› 5ubb

X-ray diffraction
2Å resolution

Crystal structure of human alpha N-terminal protein methyltransferase 1B

Released:
DOI: 10.2210/pdb5ubb/pdb
PDB entry 5ubb coloured by chain, front view.
PDB entry 5ubb coloured by chain, side view.
PDB entry 5ubb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2.
Dong C, Dong G, Li L, Zhu L, Tempel W, Liu Y, Huang R, Min J
OpenAccess logo Commun Biol 1 183 (2018)
PMID: 30417120

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + N-terminal-(A,P,S)PK-[protein] = S-adenosyl-L-homocysteine + N-terminal-N-methyl-N-(A,P,S)PK-[protein]
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-562662 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-terminal Xaa-Pro-Lys N-methyltransferase 2 Chain: A
Molecule details ›
Chain: A
Length: 222 amino acids
Theoretical weight: 25.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5VVY1 (Residues: 58-278; Coverage: 78%)
Gene names: C1orf184, METTL11B, NRMT2, NTMT2
Sequence domains: AdoMet dependent proline di-methyltransferase
Structure domains: Vaccinia Virus protein VP39

Ligands and Environments

2 bound ligands:
Ligand SAM 1 x SAM
Ligand UNX 26 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P21212
Unit cell:
a: 45.595Å b: 132.962Å c: 42.292Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.25
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Past, present, and perspectives of protein N-terminal methylation.
Diaz et al. (2021)
1 more

4 mentions without citation

Chemical Biology of Protein N-Terminal Methyltransferases.
Huang R. (2019)
3 more