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PDBsum entry 3dpg
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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
3dpg

 

 

 

 

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Contents
Protein chains
338 a.a.
DNA/RNA
Metals
_CA ×4
Waters ×471
PDB id:
3dpg
Name: Hydrolase/DNA
Title: Sgrai with noncognate DNA bound
Structure: DNA (5'- d( Dap Dap Dgp Dtp Dcp Dgp Dap Dcp Dcp Dgp Dgp Dtp Dgp Dgp Dap Dcp Dt )-3'). Chain: c, d. Engineered: yes. Sgrair restriction enzyme. Chain: a, b. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Streptomyces griseus. Organism_taxid: 1911. Gene: sgrair. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.91Å     R-factor:   0.187     R-free:   0.225
Authors: P.W.Dunten,N.C.Horton,E.J.Little
Key ref: P.W.Dunten et al. (2008). The structure of SgrAI bound to DNA; recognition of an 8 base pair target. Nucleic Acids Res, 36, 5405-5416. PubMed id: 18701646
Date:
08-Jul-08     Release date:   19-Aug-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9F6L0  (Q9F6L0_STRGR) -  SgraIR restriction enzyme from Streptomyces griseus
Seq:
Struc: 		339 a.a.
338 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains
  A-A-G-T-C-G-A-C-C-G-G-T-G-G-A-C-T 17 bases
  A-A-G-T-C-G-A-C-C-G-G-T-G-G-A-T 16 bases

 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+)

 

 
Nucleic Acids Res 36:5405-5416 (2008)
PubMed id: 18701646  
 
 
The structure of SgrAI bound to DNA; recognition of an 8 base pair target.
P.W.Dunten, E.J.Little, M.T.Gregory, V.M.Manohar, M.Dalton, D.Hough, J.Bitinaite, N.C.Horton.
 
  ABSTRACT  
 
The three-dimensional X-ray crystal structure of the 'rare cutting' type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the second bound distal from the DNA. These sites are differentially occupied by Mn(2+), with strong binding at the protein-DNA interface, but only partial occupancy of the distal site. The DNA remains uncleaved in the structures from crystals grown in the presence of either divalent cation. The structure of the dimer of SgrAI is similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC). Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via indirect readout using DNA distortion. Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21151881 C.K.Park, H.K.Joshi, A.Agrawal, M.I.Ghare, E.J.Little, P.W.Dunten, J.Bitinaite, and N.C.Horton (2010).
Domain swapping in allosteric modulation of DNA specificity.
  PLoS Biol, 8, e1000554.
PDB code: 3mq6
20571089 M.Zaremba, A.Owsicka, G.Tamulaitis, G.Sasnauskas, L.S.Shlyakhtenko, A.Y.Lushnikov, Y.L.Lyubchenko, N.Laurens, B.van den Broek, G.J.Wuite, and V.Siksnys (2010).
DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.
  Nucleic Acids Res, 38, 7142-7154.  
20140205 S.H.Chan, L.Opitz, L.Higgins, D.O'loane, and S.Y.Xu (2010).
Cofactor requirement of HpyAV restriction endonuclease.
  PLoS One, 5, e9071.  
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
19307723 P.W.Dunten, E.J.Little, and N.C.Horton (2009).
The restriction enzyme SgrAI: structure solution via combination of poor MIRAS and MR phases.
  Acta Crystallogr D Biol Crystallogr, 65, 393-398.  
19793866 R.M.Smith, J.Josephsen, and M.D.Szczelkun (2009).
An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI.
  Nucleic Acids Res, 37, 7231-7238.  
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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