8GZE

Crystal Structure of human METTL9-SAH-SLC39A7 peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for protein histidine N1-specific methylation of the "His-x-His" motifs by METTL9.

Zhao, W.Zhou, Y.Li, C.Bi, Y.Wang, K.Ye, M.Li, H.

(2023) Cell Insight 2: 100090-100090

  • DOI: https://doi.org/10.1016/j.cellin.2023.100090
  • Primary Citation of Related Structures:  
    8GZE, 8GZF

  • PubMed Abstract: 

    Histidine methylation serves as an intriguing strategy to introduce altered traits of target proteins, including metal ion chelation, histidine-based catalysis, molecular assembly, and translation regulation. As a newly identified histidine methyltransferase, METTL9 catalyzes N1-methylation of protein substrates containing the "His-x-His" motif (HxH, x denotes small side chain residue). Here our structural and biochemical studies revealed that METTL9 specifically methylates the second histidine of the "HxH" motif, while exploiting the first one as a recognition signature. We observed an intimate engagement between METTL9 and a pentapeptide motif, where the small "x" residue is embedded and confined within the substrate pocket. Upon complex formation, the N3 atom of histidine imidazole ring is stabilized by an aspartate residue such that the N1 atom is presented to S-adenosylmethionine for methylation. Moreover, METTL9 displayed a feature in preferred consecutive and "C-to-N" directional methylation of tandem "HxH" repeats that exist in many METTL9 substrates. Collectively, our work illustrates the molecular design of METTL9 in N1-specific methylation of the broadly existing "HxH" motifs, highlighting its importance in histidine methylation biology.


  • Organizational Affiliation

    MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-L-histidine N-pros-methyltransferase
A, B
266Homo sapiensMutation(s): 0 
Gene Names: METTL9DREVCGI-81
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1A3 (Homo sapiens)
Explore Q9H1A3 
Go to UniProtKB:  Q9H1A3
PHAROS:  Q9H1A3
GTEx:  ENSG00000197006 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H1A3
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc transporter SLC39A7C [auth E],
D
5Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92504 (Homo sapiens)
Explore Q92504 
Go to UniProtKB:  Q92504
PHAROS:  Q92504
GTEx:  ENSG00000112473 
Entity Groups  
UniProt GroupQ92504
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.260 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.182α = 90
b = 79.182β = 90
c = 422.365γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China92153302

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-12-13
    Changes: Database references