4C2X | pdb_00004c2x

Human N-myristoyltransferase isoform 2 (NMT2)

• PDB DOI: https://doi.org/10.2210/pdb4C2X/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-08-20 Released: 2014-10-01 
• Deposition Author(s): Thinon, E., Serwa, R.A., Brannigan, J.A., Brassat, U., Wright, M.H., Heal, W.P., Wilkinson, A.J., Mann, D.J., Tate, E.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.288 (Depositor) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Global Profiling of Co- and Post-Translationally N-Myristoylated Proteomes in Human Cells.

Thinon, E., Serwa, R.A., Broncel, M., Brannigan, J.A., Brassat, U., Wright, M.H., Heal, W.P., Wilkinson, A.J., Mann, D.J., Tate, E.W.

(2014) Nat Commun 5: 4919

• PubMed: 25255805 
• DOI: https://doi.org/10.1038/ncomms5919
• Primary Citation Related Structures: 
  4C2X, 4C2Y, 4C2Z


• PubMed Abstract: 
  

  Protein N-myristoylation is a ubiquitous co- and post-translational modification that has been implicated in the development and progression of a range of human diseases. Here, we report the global N-myristoylated proteome in human cells determined using quantitative chemical proteomics combined with potent and specific human N-myristoyltransferase (NMT) inhibition. Global quantification of N-myristoylation during normal growth or apoptosis allowed the identification of >100 N-myristoylated proteins, >95% of which are identified for the first time at endogenous levels. Furthermore, quantitative dose response for inhibition of N-myristoylation is determined for >70 substrates simultaneously across the proteome. Small-molecule inhibition through a conserved substrate-binding pocket is also demonstrated by solving the crystal structures of inhibitor-bound NMT1 and NMT2. The presented data substantially expand the known repertoire of co- and post-translational N-myristoylation in addition to validating tools for the pharmacological inhibition of NMT in living cells.

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Organizational Affiliation: 
• 1] Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK [2] Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK.
Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK.
York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK.
1] Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK [2] Department of Chemistry, Institute of Chemical Biology, Imperial College London, Exhibition Road, London SW7 2AZ, UK.
1] Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK [2] Department of Chemistry, Institute of Chemical Biology, Imperial College London, Exhibition Road, London SW7 2AZ, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.61 kDa 
• Atom Count: 3,345 
• Modeled Residue Count: 388 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 2	A	410	Homo sapiens	Mutation(s): 1  EC: 2.3.1.97 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60551 (Homo sapiens) Explore O60551  Go to UniProtKB:  O60551
PHAROS:  O60551 GTEx:  ENSG00000152465

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHW	C [auth A]	2-oxopentadecyl-CoA C36 H64 N7 O17 P3 S JKWHUJMJVNMKEF-UOCZADIYSA-J
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.288 (Depositor) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.7	α = 90
b = 72.32	β = 90
c = 114.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Thinon, E., Serwa, R.A., Brannigan, J.A., Brassat, U., Wright, M.H., Heal, W.P., Wilkinson, A.J., Mann, D.J., Tate, E.W.

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2014-10-08
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description