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Structure paper

TitleSubstrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.
Journal, issue, pagesProc. Natl. Acad. Sci. U.S.A., Vol. 115, Page 3350-3355, Year 2018
Publish dateJun 20, 2016 (structure data deposition date)
AuthorsParnell, A.E. / Mordhorst, S. / Kemper, F. / Giurrandino, M. / Prince, J.P. / Schwarzer, N.J. / Hofer, A. / Wohlwend, D. / Jessen, H.J. / Gerhardt, S. ...Parnell, A.E. / Mordhorst, S. / Kemper, F. / Giurrandino, M. / Prince, J.P. / Schwarzer, N.J. / Hofer, A. / Wohlwend, D. / Jessen, H.J. / Gerhardt, S. / Einsle, O. / Oyston, P.C.F. / Andexer, J.N. / Roach, P.L.
External linksProc. Natl. Acad. Sci. U.S.A. / PubMed:29531036
MethodsX-ray diffraction
Resolution1.903 - 2.903 Å
Structure data

PDB-5lc9:
Structure of Polyphosphate Kinase from Meiothermus ruber Apo-form
Method: X-RAY DIFFRACTION / Resolution: 1.903 Å

PDB-5lcd:
Structure of Polyphosphate Kinase from Meiothermus ruber bound to AMP
Method: X-RAY DIFFRACTION / Resolution: 2.66 Å

PDB-5ld1:
Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ATP
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-5ldb:
Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-5ll0:
Structure of Polyphosphate Kinase 2 from Francisella tularensis SCHU S4 with polyphosphate
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-5llb:
Structure of Polyphosphate Kinase 2 from Francisella tularensis with AMPPCH2PPP and polyphosphate
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-5llf:
Structure of Polyphosphate Kinase 2 mutant D117N from Francisella tularensis with polyphosphate
Method: X-RAY DIFFRACTION / Resolution: 2.31 Å

PDB-5maq:
Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP and PPi
Method: X-RAY DIFFRACTION / Resolution: 2.46 Å

PDB-5o6k:
Structure of Polyphosphate Kinase from Meiothermus ruber N121D
Method: X-RAY DIFFRACTION / Resolution: 2.903 Å

PDB-5o6m:
Structure of Polyphosphate Kinase from Meiothermus ruber N121D bound to ATP
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

Chemicals

ChemComp-PO4:
PHOSPHATE ION

ChemComp-SO4:
SULFATE ION

ChemComp-HOH:
WATER

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

ChemComp-MG:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-GOL:
GLYCEROL

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-CL:
Unknown entry

ChemComp-9PI:
bis[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] hydrogen phosphate

ChemComp-6YZ:
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]methyl]phosphinic acid

ChemComp-6YW:
[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] phosphono hydrogen phosphate

ChemComp-6YX:
[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl] phosphono hydrogen phosphate

ChemComp-6YY:
bis[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl] hydrogen phosphate

ChemComp-PPV:
PYROPHOSPHATE

ChemComp-DPO:
DIPHOSPHATE

Source
  • meiothermus ruber h328 (bacteria)
  • meiothermus ruber (bacteria)
  • francisella tularensis subsp. tularensis (strain schu s4 / schu 4) (bacteria)
KeywordsTRANSFERASE / Polyphosphate Kinase / Polyphosphate metabolism and nucleotide metabolism / Polyphosphate Kinase 2 enzyme / Complex with non-hydrolysable ATP analogue. Polyphosphate metabolism. Nucleotide metabolism / polyphosphate metabolism / nucleotide metabolism / Polyphosphate Kinase type 2 class III

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