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 

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:  

  • 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 subu ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
restriction endonuclease PacI
A
142Pseudomonas alcaligenesMutation(s): 0 
Gene Names: pacIR
Find proteins for D5MNX7 (Pseudomonas alcaligenes)
Go to UniProtKB:  D5MNX7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3')B10N/A
Entity ID: 3
MoleculeChainsLengthOrganism
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
ZN
Query on ZN
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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA
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Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4
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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PT
Query on PT
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A
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO
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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 37.089α = 90.00
b = 114.927β = 90.00
c = 114.322γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
RESOLVEphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
SOLVEphasing
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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