5XJ2

Structure of spRlmCD with U747 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

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

  • 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-resolut ...

    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.


    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized RNA methyltransferase SP_1029
A, B, C, D
454Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)EC: 2.1.1.-
Find proteins for Q97R12 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  Q97R12
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*CP*AP*CP*GP*UP*GP*CP*U)-3')G18Streptococcus pneumoniae TIGR4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B, C, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.384α = 90.00
b = 94.916β = 95.93
c = 164.164γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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