Structure of PDB 4oi4 Chain A

Receptor sequence

>4oi4A (length=428) Species: 559292 (Saccharomyces cerevisiae S288C)

TGDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYT
FQNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTMKYIYNLHFMLEKIR
MSNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINLDPQQPIF
TVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPMVKNFGLERINE
NKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHH
IIEKLNVNIMLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVD
DVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVG
RVELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEK
RRKLRVLLPVPGRLPSKAMILTSYRYLE

3D structure

• PDB: 4oi4 RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.
• Chain: A
• Resolution: 2.4 Å

Enzymatic activity

• Enzyme Commision number: 2.7.1.78: polynucleotide 5'-hydroxyl-kinase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	peptide	A	T168 S179 Q191 S192 L193 T194 S195 G196 A197 H201 N202 Q204 P205 M206 V232 Q235 R236 L239 Q242 Y332 L341 S342 F390 L406 P426 V427 P428	T151 S162 Q174 S175 L176 T177 S178 G179 A180 H184 N185 Q187 P188 M189 V215 Q218 R219 L222 Q225 Y315 L324 S325 F373 L389 P409 V410 P411
BS02	ATP	A	D33 Q35 K72 P74 Q133 G135 K136 T137 S138 G312 V313 S314	D16 Q18 K55 P57 Q116 G118 K119 T120 S121 G295 V296 S297

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0051731 polynucleotide 5'-hydroxyl-kinase activity

Biological Process

• GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation
• GO:0006396 RNA processing
• GO:0006397 mRNA processing
• GO:0031124 mRNA 3'-end processing

Cellular Component

• GO:0005634 nucleus
• GO:0005849 mRNA cleavage factor complex

External links

• PDB: RCSB:4oi4, PDBe:4oi4, PDBj:4oi4
• PDBsum: 4oi4
• PubMed: 24813946
• UniProt: Q08685|CLP1_YEAST mRNA cleavage and polyadenylation factor CLP1 (Gene Name=CLP1)