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: https://doi.org/10.1038/s42003-018-0196-2
  • Primary Citation of Related Structures:  
    5UBB, 6DUB

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha N-terminal protein methyltransferase 1BA, B222Homo sapiensMutation(s): 0 
Gene Names: METTL11B, C1orf184, NRMT2, NTMT2
EC: 2.1.1.299
UniProt
Find proteins for Q5VVY1 (Homo sapiens)
Explore Q5VVY1 
Go to UniProtKB:  Q5VVY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VVY1
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RCC1C [auth E],
D [auth F]		6Homo sapiensMutation(s): 0 
Gene Names: RCC1, CHC1
UniProt & NIH Common Fund Data Resources
Find proteins for P18754 (Homo sapiens)
Explore P18754 
Go to UniProtKB:  P18754
PHAROS:  P18754
Entity Groups  
UniProt GroupP18754
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
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],
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: https://doi.org/10.18430/m36dub
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 


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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