5TWJ

Crystal Structure of RlmH in Complex with S-Adenosylmethionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.299 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine.

Koh, C.S.Madireddy, R.Beane, T.J.Zamore, P.D.Korostelev, A.A.

(2017) Sci Rep 7: 969-969

  • DOI: 10.1038/s41598-017-01186-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Eubacterial ribosomal large-subunit methyltransferase H (RlmH) methylates 23S ribosomal RNA pseudouridine 1915 (Ψ1915), which lies near the ribosomal decoding center. The smallest member of the SPOUT superfamily of methyltransferases, RlmH lacks the ...

    Eubacterial ribosomal large-subunit methyltransferase H (RlmH) methylates 23S ribosomal RNA pseudouridine 1915 (Ψ1915), which lies near the ribosomal decoding center. The smallest member of the SPOUT superfamily of methyltransferases, RlmH lacks the RNA recognition domain found in larger methyltransferases. The catalytic mechanism of RlmH enzyme is unknown. Here, we describe the structures of RlmH bound to S-adenosyl-methionine (SAM) and the methyltransferase inhibitor sinefungin. Our structural and biochemical studies reveal catalytically essential residues in the dimer-mediated asymmetrical active site. One monomer provides the SAM-binding site, whereas the conserved C-terminal tail of the second monomer provides residues essential for catalysis. Our findings elucidate the mechanism by which a small protein dimer assembles a functionally asymmetric architecture.


    Organizational Affiliation

    RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation St, Worcester, MA 01605, USA.,RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation St, Worcester, MA 01605, USA. phillip.zamore@umassmed.edu.,RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation St, Worcester, MA 01605, USA. andrei.korostelev@umassmed.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA large subunit methyltransferase H
C, D, A, B
162Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rlmH (ybeA)
EC: 2.1.1.177
Find proteins for P0A8I8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8I8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B, C, D
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAMKd: 5580 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.299 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.530α = 90.00
b = 37.360β = 104.99
c = 122.070γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107465
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM106105
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM62862

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2020-01-01
    Type: Author supporting evidence