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Structure paper

TitleRNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.
Journal, issue, pagesMol. Cell, Vol. 54, Page 975-986, Year 2014
Publish dateJan 18, 2014 (structure data deposition date)
AuthorsDikfidan, A. / Loll, B. / Zeymer, C. / Magler, I. / Clausen, T. / Meinhart, A.
External linksMol. Cell / PubMed:24813946
MethodsX-ray diffraction
Resolution1.98 - 2.6 Å
Structure data

PDB-4ohv:
C. Elegans Clp1 bound to AMP-PNP, and Mg2+
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-4ohw:
C. Elegans Clp1 bound to ATP, and Mn2+(ATP-bound state)
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-4ohx:
C. Elegans Clp1 bound to ADP and Mg2+ (RNA released state)
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-4ohy:
C. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+(inhibited substrate bound state)
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-4ohz:
bound to ssRNA tetranucleotide GAAA, ADP, and Mg2+
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-4oi0:
bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set I)
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-4oi1:
Clp1 bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set II)
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-4oi2:
C. Elegans Clp1 and ADP and Mg2+ (turnover state)
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-4oi4:
Protein complex of Clp1 bound to ATP and Mg2+ with Pcf11deltaN454deltaC563 of S. cerevisiae
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

Chemicals

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-2PE:
NONAETHYLENE GLYCOL / precipitant*YM

ChemComp-HOH:
WATER

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

ChemComp-MN:
Unknown entry

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

ChemComp-SAR:
SARCOSINE

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

ChemComp-GOL:
GLYCEROL

Source
  • caenorhabditis elegans (invertebrata)
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsRNA BINDING PROTEIN / polynucleotide kinase / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex / TRANSCRIPTION / Clp1 / Pcf11 / cleavage factor Ia / 3'-end mRNA processing

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