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Structure paper

TitleBiosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
Journal, issue, pagesJ. Mol. Biol., Vol. 424, Page 270-282, Year 2012
Publish dateJun 1, 2012 (structure data deposition date)
AuthorsQuitterer, F. / List, A. / Beck, P. / Bacher, A. / Groll, M.
External linksJ. Mol. Biol. / PubMed:22985965
MethodsX-ray diffraction
Resolution1.5 - 2.4 Å
Structure data

PDB-4ffl:
PylC in complex with L-lysine
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-4ffm:
PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine-Ne-D-ornithine)
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-4ffn:
PylC in complex with D-ornithine and AMPPNP
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-4ffo:
PylC in complex with phosphorylated D-ornithine
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-4ffp:
PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine and D-ornithine)
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-4ffr:
SeMet-labeled PylC (remote)
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

Chemicals

ChemComp-LYS:
LYSINE

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-PO4:
PHOSPHATE ION

ChemComp-MG:
Unknown entry

ChemComp-CO3:
CARBONATE ION

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-HOH:
WATER

ChemComp-0TF:
N~6~-D-ornithyl-L-lysine

ChemComp-ORD:
D-ORNITHINE

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-0TK:
(2R)-2,5-diaminopentanoyl dihydrogen phosphate

Source
  • methanosarcina barkeri (archaea)
KeywordsLIGASE / amino acid / biosynthesis of pyrrolysine / isopeptide bond formation / ATP-grasp fold / ATP-binding / L-lysine and 3R-methyl-D-ornithine / Cytosol / LIGASE/PRODUCT / LIGASE-PRODUCT complex / LIGASE/SUBSTRATE / LIGASE-SUBSTRATE complex / LIGASE/Reaction intermediate / LIGASE-Reaction intermediate complex

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