6DUB

Crystal structure of a methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2.

Dong, C.Dong, G.Li, L.Zhu, L.Tempel, W.Liu, Y.Huang, R.Min, J.

(2018) Commun Biol 1: 183-183

  • DOI: 10.1038/s42003-018-0196-2
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • α-N-terminal methylation of proteins is an important post-translational modification that is catalyzed by two different N-terminal methyltransferases, namely NTMT1 and NTMT2. Previous studies have suggested that NTMT1 is a tri-methyltransferase, wher ...

    α-N-terminal methylation of proteins is an important post-translational modification that is catalyzed by two different N-terminal methyltransferases, namely NTMT1 and NTMT2. Previous studies have suggested that NTMT1 is a tri-methyltransferase, whereas NTMT2 is a mono-methyltransferase. Here, we report the first crystal structures, to our knowledge, of NTMT2 in binary complex with S-adenosyl-L-methionine as well as in ternary complex with S-adenosyl-L-homocysteine and a substrate peptide. Our structural observations combined with biochemical studies reveal that NTMT2 is also able to di-/tri-methylate the GPKRIA peptide and di-methylate the PPKRIA peptide, otherwise it is predominantly a mono-methyltransferase. The residue N89 of NTMT2 serves as a gatekeeper residue that regulates the binding of unmethylated versus monomethylated substrate peptide. Structural comparison of NTMT1 and NTMT2 prompts us to design a N89G mutant of NTMT2 that can profoundly alter its catalytic activities and product specificities.


    Organizational Affiliation

    Department of Physiology, University of Toronto, Toronto, M5S 1A8, ON, Canada. jr.min@utoronto.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha N-terminal protein methyltransferase 1B
A, B
222Homo sapiensMutation(s): 0 
Gene Names: METTL11BC1orf184NRMT2
EC: 2.1.1.299
Find proteins for Q5VVY1 (Homo sapiens)
Go to UniProtKB:  Q5VVY1
NIH Common Fund Data Resources
PHAROS  Q5VVY1
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RCC1
E, F
6Homo sapiensMutation(s): 0 
Gene Names: RCC1CHC1
Find proteins for P18754 (Homo sapiens)
Go to UniProtKB:  P18754
NIH Common Fund Data Resources
PHAROS  P18754
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
A, B, E, F
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 43
  • Diffraction Data DOI: 10.18430/m36dub Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.359α = 90
b = 44.359β = 90
c = 262.058γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references