3vqx Summary


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

The structure was published by Yanagisawa, T., Sumida, T., Ishii, R., and Yokoyama, S., in 2013 in a paper entitled "A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.3 Å and deposited in 2012.

The experimental data on which the structure is based was also deposited.

This PDB entry contains multiple copies of the structure of Pyrrolysine--tRNA ligase.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):

Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Pyrrolysine--tRNA ligase Not available
Methanosarcina mazeisearch < 90% 291 88%
B Pyrrolysine--tRNA ligase Not available
Methanosarcina mazeisearch < 90% 291 88%
C Pyrrolysine--tRNA ligase Q8PWY1 (185-454) (PYLS_METMA)search Methanosarcina mazei Go1search < 90% 291 88%
D Pyrrolysine--tRNA ligase Not available
Methanosarcina mazeisearch < 90% 291 88%

This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q8PWY1 (185 - 454) Pyrrolysine--tRNA ligase Methanosarcina mazei

Chain Structural classification (CATH) Sequence family (Pfam)
A, B, C, D Helix hairpin binsearch, Bira Bifunctional Protein; Domain 2search tRNA synthetase class II core domain (G, H, P, S and T)search

Chain ID Molecular function (GO) Biological process (GO)
A, B, C, D (Q8PWY1) ligase activity, forming aminoacyl-tRNA and related compoundssearch nucleotide bindingsearch aminoacyl-tRNA ligase activitysearch ATP bindingsearch tRNA aminoacylation for protein translationsearch

Chain InterPro annotation
A, B, C, D Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domainsearch Aminoacyl-tRNA synthetase, class IIsearch UPF0291 structural domainsearch Pyrrolysyl-tRNA ligase, C-terminalsearch