PDBsum entry 3vqy

Ligase

PDB id: 3vqy

Contents

Protein chain

257 a.a.

Ligands

ANP

LBY

Metals

_MG ×2

Waters ×98

PDB id:

3vqy

Name:

Ligase

Title:

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with boclys and amppnp (form 2)

Structure:

Pyrrolysine--tRNA ligase. Chain: a. Synonym: pyrrolysyl-tRNA synthetase, pylrs. Engineered: yes. Mutation: yes

Source:

Methanosarcina mazei. Organism_taxid: 2209. Strain: jcm9314. Gene: pyls. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.197 R-free: 0.231

Authors:

T.Yanagisawa,T.Sumida,R.Ishii,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

T.Yanagisawa et al. (2013). 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. Acta Crystallogr D Biol Crystallogr, 69, 5. PubMed id: 23275158

Date:

02-Apr-12 Release date: 02-Jan-13

Protein chain

No UniProt id for this chain

Struc: 257 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.26 - pyrrolysine--tRNA(Pyl) ligase.
• Reaction: tRNA(Pyl) + L-pyrrolysine + ATP = L-pyrrolysyl-tRNA(Pyl) + AMP + diphosphate

tRNA(Pyl) + L-pyrrolysine (Bound ligand (Het Group name = LBY) matches with 52.17% similarity) + ATP = L-pyrrolysyl-tRNA(Pyl) (Bound ligand (Het Group name = ANP) matches with 74.19% similarity) + AMP + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Acta Crystallogr D Biol Crystallogr 69:5 (2013)

PubMed id: 23275158

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.

T.Yanagisawa, T.Sumida, R.Ishii, S.Yokoyama.

ABSTRACT

Structures of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) have been determined in a novel crystal form. The triclinic form crystals contained two PylRS dimers (four monomer molecules) in the asymmetric unit, in which the two subunits in one dimer each bind N(ℇ)-(tert-butyloxycarbonyl)-L-lysyladenylate (BocLys-AMP) and the two subunits in the other dimer each bind AMP. The BocLys-AMP molecules adopt a curved conformation and the C(α) position of BocLys-AMP protrudes from the active site. The β7-β8 hairpin structures in the four PylRS molecules represent distinct conformations of different states of the aminoacyl-tRNA synthesis reaction. Tyr384, at the tip of the β7-β8 hairpin, moves from the edge to the inside of the active-site pocket and adopts multiple conformations in each state. Furthermore, a new crystal structure of the BocLys-AMPPNP-bound form is also reported. The bound BocLys adopts an unusually bent conformation, which differs from the previously reported structure. It is suggested that the present BocLys-AMPPNP-bound, BocLys-AMP-bound and AMP-bound complexes represent the initial binding of an amino acid (or pre-aminoacyl-AMP synthesis), pre-aminoacyl-tRNA synthesis and post-aminoacyl-tRNA synthesis states, respectively. The conformational changes of Asn346 that accompany the aminoacyl-tRNA synthesis reaction have been captured by X-ray crystallographic analyses. The orientation of the Asn346 side chain, which hydrogen-bonds to the carbonyl group of the amino-acid substrate, shifts by a maximum of 85-90° around the C(β) atom.