5H5F

The crystal structure of the yeast arginine methyltransferase SFM1 complexed with SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A flexible cofactor-binding loop in the novel arginine methyltransferase Sfm1.

Wang, C.Zeng, J.Xie, W.

(2017) FEBS Lett 591: 433-441

  • DOI: https://doi.org/10.1002/1873-3468.12533
  • Primary Citation of Related Structures:  
    5H5D, 5H5E, 5H5F

  • PubMed Abstract: 

    Arginine methylation is a common post-translational modification and is critical for many cellular processes. Sfm1 is a novel arginine methyltransferase that contains a SpoU-TrmD (SPOUT) domain, a typical fold known for RNA methylation, but acts on a ribosomal protein. The underlying mechanism is poorly understood. Here, we report cocrystal structures of Sfm1 in complex with various ligands. We found that a critical loop responsible for S-adenosyl-l-methionine (SAM) binding adopts a different conformation from previous reports, and SAM appears to exhibit double conformations. Deletion of this loop greatly reduces the affinity of Sfm1 to SAM. Additionally, by comparison to closely related tRNA-methyltransferase Trm10, our structural analyses offer a good explanation why the two enzymes utilize distinct substrates, providing insights into the molecular mechanism.


  • Organizational Affiliation

    Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase SFM1234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SFM1YOR021COR26.11
EC: 2.1.1
UniProt
Find proteins for Q12314 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12314 
Go to UniProtKB:  Q12314
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12314
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.712α = 90
b = 62.417β = 112.31
c = 44.695γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundamental Research Funds for the Central UniversitiesChina16lgjc76
the Science and Technology Program of GuangzhouChina201504010025

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description