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TitleSubstrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N-Acetylgalactosaminyltransferase 2.
Journal, issue, pagesAngew. Chem. Int. Ed. Engl., Vol. 53, Page 8206-, Year 2014
Publish dateApr 30, 2014 (structure data deposition date)
AuthorsLira-Navarrete, E. / Iglesias-Fernandez, J. / Zandberg, W.F. / Companon, I. / Kong, Y. / Corzana, F. / Pinto, B.M. / Clausen, H. / Peregrina, J.M. / Vocadlo, D. ...Lira-Navarrete, E. / Iglesias-Fernandez, J. / Zandberg, W.F. / Companon, I. / Kong, Y. / Corzana, F. / Pinto, B.M. / Clausen, H. / Peregrina, J.M. / Vocadlo, D. / Rovira, C. / Hurtado-Guerrero, R.
External linksAngew. Chem. Int. Ed. Engl. / PubMed:24954443
MethodsX-ray diffraction
Resolution2.2 - 2.85 Å
Structure data

PDB-4d0t:
GalNAc-T2 crystal soaked with UDP-GalNAc, EA2 peptide and manganese
Method: X-RAY DIFFRACTION / Resolution: 2.45 Å

PDB-4d0z:
GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 and manganese (Higher resolution dataset)
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-4d11:
GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)
Method: X-RAY DIFFRACTION / Resolution: 2.85 Å

Chemicals

ChemComp-MN:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-UD2:
URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

ChemComp-NGA:
2-acetamido-2-deoxy-beta-D-galactopyranose

ChemComp-HOH:
WATER

ChemComp-BBK:
2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose

ChemComp-HWU:
(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSFERASE / RETAINING GALNAC-T2 / SUBSTRATE-GUIDED SNI-TYPE REACTION / QM/MM METADYNAMICS / BI-BI KINETIC MECHANISM / SUBSTRATE SPECIFICITY / PROTEIN X-RAY CRYSTALLOGRAPHY / ACETAMIDO GROUP / TRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX

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