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PDBsum entry 3bvq

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
3bvq
Jmol
Contents
Protein chains
342 a.a.
Ligands
SO4 ×2
Metals
_FE ×2
PDB id:
3bvq
Name: Hydrolase
Title: Crystal structure of apo noti restriction endonuclease
Structure: Noti restriction endonuclease. Chain: a, b. Engineered: yes
Source: Nocardia otitidiscaviarum. Organism_taxid: 1823. Gene: notir. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.80Å     R-factor:   0.266     R-free:   0.335
Authors: A.R.Lambert,D.Sussman,B.Shen,B.L.Stoddard
Key ref:
A.R.Lambert et al. (2008). Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Structure, 16, 558-569. PubMed id: 18400177 DOI: 10.1016/j.str.2008.01.017
Date:
07-Jan-08     Release date:   22-Jan-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q2I6W2  (Q2I6W2_9NOCA) -  NotI restriction endonuclease
Seq:
Struc:
383 a.a.
342 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  

 

 
DOI no: 10.1016/j.str.2008.01.017 Structure 16:558-569 (2008)
PubMed id: 18400177  
 
 
Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding.
A.R.Lambert, D.Sussman, B.Shen, R.Maunus, J.Nix, J.Samuelson, S.Y.Xu, B.L.Stoddard.
 
  ABSTRACT  
 
The structure of the rare-cutting restriction endonuclease NotI, which recognizes the 8 bp target 5'-GCGGCCGC-3', has been solved with and without bound DNA. Because of its specificity (recognizing a site that occurs once per 65 kb), NotI is used to generate large genomic fragments and to map DNA methylation status. NotI contains a unique metal binding fold, found in a variety of putative endonucleases, occupied by an iron atom coordinated within a tetrahedral Cys4 motif. This domain positions nearby protein elements for DNA recognition, and serves a structural role. While recognition of the central six base pairs of the target is accomplished via a saturated hydrogen bond network typical of restriction enzymes, the most peripheral base pairs are engaged in a single direct contact in the major groove, reflecting reduced pressure to recognize those positions. NotI may represent an evolutionary intermediate between mobile endonucleases (which recognize longer target sites) and canonical restriction endonucleases.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Homodimeric NotI REase
Domains are colored as described in Figure 1. Select secondary structural elements are numbered for reference. The NotI dimer interface is formed by the domain-swapped α helices (cyan) and the DNA recognition helices (red).
Figure 6.
Figure 6. The NotI Active Site
(A) Active site residues Glu145, Asp160, Glu182, and Gln184 are colored yellow. The bound DNA is colored white, with the scissile phosphate designated orange. The nucleophilic water molecule is shown as a blue sphere and two calcium ions are depicted as magenta spheres. Dashed lines represent interactions between atoms in the active site and numbers indicate distances in angstroms (as average values calculated between the two active sites of the NotI homodimer).
(B) Superposition of active site residues of the P(D)…(D/E)xK active site motif from NotI (green) and BglII (orange). Both REases have a glutamine in the general base position typically occupied by a lysine residue.
(C) Superposition of the two-metal ion active sites of NotI (green) and BamHI (purple). Asp160/Asp94, Glu182/Glu111, and Gln184/Glu113 are residues belonging to the canonical PD…(D/E)xK nuclease motif, while the third acidic residue, Glu145/Glu77, helps coordinate a second metal ion in the active site. The position of this third acidic residue is conserved between the NotI and BamHI enzymes.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 558-569) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21146395 E.S.Kim, B.J.Hong, C.W.Park, Y.Kim, J.W.Park, and K.Y.Choi (2011).
Effects of lateral spacing on enzymatic on-chip DNA polymerization.
  Biosens Bioelectron, 26, 2566-2573.  
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
20047321 J.C.Genereux, A.K.Boal, and J.K.Barton (2010).
DNA-mediated charge transport in redox sensing and signaling.
  J Am Chem Soc, 132, 891-905.  
19747545 P.Zhang, P.H.Too, J.C.Samuelson, S.H.Chan, T.Vincze, S.Doucette, S.Bäckström, K.D.Potamousis, T.M.Schramm, D.Forrest, D.C.Schwartz, and S.Y.Xu (2010).
Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.
  Protein Expr Purif, 69, 226-234.  
19089001 C.Liu, and L.Wang (2009).
DNA hydrolytic cleavage catalyzed by synthetic multinuclear metallonucleases.
  Dalton Trans, (), 227-239.  
19729506 D.Golovenko, E.Manakova, G.Tamulaitiene, S.Grazulis, and V.Siksnys (2009).
Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.
  Nucleic Acids Res, 37, 6613-6624.
PDB codes: 3hqf 3hqg
19129187 J.T.Yeeles, R.Cammack, and M.S.Dillingham (2009).
An Iron-Sulfur Cluster Is Essential for the Binding of Broken DNA by AddAB-type Helicase-Nucleases.
  J Biol Chem, 284, 7746-7755.  
18400171 G.Tamulaitiene, and V.Siksnys (2008).
NotI is not boring.
  Structure, 16, 497-498.  
18701646 P.W.Dunten, E.J.Little, M.T.Gregory, V.M.Manohar, M.Dalton, D.Hough, J.Bitinaite, and N.C.Horton (2008).
The structure of SgrAI bound to DNA; recognition of an 8 base pair target.
  Nucleic Acids Res, 36, 5405-5416.
PDB codes: 3dpg 3dvo 3dw9
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.