Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 64.13 kDa 
• Atom Count: 4525 
• Modelled Residue Count: 549 
• Deposited Residue Count: 562 
• Unique protein chains: 1

3BK2

Crystal Structure Analysis of the RNase J/UMP complex

• PDB DOI: 10.2210/pdb3BK2/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB27
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-05 Released: 2008-01-22 
• Deposition Author(s): de la Sierra-Gallay, I.L., Zig, L., Putzer, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.217 
• R-Value Observed: 0.227 

Literature

Structural insights into the dual activity of RNase J

de la Sierra-Gallay, I.L., Zig, L., Jamalli, A., Putzer, H.

(2008) Nat Struct Mol Biol 15: 206-212

• PubMed: 18204464 
• DOI: 10.1038/nsmb.1376
• Primary Citation of Related Structures:  
  3BK1, 3BK2


• PubMed Abstract: 
  

The maturation and stability of RNA transcripts is controlled by a combination of endo- and exoRNases. RNase J is unique, as it combines an RNase E-like endoribonucleolytic and a 5'-to-3' exoribonucleolytic activity in a single polypeptide. The structural basis for this dual activity is unknown. Here we report the crystal structures of Thermus thermophilus RNase J and its complex with uridine 5'-monophosphate. A binding pocket coordinating the phosphate and base moieties of the nucleotide in the vicinity of the catalytic center provide a rationale for the 5'-monophosphate-dependent 5'-to-3' exoribonucleolytic activity. We show that this dependence is strict; an initial 5'-PPP transcript cannot be degraded exonucleolytically from the 5'-end. Our results suggest that RNase J might switch promptly from endo- to exonucleolytic mode on the same RNA, a property that has important implications for RNA metabolism in numerous prokaryotic organisms and plant organelles containing RNase J orthologs.

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Organizational Affiliation: 

FRC550, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal dependent hydrolase	A	562	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: TTC0775, rnj, TT_C0775 EC: 3 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for Q72JJ7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72JJ7  Go to UniProtKB:  Q72JJ7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	E [auth A]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.217 
• R-Value Observed: 0.227 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.08	α = 90
b = 118	β = 90
c = 228.32	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-12-05 
• Released Date: 2008-01-22 
Deposition Author(s): de la Sierra-Gallay, I.L., Zig, L., Putzer, H.

Revision History  

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance