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 

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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
  • Primary Citation of Related Structures:  
    6DUB, 5UBB

  • 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, whereas NTMT2 is a mono-methyltransferase ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha N-terminal protein methyltransferase 1BA, B222Homo sapiensMutation(s): 0 
Gene Names: METTL11BC1orf184NRMT2
EC: 2.1.1.299
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VVY1 (Homo sapiens)
Explore Q5VVY1 
Go to UniProtKB:  Q5VVY1
PHAROS:  Q5VVY1
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RCC1C [auth E], D [auth F]6Homo sapiensMutation(s): 0 
Gene Names: RCC1CHC1
UniProt & NIH Common Fund Data Resources
Find proteins for P18754 (Homo sapiens)
Explore P18754 
Go to UniProtKB:  P18754
PHAROS:  P18754
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
E [auth A], PA [auth B]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], QA [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth A] , AB [auth B] , BA [auth A] , BB [auth B] , CA [auth A] , CB [auth B] , DA [auth A] , DB [auth B] , 
AA [auth A],  AB [auth B],  BA [auth A],  BB [auth B],  CA [auth A],  CB [auth B],  DA [auth A],  DB [auth B],  EA [auth A],  EB [auth B],  FA [auth A],  FB [auth B],  GA [auth A],  GB [auth B],  H [auth A],  HA [auth A],  HB [auth B],  I [auth A],  IA [auth A],  IB [auth B],  J [auth A],  JA [auth A],  JB [auth B],  K [auth A],  KA [auth A],  KB [auth B],  L [auth A],  LA [auth A],  LB [auth B],  M [auth A],  MA [auth A],  MB [auth B],  N [auth A],  NA [auth A],  NB [auth E],  O [auth A],  OA [auth A],  OB [auth E],  P [auth A],  PB [auth E],  Q [auth A],  QB [auth F],  R [auth A],  RA [auth B],  S [auth A],  SA [auth B],  T [auth A],  TA [auth B],  U [auth A],  UA [auth B],  V [auth A],  VA [auth B],  W [auth A],  WA [auth B],  X [auth A],  XA [auth B],  Y [auth A],  YA [auth B],  Z [auth A],  ZA [auth B]
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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