Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 52.09 kDa 
• Atom Count: 3903 
• Modelled Residue Count: 453 
• Deposited Residue Count: 454 
• Unique protein chains: 1

5XJ1

Crystal structure of spRlmCD

• PDB DOI: 10.2210/pdb5XJ1/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-04-28 Released: 2017-11-01 
• Deposition Author(s): Jiang, Y., Gong, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD

Jiang, Y., Li, F., Wu, J., Shi, Y., Gong, Q.

(2017) PLoS One 12: e0185226-e0185226

• PubMed: 28949991 
• DOI: 10.1371/journal.pone.0185226
• Primary Citation of Related Structures:  
  5XJ1, 5XJ2


• PubMed Abstract: 
  

RlmCD has recently been identified as the S-adenosyl methionine (SAM)-dependent methyltransferase responsible for the formation of m5U at U747 and U1939 of 23S ribosomal RNA in Streptococcus pneumoniae. In this research, we determine the high-resolution crystal structures of apo-form RlmCD and its complex with SAH. Using an in-vitro methyltransferase assay, we reveal the crucial residues for its catalytic functions. Furthermore, structural comparison between RlmCD and its structural homologue RumA, which only catalyzes the m5U1939 in Escherichia coli, implicates that a unique long linker in the central domain of RlmCD is the key factor in determining its substrate selectivity. Its significance in the enzyme activity of RlmCD is further confirmed by in-vitro methyltransferase assay.

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Organizational Affiliation: 

Hefei National Laboratory For Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized RNA methyltransferase SP_1029	A	454	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: SP_1029 EC: 2.1.1
UniProt
Find proteins for Q97R12 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q97R12  Go to UniProtKB:  Q97R12

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	D [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
EPE	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.452	α = 90
b = 101.772	β = 110.11
c = 63.037	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-04-28 
• Released Date: 2017-11-01 
Deposition Author(s): Jiang, Y., Gong, Q.

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release