3M7K

Crystal structure of PacI-DNA Enzyme product complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.

Shen, B.W., Heiter, D.F., Chan, S.H., Wang, H., Xu, S.Y., Morgan, R.D., Wilson, G.G., Stoddard, B.L.

(2010) Structure 18: 734-743

  • DOI: 10.1016/j.str.2010.03.009
  • Primary Citation of Related Structures:  
    3LDY, 3M7K

  • PubMed Abstract: 

    • The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with its eight-base-pair target recognition sequence 5'-TTAATTAA-3' has been determined to 1.9 A resolution. The enzyme forms an extended homodimer, with each subunit containing two zinc-bound motifs surrounding a betabetaalpha-metal catalytic site ...

    The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with its eight-base-pair target recognition sequence 5'-TTAATTAA-3' has been determined to 1.9 A resolution. The enzyme forms an extended homodimer, with each subunit containing two zinc-bound motifs surrounding a betabetaalpha-metal catalytic site. The latter is unusual in that a tyrosine residue likely initiates strand cleavage. PacI dramatically distorts its target sequence from Watson-Crick duplex DNA base pairing, with every base separated from its original partner. Two bases on each strand are unpaired, four are engaged in noncanonical A:A and T:T base pairs, and the remaining two bases are matched with new Watson-Crick partners. This represents a highly unusual DNA binding mechanism for a restriction endonuclease, and implies that initial recognition of the target site might involve significantly different contacts from those visualized in the DNA-bound cocrystal structures.

    Organizational Affiliation: 

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. A3-025, Seattle, WA 98109, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
restriction endonuclease PacIA142Pseudomonas alcaligenesMutation(s): 0 
Gene Names: pacIR
Find proteins for D5MNX7 (Pseudomonas alcaligenes)
Explore D5MNX7 
Go to UniProtKB:  D5MNX7
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3')B10N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3')C8N/A
      Small Molecules
      Ligands 6 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PT
      Query on PT
      Download Ideal Coordinates CCD File 
      		 G [auth A]PLATINUM (II) ION
      Pt
      HRGDZIGMBDGFTC-UHFFFAOYSA-N      		 Ligand Interaction
      SO4
      Query on SO4
      Download Ideal Coordinates CCD File 
      		 P [auth A], Q [auth A]SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L      		 Ligand Interaction
      ZN
      Query on ZN
      Download Ideal Coordinates CCD File 
      		 D [auth A], E [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N      		 Ligand Interaction
      EDO
      Query on EDO
      Download Ideal Coordinates CCD File 
      		 O [auth A]1,2-ETHANEDIOL
      C2 H6 O2
      LYCAIKOWRPUZTN-UHFFFAOYSA-N      		 Ligand Interaction
      MG
      Query on MG
      Download Ideal Coordinates CCD File 
      		 F [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N      		 Ligand Interaction
      NA
      Query on NA
      Download Ideal Coordinates CCD File 
      H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , N [auth A] , R [auth B] , 
      H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  R [auth B],  S [auth C]
      		SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.92 Å
      • R-Value Free: 0.201 
      • R-Value Work: 0.172 
      • R-Value Observed: 0.173 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 37.089α = 90
      b = 114.927β = 90
      c = 114.322γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      SOLVEphasing
      RESOLVEphasing
      REFMACrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data collection
      HKL-2000data reduction

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2010-04-21
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance
      • Version 1.2: 2011-07-20
        Changes: Database references
      • Version 1.3: 2017-11-08
        Changes: Refinement description