1J3L

Structure of the RNA-processing inhibitor RraA from Thermus thermophilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the RNA-processing inhibitor RraA from Thermus thermophilis.

Rehse, P.H.Kuroishi, C.Tahirov, T.H.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1997-2002

  • DOI: 10.1107/S0907444904021146
  • Primary Citation of Related Structures:  
    1J3L

  • PubMed Abstract: 
  • The menG gene product, thought to catalyze the final methylation in vitamin K(2) synthesis, has recently been shown to inhibit RNase E in Eschericha coli. The structure of the protein, since renamed RraA, has been solved to 2.3 A using the multiple-wavelength anomalous diffraction method and selenomethionine-substituted protein from Thermus thermophilus ...

    The menG gene product, thought to catalyze the final methylation in vitamin K(2) synthesis, has recently been shown to inhibit RNase E in Eschericha coli. The structure of the protein, since renamed RraA, has been solved to 2.3 A using the multiple-wavelength anomalous diffraction method and selenomethionine-substituted protein from Thermus thermophilus. The six molecules in the asymmetric unit are arranged as two similar trimers which have a degree of interaction, suggesting biological significance. The fold does not support the postulated methylation function. Genomic analysis, specifically a lack of an RNase E homologue in cases where homologues to RraA exist, indicates that the function is still obscure.


    Organizational Affiliation

    Highthroughput Factory, RIKEN Harima Institute, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Demethylmenaquinone Methyltransferase
A, B, C, D, E, F
A, B, C, D, E, F
164Thermus thermophilusMutation(s): 0 
EC: 2.1.1 (PDB Primary Data), 4.1.3.17 (UniProt), 4.1.1.112 (UniProt)
UniProt
Find proteins for Q5SIP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIP7 
Go to UniProtKB:  Q5SIP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIP7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.872α = 90
b = 109.068β = 90
c = 270.319γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance