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Structure paper

TitleMolecular mechanism of allosteric substrate activation in a thiamine diphosphate-dependent decarboxylase.
Journal, issue, pagesJ. Biol. Chem., Vol. 282, Page 35269-35278, Year 2007
Publish dateJun 1, 2007 (structure data deposition date)
AuthorsVersees, W. / Spaepen, S. / Wood, M.D. / Leeper, F.J. / Vanderleyden, J. / Steyaert, J.
External linksJ. Biol. Chem. / PubMed:17905741
MethodsX-ray diffraction
Resolution1.85 - 3.2 Å
Structure data

PDB-2q5j:
X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-2q5l:
X-ray structure of phenylpyruvate decarboxylase in complex with 2-(1-hydroxyethyl)-3-deaza-ThDP
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-2q5o:
X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and phenylpyruvate
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-2q5q:
X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and 5-phenyl-2-oxo-valeric acid
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-TPW:
2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE

ChemComp-HOH:
WATER

ChemComp-CL:
Unknown entry

ChemComp-S1T:
2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1S)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE

ChemComp-R1T:
2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE

ChemComp-GOL:
GLYCEROL

ChemComp-PPY:
3-PHENYLPYRUVIC ACID

ChemComp-KPV:
5-PHENYL-2-KETO-VALERIC ACID

ChemComp-TLA:
L(+)-TARTARIC ACID

Source
  • azospirillum brasilense (bacteria)
KeywordsLYASE / thiamine diphosphate / asymmetric dimer of dimers / open active site loops / cofactor analogue / open active site loop / covalent intermediate analogue / symmetrical dimer of dimers / closed active site loops / substrate complex

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