6EHJ | pdb_00006ehj

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

• PDB DOI: https://doi.org/10.2210/pdb6EHJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-13 Released: 2019-03-27 
• Deposition Author(s): Perez-Dorado, I., Ritzefeld, M., Tate, E.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

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

• PubMed: 32111831 
• DOI: https://doi.org/10.1038/s41467-020-14847-3
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France.
Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK.
Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, SW7 2AZ, UK.
Evotec Ltd, 114 Innovation Dr, Milton Park, Milton, Abingdon, OX14 4RZ, UK.
Synchrotron SOLEIL, Gif-sur-Yvette, Cedex, 91192, France.
Evotec SE, Essener Bogen 7, Hamburg, 22419, Germany.
Oakland Innovation, Mill Rd, Harston, Cambridge, CB22 7GG, UK.
Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France. [e-mail].
Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK. [e-mail].
The Francis Crick Institute, 1 Midland Rd, London, NW 1AT, UK. [e-mail].
Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.19 kDa 
• Atom Count: 6,609 
• Modeled Residue Count: 747 
• Deposited Residue Count: 782 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase 1	A, B	391	Homo sapiens	Mutation(s): 0  Gene Names: NMT1, NMT EC: 2.3.1.97 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens) Explore P30419  Go to UniProtKB:  P30419
PHAROS:  P30419 GTEx:  ENSG00000136448

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA (Subject of Investigation/LOI)	E [auth A]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
COA	O [auth A], R [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
MYR	N [auth A], S [auth B]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
LYS	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
ASN	H [auth A], V [auth B]	ASPARAGINE C4 H8 N2 O3 DCXYFEDJOCDNAF-REOHCLBHSA-N
PRO	L [auth A], Z [auth B]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
SER	G [auth A], J [auth A], U [auth B], X [auth B]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
GOL	C [auth A], D [auth A], P [auth B], Q [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY	F [auth A], T [auth B]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.25	α = 90
b = 177.54	β = 90
c = 58.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Perez-Dorado, I., Ritzefeld, M., Tate, E.W.

Revision History  

• 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
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description