1J3L | pdb_00001j3l

Structure of the RNA-processing inhibitor RraA from Thermus thermophilis

• PDB DOI: https://doi.org/10.2210/pdb1J3L/pdb

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


• Deposited: 2003-02-04 Released: 2004-02-17 
• Deposition Author(s): Rehse, P.H., Miyano, M., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.274 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

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

• PubMed: 15502308 
• DOI: https://doi.org/10.1107/S0907444904021146
• Primary Citation 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 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 104.84 kDa 
• Atom Count: 7,692 
• Modeled Residue Count: 974 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Demethylmenaquinone Methyltransferase	A, B, C, D, E, F	164	Thermus thermophilus	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	H [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.274 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.872	α = 90
b = 109.068	β = 90
c = 270.319	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-17 
Deposition Author(s): Rehse, P.H., Miyano, M., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• 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
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Structure summary