5E1D

NTMT1 in complex with YPKRIA peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for substrate recognition by the human N-terminal methyltransferase 1.

Dong, C.Mao, Y.Tempel, W.Qin, S.Li, L.Loppnau, P.Huang, R.Min, J.

(2015) Genes Dev. 29: 2343-2348

  • DOI: 10.1101/gad.270611.115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • α-N-terminal methylation represents a highly conserved and prevalent post-translational modification, yet its biological function has remained largely speculative. The recent discovery of α-N-terminal methyltransferase 1 (NTMT1) and its physiological ...

    α-N-terminal methylation represents a highly conserved and prevalent post-translational modification, yet its biological function has remained largely speculative. The recent discovery of α-N-terminal methyltransferase 1 (NTMT1) and its physiological substrates propels the elucidation of a general role of α-N-terminal methylation in mediating DNA-binding ability of the modified proteins. The phenotypes, observed from both NTMT1 knockdown in breast cancer cell lines and knockout mouse models, suggest the potential involvement of α-N-terminal methylation in DNA damage response and cancer development. In this study, we report the first crystal structures of human NTMT1 in complex with cofactor S-adenosyl-L-homocysteine (SAH) and six substrate peptides, respectively, and reveal that NTMT1 contains two characteristic structural elements (a β hairpin and an N-terminal extension) that contribute to its substrate specificity. Our complex structures, coupled with mutagenesis, binding, and enzymatic studies, also present the key elements involved in locking the consensus substrate motif XPK (X indicates any residue type other than D/E) into the catalytic pocket for α-N-terminal methylation and explain why NTMT1 prefers an XPK sequence motif. We propose a catalytic mechanism for α-N-terminal methylation. Overall, this study gives us the first glimpse of the molecular mechanism of α-N-terminal methylation and potentially contributes to the advent of therapeutic agents for human diseases associated with deregulated α-N-terminal methylation.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-terminal Xaa-Pro-Lys N-methyltransferase 1
A, B
241Homo sapiensMutation(s): 0 
Gene Names: NTMT1 (C9orf32, METTL11A, NRMT, NRMT1)
EC: 2.1.1.244
Find proteins for Q9BV86 (Homo sapiens)
Go to Gene View: NTMT1
Go to UniProtKB:  Q9BV86
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RCC1
D, E
6Homo sapiensMutation(s): 0 
Gene Names: RCC1 (CHC1)
Find proteins for P18754 (Homo sapiens)
Go to Gene View: RCC1
Go to UniProtKB:  P18754
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.154 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 107.082α = 90.00
b = 107.082β = 90.00
c = 205.946γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-18
    Type: Database references
  • Version 1.2: 2015-12-02
    Type: Database references