8HL6

Crystal structure of human valosin-containing protein methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for recognition and methylation of p97 by METTL21D, a valosin-containing protein lysine methyltransferase.

Nguyen, T.Q.Koh, S.Kwon, J.Jang, S.Kang, W.Yang, J.K.

(2023) iScience 26: 107222-107222

  • DOI: https://doi.org/10.1016/j.isci.2023.107222
  • Primary Citation of Related Structures:  
    8HL6, 8HL7

  • PubMed Abstract: 

    p97 is a human AAA+ (ATPase associated with diverse cellular activities, also known as valosin-containing protein [VCP]) ATPase, which is involved in diverse cellular processes such as membrane fusion and proteolysis. Lysine-specific methyltransferase of p97 (METTL21D) was identified as a class I methyltransferase that catalyzes the trimethylation of Lys315 of p97, a so-called VCP lysine methyltransferase (VCPKMT). Interestingly, VCPKMT disassembles a single hexamer ring consisting of p97-D1 domain and methylates Lys315 residue. Herein, the structures of S-adenosyl-L-methionine-bound VCPKMT and S-adenosyl-L-homocysteine-bound VCPKMT in complex with p97 N/D1 (N21-Q458) were reported at a resolution of 1.8 Å and 2.8 Å, respectively. The structures revealed the molecular details for the recognition and methylation of monomeric p97 by VCPKMT. Using biochemical analysis, we also investigated whether the methylation of full-length p97 could be sufficiently enhanced through cooperation between VCPKMT and the C terminus of alveolar soft part sarcoma locus (ASPL). Our study provides the groundwork for future structural and mechanistic studies of p97 and inhibitors.


  • Organizational Affiliation

    Department of Chemistry and Integrative Institute of Basic Science, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein N-lysine methyltransferase METTL21D235Homo sapiensMutation(s): 0 
Gene Names: METTL21D
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H867 (Homo sapiens)
Explore Q9H867 
Go to UniProtKB:  Q9H867
PHAROS:  Q9H867
GTEx:  ENSG00000100483 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H867
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
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

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.17α = 90
b = 58.17β = 90
c = 129.291γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2021R1A6A1A10044154
National Research Foundation (NRF, Korea)Korea, Republic Of2022R1C1C1004221

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection