res, 37, 2560-2573.  
19474347 R.J.Heinze, L.Giron-Monzon, A.Solovyova, S.L.Elliot, S.Geisler, C.G.Cupples, B.A.Connolly, and P.Friedhoff (2009).
Physical and functional interactions between Escherichia coli MutL and the Vsr repair endonuclease.
  Nucleic Acids Res, 37, 4453-4463.  
17584917 L.Knizewski, L.N.Kinch, N.V.Grishin, L.Rychlewski, and K.Ginalski (2007).
Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
  BMC Struct Biol, 7, 40.  
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
16011798 J.Kosinski, M.Feder, and J.M.Bujnicki (2005).
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.
  BMC Bioinformatics, 6, 172.  
15882618 J.R.Horton, K.Liebert, S.Hattman, A.Jeltsch, and X.Cheng (2005).
Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase.
  Cell, 121, 349-361.
PDB codes: 1yf3 1yfj 1yfl
15972856 L.N.Kinch, K.Ginalski, L.Rychlewski, and N.V.Grishin (2005).
Identification of novel restriction endonuclease-like fold families among hypothetical proteins.
  Nucleic Acids Res, 33, 3598-3605.  
15240833 J.Gallego (2004).
Sequence-dependent nucleotide dynamics revealed by intercalated ring rotation in DNA-bisnaphthalimide complexes.
  Nucleic Acids Res, 32, 3607-3614.  
12512075 I.Gómez-Pinto, V.Marchán, F.Gago, A.Grandas, and C.González (2003).
Solution structure and stability of tryptophan-containing nucleopeptide duplexes.
  Chembiochem, 4, 40-49.
PDB code: 1j9n
12626704 K.A.Bunting, S.M.Roe, A.Headley, T.Brown, R.Savva, and L.H.Pearl (2003).
Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.
  Nucleic Acids Res, 31, 1633-1639.
PDB code: 1odg
12655008 M.Laging, E.Lindner, H.J.Fritz, and W.Kramer (2003).
Repair of hydrolytic DNA deamination damage in thermophilic bacteria: cloning and characterization of a Vsr endonuclease homolog from Bacillus stearothermophilus.
  Nucleic Acids Res, 31, 1913-1920.  
12067333 A.S.Bhagwat, and M.Lieb (2002).
Cooperation and competition in mismatch repair: very short-patch repair and methyl-directed mismatch repair in Escherichia coli.
  Mol Microbiol, 44, 1421-1428.  
12356742 M.Mücke, G.Grelle, J.Behlke, R.Kraft, D.H.Krüger, and M.Reuter (2002).
EcoRII: a restriction enzyme evolving recombination functions?
  EMBO J, 21, 5262-5268.  
11742344 N.C.Horton, L.F.Dorner, and J.J.Perona (2002).
Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation.
  Nat Struct Biol, 9, 42-47.
PDB code: 1kc6
11920679 T.M.Marti, C.Kunz, and O.Fleck (2002).
DNA mismatch repair and mutation avoidance pathways.
  J Cell Physiol, 191, 28-41.  
12361800 Y.W.Kow (2002).
Repair of deaminated bases in DNA.
  Free Radic Biol Med, 33, 886-893.  
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
11557807 I.Kobayashi (2001).
Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.
  Nucleic Acids Res, 29, 3742-3756.  
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
11591694 M.Lieb, S.Rehmat, and A.S.Bhagwat (2001).
Interaction of MutS and Vsr: some dominant-negative mutS mutations that disable methyladenine-directed mismatch repair are active in very-short-patch repair.
  J Bacteriol, 183, 6487-6490.  
11557809 S.E.Tsutakawa, and K.Morikawa (2001).
The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease.
  Nucleic Acids Res, 29, 3775-3783.  
11179891 T.K.Sixma (2001).
DNA mismatch repair: MutS structures bound to mismatches.
  Curr Opin Struct Biol, 11, 47-52.  
10911996 A.B.Hickman, Y.Li, S.V.Mathew, E.W.May, N.L.Craig, and F.Dyda (2000).
Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
  Mol Cell, 5, 1025-1034.
PDB code: 1f1z
11071943 H.Daiyasu, K.Komori, S.Sakae, Y.Ishino, and H.Toh (2000).
Hjc resolvase is a distantly related member of the type II restriction endonuclease family.
  Nucleic Acids Res, 28, 4540-4543.  
11188699 K.P.Hopfner, and J.A.Tainer (2000).
DNA mismatch repair: the hands of a genome guardian.
  Structure, 8, R237-R241.  
10871403 K.R.Fox, S.L.Allinson, H.Sahagun-Krause, and T.Brown (2000).
Recognition of GT mismatches by Vsr mismatch endonuclease.
  Nucleic Acids Res, 28, 2535-2540.  
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.  
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.

 

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