Structure of PDB 8cee Chain C

Receptor sequence

>8ceeC (length=708) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

KEAFMEKLLSFMKEEAYKPLTVQELEEMLNITEAEEFKELVKALVALEEK
GLIVRTRSDRYGIPEKMNLIKGKISAHAKGFAFLLPEDTSLSDVFIPPNE
LNTAMNGDIVMVRLNSQSSGSRQEGTVIRILERAIQRVVGTYTETRNFGF
VIPDDKKITSDIFIPKNGKNGAAEGHKVVVKLTSYPEGRMNAEGEVETIL
GHKNDPGIDILSVIHKHGLPGEFPADAMEQASSTPDTIDEKDLKDRRDLR
DQVIVTIDGADAKDLDDAVTVTKLDDGSYKLGVHIADVSHYVTENSPIDK
EALERGTSVYLVDRVIPMIPHRLSNGICSLNPKVDRLTLSCEMTINSQGQ
VTEHEIFQSVIKTTERMTYSDVNKILVDDDEELKQKYEPLVPMFKDMERL
AQILRDKRMDRGAVDFDFKEAKVLVDDEGAVKDVVIRERSVAEKLIEEFM
LVANETVAEHFHWMNVPFIYRIHEEPNAEKLQKFLEFVTTFGYVVKGTAG
NIHPRALQSILDAVRDRPEETVISTVMLRSMKQAKYDPQSLGHFGLSTEF
YTHFTSPIRRYPDLIVHRLIRTYLINGKVDEATQEKWAERLPDIAEHTSS
MERRAVDAERETDDLKKAEYMLDKIGEEFDGMISSVTNFGMFVELPNTIE
GLVHVSFMTDDYYRFDEQHFAMIGERTGNVFRIGDEITVKVVDVNKDERN
IDFEIVGM

3D structure

• PDB: 8cee Structural basis of ribosomal 30S subunit degradation by RNase R
• Chain: C
• Resolution: 3.7 Å

Enzymatic activity

• Enzyme Commision number: 3.1.13.1: exoribonuclease II.

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	rna	C	R148 E176 R191	R146 E174 R189
BS02	rna	C	D269 Y312 F418 F420 E422 R439 E449 H475 L530 R531 Q535 A536 H545 R561 R562 R612 F644 E652	D267 Y310 F416 F418 E420 R437 E447 H473 L528 R529 Q533 A534 H543 R559 R560 R610 F642 E650

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0004518 nuclease activity
• GO:0004527 exonuclease activity
• GO:0004540 RNA nuclease activity
• GO:0008859 exoribonuclease II activity

Biological Process

• GO:0006402 mRNA catabolic process
• GO:0016070 RNA metabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:8cee, PDBe:8cee, PDBj:8cee
• PDBsum: 8cee
• PubMed: 38326618
• UniProt: O32231|RNR_BACSU Ribonuclease R (Gene Name=rnr)