PDBsum entry 2ost

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
148 a.a.
138 a.a.
_CA ×2
Waters ×16
PDB id:
Name: Hydrolase/DNA
Title: The structure of a bacterial homing endonuclease : i-ssp6803
Structure: Synthetic DNA 29 mer. Chain: y. Engineered: yes. Synthetic DNA 29 mer. Chain: z. Engineered: yes. Putative endonuclease. Chain: a, b, c, d. Engineered: yes.
Source: Synthetic: yes. Other_details: synthetic construct containing natural homin i-sspi6803i. Synechocystis sp.. Organism_taxid: 1148. Strain: pcc 6803. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
3.10Å     R-factor:   0.281     R-free:   0.328
Authors: L.Zhao,R.P.Bonocora,D.A.Shub,B.L.Stoddard
Key ref:
L.Zhao et al. (2007). The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. EMBO J, 26, 2432-2442. PubMed id: 17410205 DOI: 10.1038/sj.emboj.7601672
06-Feb-07     Release date:   20-Mar-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q57253  (Q57253_SYNY3) -  Putative endonuclease
150 a.a.
148 a.a.*
Protein chains
Pfam   ArchSchema ?
Q57253  (Q57253_SYNY3) -  Putative endonuclease
150 a.a.
138 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 10 residue positions (black crosses)

 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: 10.1038/sj.emboj.7601672 EMBO J 26:2432-2442 (2007)
PubMed id: 17410205  
The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.
L.Zhao, R.P.Bonocora, D.A.Shub, B.L.Stoddard.
The homing endonuclease I-Ssp6803I causes the insertion of a group I intron into a bacterial tRNA gene-the only example of an invasive mobile intron within a bacterial genome. Using a computational fold prediction, mutagenic screen and crystal structure determination, we demonstrate that this protein is a tetrameric PD-(D/E)-XK endonuclease - a fold normally used to protect a bacterial genome from invading DNA through the action of restriction endonucleases. I-Ssp6803I uses its tetrameric assembly to promote recognition of a single long target site, whereas restriction endonuclease tetramers facilitate cooperative binding and cleavage of two short sites. The limited use of the PD-(D/E)-XK nucleases by mobile introns stands in contrast to their frequent use of LAGLIDADG and HNH endonucleases - which in turn, are rarely incorporated into restriction/modification systems.
  Selected figure(s)  
Figure 3.
Figure 3 Structural comparison of protein subunits from the I-Ssp6803I homing endonuclease, the Hjc Holliday junction resolvase and the PvuII restriction endonuclease. (A) Structure and topology diagram of a single homing endonuclease subunit. The secondary structural elements are labeled and colored as follows: the PD-(D/E)-XK catalytic core region is pink and peripheral elaborations on that core are green. The N- and C-terminal residues of the secondary structural elements are indicated in the topology diagram. Catalytic residues are shown as sticks in the model on the left and labeled in red on the right. Regions involved in DNA recognition are indicated by dotted boxes and are numbered as shown in Figure 6 and described in the text. (B) The Hjc Holliday junction resolvase subunit. This structure has not been determined in the presence of DNA. (C) The PvuII restriction endonuclease subunit. Inlay: superposition of the I-SspI and Hjc catalytic cores (r.m.s.d. 1.9 Å).
Figure 7.
Figure 7 The active site of I-Ssp6803I. (A) The active site of I-Ssp6803I is shown as a ball-and-stick representation. The observed calcium ion position is shown as a red sphere. The anomalous difference map calculated from a native data set collected on a rotating anode X-ray source (CuK ; =1.54 Å) is shown in blue and contoured at 4.5 . The predicted location of the water nucleophile and direction of its attack is indicated by the arrow; the scissile phosphodiester bond is indicated with a red star. (B) Superimposed active sites of I-SspI with EcoRV and Hjc. K51, D36 and E11 are conserved; Q49 is replaced by D and E, respectively in EcoRV and Hjc.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 2432-2442) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21220111 B.L.Stoddard (2011).
Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.
  Structure, 19, 7.  
21047873 S.Arnould, C.Delenda, S.Grizot, C.Desseaux, F.Pâques, G.H.Silva, and J.Smith (2011).
The I-CreI meganuclease and its engineered derivatives: applications from cell modification to gene therapy.
  Protein Eng Des Sel, 24, 27-31.  
20805246 S.H.Chan, B.L.Stoddard, and S.Y.Xu (2011).
Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.
  Nucleic Acids Res, 39, 1.  
20061372 B.P.Kleinstiver, A.D.Fernandes, G.B.Gloor, and D.R.Edgell (2010).
A unified genetic, computational and experimental framework identifies functionally relevant residues of the homing endonuclease I-BmoI.
  Nucleic Acids Res, 38, 2411-2427.  
19915993 M.J.Marcaida, I.G.Muñoz, F.J.Blanco, J.Prieto, and G.Montoya (2010).
Homing endonucleases: from basics to therapeutic applications.
  Cell Mol Life Sci, 67, 727-748.  
  19937653 P.Singh, P.Tripathi, and K.Muniyappa (2010).
Mutational analysis of active-site residues in the Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease: Asp(122) and Asp(193) are crucial to the double-stranded DNA cleavage activity whereas Asp(218) is not.
  Protein Sci, 19, 111-123.  
20375162 S.K.Menon, B.J.Eilers, M.J.Young, and C.M.Lawrence (2010).
The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily.
  J Virol, 84, 5890-5897.
PDB code: 2w8m
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.  
19597163 J.Sethuraman, A.Majer, N.C.Friedrich, D.R.Edgell, and G.Hausner (2009).
Genes within genes: multiple LAGLIDADG homing endonucleases target the ribosomal protein S3 gene encoded within an rnl group I intron of Ophiostoma and related taxa.
  Mol Biol Evol, 26, 2299-2315.  
19038269 L.Zhao, S.Pellenz, and B.L.Stoddard (2009).
Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I.
  J Mol Biol, 385, 1498-1510.  
19605345 P.Singh, P.Tripathi, G.H.Silva, A.Pingoud, and K.Muniyappa (2009).
Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA binding, helical distortion, and cleavage compared with a canonical LAGLIDADG homing endonuclease.
  J Biol Chem, 284, 25912-25928.  
19200727 R.P.Bonocora, and D.A.Shub (2009).
A likely pathway for formation of mobile group I introns.
  Curr Biol, 19, 223-228.  
19666710 R.Raghavan, and M.F.Minnick (2009).
Group I introns and inteins: disparate origins but convergent parasitic strategies.
  J Bacteriol, 191, 6193-6202.  
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
18992156 D.Milstein, M.C.Oliveira, F.M.Martins, and S.R.Matioli (2008).
Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the Eastern coast of South America.
  BMC Evol Biol, 8, 308.  
18032435 D.Nord, and B.M.Sjöberg (2008).
Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group.
  Nucleic Acids Res, 36, 300-310.  
17947319 J.H.Eastberg, A.McConnell Smith, L.Zhao, J.Ashworth, B.W.Shen, and B.L.Stoddard (2007).
Thermodynamics of DNA target site recognition by homing endonucleases.
  Nucleic Acids Res, 35, 7209-7221.  
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.