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TitleThe first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
Journal, issue, pagesJ. Biol. Chem., Vol. 292, Page 12126-12138, Year 2017
Publish dateJan 18, 2017 (structure data deposition date)
AuthorsSato, M. / Liebschner, D. / Yamada, Y. / Matsugaki, N. / Arakawa, T. / Wills, S.S. / Hattie, M. / Stubbs, K.A. / Ito, T. / Senda, T. ...Sato, M. / Liebschner, D. / Yamada, Y. / Matsugaki, N. / Arakawa, T. / Wills, S.S. / Hattie, M. / Stubbs, K.A. / Ito, T. / Senda, T. / Ashida, H. / Fushinobu, S.
External linksJ. Biol. Chem. / PubMed:28546425
MethodsX-ray diffraction
Resolution1.9 - 2.79 Å
Structure data

PDB-5wzn:
Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - GalNAc complex
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5wzp:
Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - ligand free
Method: X-RAY DIFFRACTION / Resolution: 2.64 Å

PDB-5wzq:
Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - quadruple mutant
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-5wzr:
Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex
Method: X-RAY DIFFRACTION / Resolution: 2.79 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-A2G:
2-acetamido-2-deoxy-alpha-D-galactopyranose

ChemComp-CA:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-GOL:
GLYCEROL

ChemComp-DJN:
N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide

Source
  • bifidobacterium bifidum (bacteria)
KeywordsHYDROLASE / Glycoside Hydrolase

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