3S1S

Characterization and crystal structure of the type IIG restriction endonuclease BpuSI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI.

Shen, B.W.Xu, D.Chan, S.H.Zheng, Y.Zhu, Z.Xu, S.Y.Stoddard, B.L.

(2011) Nucleic Acids Res 39: 8223-8236

  • DOI: 10.1093/nar/gkr543
  • Primary Citation of Related Structures:  
    3S1S

  • PubMed Abstract: 
  • A type IIG restriction endonuclease, RM.BpuSI from Bacillus pumilus, has been characterized and its X-ray crystal structure determined at 2.35Å resolution. The enzyme is comprised of an array of 5-folded domains that couple the enzyme's N-terminal endonuclease domain to its C-terminal target recognition and methylation activities ...

    A type IIG restriction endonuclease, RM.BpuSI from Bacillus pumilus, has been characterized and its X-ray crystal structure determined at 2.35Å resolution. The enzyme is comprised of an array of 5-folded domains that couple the enzyme's N-terminal endonuclease domain to its C-terminal target recognition and methylation activities. The REase domain contains a PD-x(15)-ExK motif, is closely superimposable against the FokI endonuclease domain, and coordinates a single metal ion. A helical bundle domain connects the endonuclease and methyltransferase (MTase) domains. The MTase domain is similar to the N6-adenine MTase M.TaqI, while the target recognition domain (TRD or specificity domain) resembles a truncated S subunit of Type I R-M system. A final structural domain, that may form additional DNA contacts, interrupts the TRD. DNA binding and cleavage must involve large movements of the endonuclease and TRD domains, that are probably tightly coordinated and coupled to target site methylation status.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
restriction endonuclease BpuSIA878Bacillus pumilusMutation(s): 0 
Gene Names: Bacillus pumilus
EC: 2.1.1.72
Find proteins for G1K3S1 (Bacillus pumilus)
Explore G1K3S1 
Go to UniProtKB:  G1K3S1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth A] , AB [auth A] , BA [auth A] , BB [auth A] , CA [auth A] , CB [auth A] , DA [auth A] , DB [auth A] , 
AA [auth A],  AB [auth A],  BA [auth A],  BB [auth A],  CA [auth A],  CB [auth A],  DA [auth A],  DB [auth A],  EA [auth A],  EB [auth A],  FA [auth A],  FB [auth A],  GA [auth A],  GB [auth A],  HA [auth A],  HB [auth A],  IA [auth A],  IB [auth A],  JA [auth A],  KA [auth A],  LA [auth A],  MA [auth A],  NA [auth A],  OA [auth A],  PA [auth A],  QA [auth A],  RA [auth A],  SA [auth A],  TA [auth A],  UA [auth A],  VA [auth A],  WA [auth A],  X [auth A],  XA [auth A],  Y [auth A],  YA [auth A],  Z [auth A],  ZA [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , 
C [auth A],  D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
W [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.472α = 90
b = 215.732β = 90
c = 73.71γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2011-10-19
    Changes: Database references