› 6pau

X-ray diffraction
1.93Å resolution

Structure of Human NMT2 with myristoyl-lysine peptide and CoA products

Released:
DOI: 10.2210/pdb6pau/pdb
PDB entry 6pau coloured by chain, front view.
PDB entry 6pau coloured by chain, side view.
PDB entry 6pau 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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130016 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Glycylpeptide N-tetradecanoyltransferase 2 Chain: A
Molecule details ›
Chain: A
Length: 383 amino acids
Theoretical weight: 44.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60551 (Residues: 116-498; Coverage: 77%)
Gene name: NMT2
Sequence domains:
ADP-ribosylation factor 6 Chain: C
Molecule details ›
Chain: C
Length: 7 amino acids
Theoretical weight: 836 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62330 (Residues: 3-9; Coverage: 4%)
Gene name: ARF6

Ligands and Environments

5 bound ligands:
Ligand MG 1 x MG
Ligand GOL 9 x GOL
Ligand 4PS 1 x 4PS
Ligand SO4 1 x SO4
Ligand MYR 1 x MYR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 63.162Å b: 46.35Å c: 74.395Å
α: 90° β: 114.25° γ: 90°
R-values:
R R work R free
0.198 0.197 0.218
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

Lysine Fatty Acylation: Regulatory Enzymes, Research Tools, and Biological Function.
Komaniecki et al. (2021)