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Structure paper

TitleCrystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism
Journal, issue, pagesJ. Biol. Chem., Vol. 285, Page 34279-34287, Year 2010
Publish dateApr 22, 2010 (structure data deposition date)
AuthorsSuzuki, R. / Katayama, T. / Kim, B.-J. / Wakagi, T. / Shoun, H. / Ashida, H. / Yamamoto, K. / Fushinobu, S.
External linksJ. Biol. Chem. / PubMed:20739284
MethodsX-ray diffraction
Resolution1.7 - 2.3 Å
Structure data

PDB-3ahc:
Resting form of Phosphoketolase from Bifidobacterium Breve
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-3ahd:
Phosphoketolase from Bifidobacterium Breve complexed with 2-acetyl-thiamine diphosphate
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-3ahe:
Phosphoketolase from Bifidobacterium Breve complexed with dihydroxyethyl thiamine diphosphate
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-3ahf:
Phosphoketolase from Bifidobacterium Breve complexed with inorganic phosphate
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3ahg:
H64A mutant of Phosphoketolase from Bifidobacterium Breve complexed with a tricyclic ring form of thiamine diphosphate
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-3ahh:
H142A mutant of Phosphoketolase from Bifidobacterium Breve complexed with acetyl thiamine diphosphate
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-3ahi:
H320A mutant of Phosphoketolase from Bifidobacterium Breve complexed with acetyl thiamine diphosphate
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-3ahj:
H553A mutant of Phosphoketolase from Bifidobacterium Breve
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-TPP:
THIAMINE DIPHOSPHATE / Thiamine pyrophosphate

ChemComp-NA:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-2PE:
NONAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-HOH:
WATER / Water

ChemComp-HTL:
2-ACETYL-THIAMINE DIPHOSPHATE

ChemComp-THD:
2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-HTD:
2-[(9aR)-2,7-dimethyl-9a,10-dihydro-5H-pyrimido[4,5-d][1,3]thiazolo[3,2-a]pyrimidin-8-yl]ethyl trihydrogen diphosphate

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

Source
  • bifidobacterium breve (bacteria)
KeywordsLYASE / THIAMINE DIPHOSPHATE-DEPENDENT ENZYME / ALPHA-BETA FOLD / HOMODIMER / LIGAND-FREE STRUCTURE / ACETYL THIAMINE DIPHOSPHATE / DIHYDROXYETHYL THIAMINE DIPHOSPHATE / INORGANIC PHOSPHATE / DIHYDROTHIACHROMINE FORM OF THIAMINE DIPHOSPHATE

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