3TWH

Selenium Derivatized RNA/DNA Hybrid in complex with RNase H Catalytic Domain D132N Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides.

Abdur, R.Gerlits, O.O.Gan, J.Jiang, J.Salon, J.Kovalevsky, A.Y.Chumanevich, A.A.Weber, I.T.Huang, Z.

(2014) Acta Crystallogr.,Sect.D 70: 354-361

  • DOI: 10.1107/S1399004713027922

  • PubMed Abstract: 
  • The crystal structures of protein-nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein-nucleic acid complex structure determined using selenium-derivatized nucleic acids is ...

    The crystal structures of protein-nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein-nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H-RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.


    Organizational Affiliation

    Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease H
A
138Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)Mutation(s): 1 
Gene Names: rnhA
EC: 3.1.26.4
Find proteins for Q9KEI9 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9KEI9
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')B6N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*(SDG)P*TP*CP*(SDG))-3')C6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SDG
Query on SDG
C
DNA LINKINGC10 H14 N5 O6 P SeDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 80.660α = 90.00
b = 37.819β = 96.60
c = 61.937γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
SHELXSphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2014-02-12
    Type: Database references
  • Version 1.2: 2014-09-24
    Type: Database references