› 6pav

X-ray diffraction
2.52Å resolution

Structure of Human NMT1 with products CoA and myristoyl-lysine peptide with acetylated N-terminus

Released:
DOI: 10.2210/pdb6pav/pdb
PDB entry 6pav coloured by chain, front view.
PDB entry 6pav coloured by chain, side view.
PDB entry 6pav coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle.
Kosciuk T, Price IR, Zhang X, Zhu C, Johnson KN, Zhang S, Halaby SL, Komaniecki GP, Yang M, DeHart CJ, Thomas PM, Kelleher NL, Fromme JC, Lin H
Nat Commun 11 1067 (2020)
PMID: 32103017

Function and Biology Details

Reactions catalysed: 
Tetradecanoyl-CoA + an N-terminal-glycyl-[protein] = CoA + an N-terminal-N-tetradecanoylglycyl-[protein]
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151737 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Glycylpeptide N-tetradecanoyltransferase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 388 amino acids
Theoretical weight: 45.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P30419 (Residues: 109-496; Coverage: 78%)
Gene names: NMT, NMT1
Sequence domains:
ADP-ribosylation factor 6 Chain: D
Molecule details ›
Chain: D
Length: 8 amino acids
Theoretical weight: 862 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62330 (Residues: 3-9; Coverage: 4%)
Gene name: ARF6
ADP-ribosylation factor 6 Chain: C
Molecule details ›
Chain: C
Length: 8 amino acids
Theoretical weight: 893 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62330 (Residues: 2-9; Coverage: 5%)
Gene name: ARF6

Ligands and Environments


Cofactor: Ligand COA 2 x COA
2 bound ligands:
Ligand GOL 4 x GOL
Ligand MYR 2 x MYR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: C2
Unit cell:
a: 92.361Å b: 58.217Å c: 154.035Å
α: 90° β: 90.66° γ: 90°
R-values:
R R work R free
0.266 0.265 0.28
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

15 review citations

Protein N-myristoylation: functions and mechanisms in control of innate immunity.
Wang et al. (2021)
14 more

1 mention without citation

Identification of potent and selective N-myristoyltransferase inhibitors of Plasmodium vivax liver stage hypnozoites and schizonts.
Rodríguez-Hernández et al. (2023)