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Structure paper

TitleCrystal Structure of the Mannose-6-Phosphate Uncovering Enzyme.
Journal, issue, pagesStructure, Vol. 28, Page 426-436.e3, Year 2020
Publish dateJun 29, 2019 (structure data deposition date)
AuthorsGorelik, A. / Illes, K. / Nagar, B.
External linksStructure / PubMed:32109365
MethodsX-ray diffraction
Resolution1.6 - 3 Å
Structure data

PDB-6pkg:
Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain auto-inhibited by pro-peptide
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-6pkh:
Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain auto-inhibited by pro-peptide
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-6pki:
Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain (C56S C230S) in complex with N-acetyl-alpha-D-glucosamine (alpha-GlcNAc) and mannose 6-phosphate (M6P)
Method: X-RAY DIFFRACTION / Resolution: 2.293 Å

PDB-6pku:
Guinea pig N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain (C51S C221S) in complex with N-acetyl-alpha-D-glucosamine (alpha-GlcNAc) and mannose 6-phosphate (M6P)
Method: X-RAY DIFFRACTION / Resolution: 1.949 Å

PDB-6pky:
Guinea pig N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain auto-inhibited by pro-peptide
Method: X-RAY DIFFRACTION / Resolution: 3 Å

PDB-6u11:
Xenopus laevis N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) (C46S C219S C453S C480S C486S) with CTD mostly flexible
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-IOD:
IODIDE ION

ChemComp-I2I:
molecular iodine

ChemComp-P6G:
HEXAETHYLENE GLYCOL / precipitant*YM

ChemComp-HOH:
WATER

ChemComp-NDG:
2-acetamido-2-deoxy-alpha-D-glucopyranose

ChemComp-M6P:
6-O-phosphono-alpha-D-mannopyranose

ChemComp-1PE:
PENTAETHYLENE GLYCOL / precipitant*YM

ChemComp-CL:
Unknown entry

ChemComp-BR:
BROMIDE ION

ChemComp-K:
Unknown entry

Source
  • danio rerio (zebrafish)
  • cavia porcellus (domestic guinea pig)
  • xenopus laevis (African clawed frog)
KeywordsHYDROLASE / uncovering enzyme / mannose 6-phosphate / glycosidase / pro-peptide / n-acetylglucosamine

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