6EHJ

Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and peptide bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 


Literature

High-resolution snapshots of human N-myristoyltransferase in action illuminate a mechanism promoting N-terminal Lys and Gly myristoylation.

Dian, C., Perez-Dorado, I., Riviere, F., Asensio, T., Legrand, P., Ritzefeld, M., Shen, M., Cota, E., Meinnel, T., Tate, E.W., Giglione, C.

(2020) Nat Commun 11: 1132-1132

  • DOI: 10.1038/s41467-020-14847-3
  • Primary Citation of Related Structures:  
    6EHJ, 6QRM, 6SJZ, 6SK2, 6SK3, 6SK8, 6SKJ

  • PubMed Abstract: 

    • The promising drug target N-myristoyltransferase (NMT) catalyses an essential protein modification thought to occur exclusively at N-terminal glycines (Gly). Here, we present high-resolution human NMT1 structures co-crystallised with reactive cognate lipid and peptide substrates, revealing high-resolution snapshots of the entire catalytic mechanism from the initial to final reaction states ...

    The promising drug target N-myristoyltransferase (NMT) catalyses an essential protein modification thought to occur exclusively at N-terminal glycines (Gly). Here, we present high-resolution human NMT1 structures co-crystallised with reactive cognate lipid and peptide substrates, revealing high-resolution snapshots of the entire catalytic mechanism from the initial to final reaction states. Structural comparisons, together with biochemical analysis, provide unforeseen details about how NMT1 reaches a catalytically competent conformation in which the reactive groups are brought into close proximity to enable catalysis. We demonstrate that this mechanism further supports efficient and unprecedented myristoylation of an N-terminal lysine side chain, providing evidence that NMT acts both as N-terminal-lysine and glycine myristoyltransferase.

    Organizational Affiliation: 

    Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France. carmela.giglione@i2bc.paris-saclay.fr.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase 1A, B391Homo sapiensMutation(s): 0 
Gene Names: NMT1, NMT
EC: 2.3.1.97
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens)
Explore P30419 
Go to UniProtKB:  P30419
PHAROS:  P30419
GTEx:  ENSG00000136448 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30419
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYA (Subject of Investigation/LOI)
Query on MYA
Download Ideal Coordinates CCD File 
E [auth A]TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-GLTUGWJXDB		 Ligand Interaction
COA
Query on COA
Download Ideal Coordinates CCD File 
O [auth A],
R [auth B]		COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N		 Ligand Interaction
MYR
Query on MYR
Download Ideal Coordinates CCD File 
N [auth A],
S [auth B]		MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N		 Ligand Interaction
LYS
Query on LYS
Download Ideal Coordinates CCD File 
AA [auth B],
I [auth A],
K [auth A],
M [auth A],
W [auth B],
AA [auth B],
I [auth A],
K [auth A],
M [auth A],
W [auth B],
Y [auth B]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O		 Ligand Interaction
ASN
Query on ASN
Download Ideal Coordinates CCD File 
H [auth A],
V [auth B]		ASPARAGINE
C4 H8 N2 O3
DCXYFEDJOCDNAF-REOHCLBHSA-N		 Ligand Interaction
PRO
Query on PRO
Download Ideal Coordinates CCD File 
L [auth A],
Z [auth B]		PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N		 Ligand Interaction
SER
Query on SER
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G [auth A],
J [auth A],
U [auth B],
X [auth B]		SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
P [auth B],
Q [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
GLY
Query on GLY
Download Ideal Coordinates CCD File 
F [auth A],
T [auth B]		GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.25α = 90
b = 177.54β = 90
c = 58.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
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: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection
  • Version 2.0: 2020-04-22
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary