Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42989.96 
• Atom Count: 2866 
• Residue Count: 309 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

4PY5

Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA

• DOI: 10.2210/pdb4PY5/pdb
• NDB: NA2974

• Classification: Hydrolase/DNA/RNA
• Organism(s): Thermovibrio ammonificans (strain DSM 15698 / JCM 12110 / HB-1)
• Expression System: Escherichia coli BL21
• Mutation(s): 1 


• Deposited: 2014-03-26 Released: 2014-07-30 
• Deposition Author(s): Figiel, M., Nowotny, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.233 
• R-Value Work: 0.183 

Literature

Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition.

Figiel, M., Nowotny, M.

(2014) Nucleic Acids Res. 42: 9285-9294

• PubMed: 25016521 
• DOI: 10.1093/nar/gku615


• PubMed Abstract: 
  

RNases H participate in the replication and maintenance of genomic DNA. RNase H1 cleaves the RNA strand of RNA/DNA hybrids, and RNase H2 in addition hydrolyzes the RNA residue of RNA-DNA junctions. RNase H3 is structurally closely related to RNases H2, but its biochemical properties are similar to type 1 enzymes. Its unique N-terminal substrate-binding domain (N-domain) is related to TATA-binding protein. Here, we report the first crystal structure of RNase H3 in complex with its RNA/DNA substrate. Just like RNases H1, type 3 enzyme recognizes the 2'-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation. Moreover, the N-domain recognizes RNA and DNA in a manner that is highly similar to the hybrid-binding domain of RNases H1. Our structure demonstrates a remarkable example of parallel evolution of the elements used in the specific recognition of RNA and DNA.

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Organizational Affiliation: 

Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ribonuclease	A	271	Thermovibrio ammonificans (strain DSM 15698 / JCM 12110 / HB-1)	Mutation(s): 1  EC: 3.1.26.4
Find proteins for E8T217 (Thermovibrio ammonificans (strain DSM 15698 / JCM 12110 / HB-1)) Go to UniProtKB:  E8T217

Entity ID: 2
Molecule	Chains	Length	Organism
5'-R(*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'	B	19	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*C)-3'	C	19	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.233 
• R-Value Work: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 58.449	α = 90.00
b = 67.661	β = 90.00
c = 107.514	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	phasing
PHENIX	refinement
XDS	data scaling
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-03-26 
• Released Date: 2014-07-30 
• Deposition Author(s): Figiel, M., Nowotny, M.

Revision History 

• Version 1.0: 2014-07-30
  Type: Initial release
• Version 1.1: 2014-08-27
  Type: Database references
• Version 1.2: 2014-10-29
  Type: Structure summary