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TitleStructures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation.
Journal, issue, pagesNat Commun, Vol. 12, Page 6635-6635, Year 2021
Publish dateJun 23, 2021 (structure data deposition date)
AuthorsCui, H. / Muller, A.U. / Leibundgut, M. / Tian, J. / Ban, N. / Weber-Ban, E.
External linksNat Commun / PubMed:34789727
MethodsX-ray diffraction
Resolution1.394 - 1.88 Å
Structure data

PDB-7oxv:
Crystal structure of depupylase Dop in the Dop-loop-inserted state
Method: X-RAY DIFFRACTION / Resolution: 1.394 Å

PDB-7oxy:
Crystal structure of depupylase Dop in complex with Pup and AMP-PCP
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7oy3:
Crystal structure of depupylase Dop in complex with phosphorylated Pup and ADP
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7oyf:
Crystal structure of depupylase Dop in complex with Pup and ADP/trifluoromagnesate
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-7oyh:
Crystal structure of depupylase Dop in complex with Pup and ADP/tetrafluoromagnesate
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

Chemicals

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-SCN:
THIOCYANATE ION

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-HOH:
WATER

ChemComp-MG:
Unknown entry

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

ChemComp-ACT:
ACETATE ION

ChemComp-K:
Unknown entry

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

ChemComp-KQB:
trifluoromagnesate monohydrate

ChemComp-SO4:
SULFATE ION

ChemComp-MF4:
TETRAFLUOROMAGNESATE(2-)

Source
  • acidothermus cellulolyticus (bacteria)
  • acidothermus cellulolyticus (strain atcc 43068 / 11b) (bacteria)
KeywordsHYDROLASE / depupylase / Dop-loop / deamidase / Pup / ATP hydrolysis / Pup binding / phosphorylated Pup binding / transition state / product state

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