4LWP

Crystal structure of PRMT6-SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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Literature

Crystal Structure of Arginine Methyltransferase 6 from Trypanosoma brucei

Wang, C.Zhu, Y.Chen, J.Li, X.Peng, J.Chen, J.Zou, Y.Zhang, Z.Jin, H.Yang, P.Wu, J.Niu, L.Gong, Q.Teng, M.Shi, Y.

(2014) PLoS One 9: e87267-e87267

  • DOI: https://doi.org/10.1371/journal.pone.0087267
  • Primary Citation of Related Structures:  
    4LWO, 4LWP

  • PubMed Abstract: 

    Arginine methylation plays vital roles in the cellular functions of the protozoan Trypanosoma brucei. The T. brucei arginine methyltransferase 6 (TbPRMT6) is a type I arginine methyltransferase homologous to human PRMT6. In this study, we report the crystal structures of apo-TbPRMT6 and its complex with the reaction product S-adenosyl-homocysteine (SAH). The structure of apo-TbPRMT6 displays several features that are different from those of type I PRMTs that were structurally characterized previously, including four stretches of insertion, the absence of strand β15, and a distinct dimerization arm. The comparison of the apo-TbPRMT6 and SAH-TbPRMT6 structures revealed the fine rearrangements in the active site upon SAH binding. The isothermal titration calorimetry results demonstrated that SAH binding greatly increases the affinity of TbPRMT6 to a substrate peptide derived from bovine histone H4. The western blotting and mass spectrometry results revealed that TbPRMT6 methylates bovine histone H4 tail at arginine 3 but cannot methylate several T. brucei histone tails. In summary, our results highlight the structural differences between TbPRMT6 and other type I PRMTs and reveal that the active site rearrangement upon SAH binding is important for the substrate binding of TbPRMT6.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arginine N-methyltransferase, putativeA [auth B],
B [auth A]
368Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb927.5.3960
UniProt
Find proteins for Q57U70 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57U70 
Go to UniProtKB:  Q57U70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57U70
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
I [auth B],
J [auth A]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
N [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
C [auth B]
D [auth B]
E [auth B]
F [auth B]
G [auth B]
C [auth B],
D [auth B],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
K [auth A],
L [auth A],
M [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH Binding MOAD:  4LWP Kd: 4.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.428α = 90
b = 108.465β = 90
c = 137.865γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations