Structure of PDB 4oi4 Chain C

Receptor sequence

>4oi4C (length=427) Species: 559292 (Saccharomyces cerevisiae S288C)

GDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTF
QNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTMKYIYNLHFMLEKIRM
SNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFT
VPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPMVKNFGLERINEN
KDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHI
IEKLNVNIMLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDD
VYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGR
VELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKR
RKLRVLLPVPGRLPSKAMILTSYRYLE

3D structure

• PDB: 4oi4 RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.
• Chain: C
• 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	C	T168 S179 Q191 S192 L193 T194 S195 G196 A197 Q204 M206 K208 V232 Q235 R236 L239 Y332 L341 S342 F390 P404 I405 L406 P426 V427 P428	T150 S161 Q173 S174 L175 T176 S177 G178 A179 Q186 M188 K190 V214 Q217 R218 L221 Y314 L323 S324 F372 P386 I387 L388 P408 V409 P410
BS02	ATP	C	D33 Q35 K72 P74 Q133 G135 K136 T137 S138 G312 V313 S314	D15 Q17 K54 P56 Q115 G117 K118 T119 S120 G294 V295 S296

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)