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Structure paper

TitlePhosphate Binding in PNP Alters Transition-State Analogue Affinity and Subunit Cooperativity.
Journal, issue, pagesBiochemistry, Vol. 62, Page 3116-3125, Year 2023
Publish dateMay 19, 2023 (structure data deposition date)
AuthorsMinnow, Y.V.T. / Schramm, V.L. / Almo, S.C. / Ghosh, A.
External linksBiochemistry / PubMed:37812583
MethodsX-ray diffraction
Resolution1.66 - 2.34 Å
Structure data

PDB-8swp:
Structure of K. lactis PNP bound to hypoxanthine
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-8swq:
Structure of K. lactis PNP bound to transition state analog DADMe-IMMUCILLIN H and sulfate
Method: X-RAY DIFFRACTION / Resolution: 1.979 Å

PDB-8swr:
Structure of K. lactis PNP S42E variant bound to transition state analog DADMe-IMMUCILLIN G and sulfate
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-8sws:
Structure of K. lactis PNP S42E-H98R variant bound to transition state analog DADMe-IMMUCILLIN G and sulfate
Method: X-RAY DIFFRACTION / Resolution: 1.99 Å

PDB-8swt:
Structure of Bacteroides fragilis PNP bound to transition state analog IMMUCILLIN H and sulfate
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-8swu:
Structure of Clostridium perfringens PNP bound to transition state analog IMMUCILLIN H and sulfate
Method: X-RAY DIFFRACTION / Resolution: 2.34 Å

Chemicals

ChemComp-HPA:
HYPOXANTHINE

ChemComp-ACT:
ACETATE ION

ChemComp-HOH:
WATER

ChemComp-DIH:
7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one

ChemComp-SO4:
SULFATE ION

ChemComp-GOL:
GLYCEROL

ChemComp-IM5:
2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one

ChemComp-GUN:
GUANINE

ChemComp-IMH:
1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / inhibitor*YM

Source
  • kluyveromyces lactis nrrl y-1140 (yeast)
  • bacteroides fragilis nctc 9343 (bacteria)
  • clostridium perfringens atcc 13124 (bacteria)
KeywordsTRANSFERASE / PENTOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE

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