Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 43.07 kDa 
• Atom Count: 2999 
• Modelled Residue Count: 360 
• Deposited Residue Count: 375 
• Unique protein chains: 1

4DCM

Crystal Structure of methyltransferase RlmG modifying G1835 of 23S rRNA in Escherichia coli

• DOI: 10.2210/pdb4DCM/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-17 Released: 2012-08-01 
• Deposition Author(s): Zhang, H., Gao, Z.Q., Dong, Y.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Structural insights into the function of 23S rRNA methyltransferase RlmG (m2G1835) from Escherichia coli.

Zhang, H., Gao, Z.Q., Wei, Y., Wang, W.J., Liu, G.F., Shtykova, E.V., Xu, J.H., Dong, Y.H.

(2012) RNA 18: 1500-1509

• PubMed: 22753782 
• DOI: 10.1261/rna.033407.112
• Primary Citation of Related Structures:  
  4DCM


• PubMed Abstract: 
  

RlmG is a specific AdoMet-dependent methyltransferase (MTase) responsible for N²-methylation of G1835 in 23S rRNA of Escherichia coli. Methylation of m²G1835 specifically enhances association of ribosomal subunits and provides a significant advantage for bacteria in osmotic and oxidative stress. Here, the crystal structure of RlmG in complex with AdoMet and its structure in solution were determined. The structure of RlmG is similar to that of the MTase RsmC, consisting of two homologous domains: the N-terminal domain (NTD) in the recognition and binding of the substrate, and the C-terminal domain (CTD) in AdoMet-binding and the catalytic process. However, there are distinct positively charged protuberances and a distribution of conserved residues contributing to the charged surface patch, especially in the NTD of RlmG for direct binding of protein-free rRNA. The RNA-binding properties of the NTD and CTD characterized by both gel electrophoresis mobility shift assays and isothermal titration calorimetry showed that NTD could bind RNA independently and RNA binding was achieved by the NTD, accomplished by a coordinating role of the CTD. The model of the RlmG-AdoMet-RNA complex suggested that RlmG may unfold its substrate RNA in the positively charged cleft between the NTD and CTD, and then G1835 disengages from its Watson-Crick pairing with C1905 and flips out to insert into the active site. Our structure and biochemical studies provide novel insights into the catalytic mechanism of G1835 methylation.

---

Organizational Affiliation: 

Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA large subunit methyltransferase G	A	375	Escherichia coli K-12	Mutation(s): 0  Gene Names: b3084, JW5513, rlmG, ygjO EC: 2.1.1.174
UniProt
Find proteins for P42596 (Escherichia coli (strain K12)) Explore P42596  Go to UniProtKB:  P42596

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
PEG	C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-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: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.185	α = 90
b = 42.134	β = 104.46
c = 72.429	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-17 
• Released Date: 2012-08-01 
Deposition Author(s): Zhang, H., Gao, Z.Q., Dong, Y.H.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description