Function and Biology

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in triclinic crystal form

Source organism: Methanosarcina mazei
Biochemical function: aminoacyl-tRNA ligase activity
Biological process: tRNA aminoacylation
Cellular component: cytoplasm

EC 6.1.1.26: Pyrrolysine--tRNA(Pyl) ligase

Reaction catalysed:
ATP + L-pyrrolysine + tRNA(Pyl) = AMP + diphosphate + L-pyrrolysyl- tRNA(Pyl).
Comments:
  • In organisms such as Methanosarcina barkeri that incorporate the modified amino acid pyrrolysine (Pyl) into certain methylamine methyltransferases, an unusual tRNA(Pyl), with a CUA anticodon, can be charged directly with pyrrolysine by this class II aminoacyl- -tRNA ligase.
  • Specific for pyrrolysine as substrate as it cannot be replaced by lysine or any of the other natural amino acids.
Systematic name:
L-pyrrolysine:tRNA(Pyl) ligase (AMP-forming)
Alternative Name(s):
  • PylS
  • Pyrrolysyl-tRNA synthetase
  • PylRS

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence family

Pfam Protein family (Pfam)
PF01409
Domain description: tRNA synthetases class II core domain (F)
Occurring in:
  1. Pyrrolysine--tRNA ligase

InterPro InterPro annotations
IPR002319
Domain description: Phenylalanyl-tRNA synthetase
Occurring in:
  1. Pyrrolysine--tRNA ligase
IPR006195
Domain description: Aminoacyl-tRNA synthetase, class II
Occurring in:
  1. Pyrrolysine--tRNA ligase
IPR023877
Domain description: Pyrrolysyl-tRNA ligase, C-terminal
Occurring in:
  1. Pyrrolysine--tRNA ligase
IPR014729
Domain description: Rossmann-like alpha/beta/alpha sandwich fold
Occurring in:
  1. Pyrrolysine--tRNA ligase

Structure domains

CATH CATH domains
1.10.287.540
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Helix Hairpins
Homology: Helix hairpin bin
Occurring in:
  1. Pyrrolysine--tRNA ligase
1 copy of CATH domain 1.10.287.540 (Helix Hairpins) in Pyrrolysine--tRNA ligase in PDB 3vqx.
3.30.930.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: BirA Bifunctional Protein; domain 2
Homology: Bira Bifunctional Protein; Domain 2
Occurring in:
  1. Pyrrolysine--tRNA ligase
1 copy of CATH domain 3.30.930.10 (BirA Bifunctional Protein; domain 2) in Pyrrolysine--tRNA ligase in PDB 3vqx.