5TWJ

Crystal Structure of RlmH in Complex with S-Adenosylmethionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1038/s41598-017-01186-5
  • Primary Citation of Related Structures:  
    5TWJ, 5TWK

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA large subunit methyltransferase HA [auth C],
B [auth D],
C [auth A],
D [auth B]
162Escherichia coliMutation(s): 0 
Gene Names: rlmH
EC: 2.1.1.177
UniProt
Find proteins for P0A8I8 (Escherichia coli (strain K12))
Explore P0A8I8 
Go to UniProtKB:  P0A8I8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8I8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.53α = 90
b = 37.36β = 104.99
c = 122.07γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description