ISDA

Deposition Date 2014-04-11

Release Date 2014-04-23

Last Version Date 2024-11-27

Entry Detail

PDB ID:

4Q3D

Keywords:

OXIDOREDUCTASE

Title:

PylD cocrystallized with L-Ornithine-Nd-D-ornithine and NAD+

Biological Source:

Source Organism:

Methanosarcina barkeri (Taxon ID: 269797)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Free:

0.23

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 21 21 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PYLD, pyrrolysine synthase
Gene (Uniprot):pylD
Chain IDs:A, B, C, D
Chain Length:260
Number of Molecules:4
Biological Source:Methanosarcina barkeri

UniProt ID:Q46E80 Pfam ID:PF21455

Ligand Molecules

2YH

EDO

GOL

NAD

PEG

Primary Citation

The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD).

Quitterer, F, Beck, P, Bacher, A, Groll, M.Show

Angew.Chem.Int.Ed.Engl. 53 8150 8153 (2014)

PMID: 24916332 DOI: 10.1002/anie.201402595

Abstact

The dehydrogenase PylD catalyzes the ultimate step of the pyrrolysine pathway by converting the isopeptide L-lysine-Nε-3R-methyl-D-ornithine to the 22nd proteinogenic amino acid. In this study, we demonstrate how PylD can be harnessed to oxidize various isopeptides to novel amino acids by combining chemical synthesis with enzyme kinetics and X-ray crystallography. The data enable a detailed description of the PylD reaction trajectory for the biosynthesis of pyrroline and tetrahydropyridine rings as constituents of pyrrolysine analogues.

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Primary Citation of related structures