Structure of PDB 7dcy Chain A

Receptor sequence

>7dcyA (length=644) Species: 243273 (Mycoplasmoides genitalium G37)

LQGILTLGNKNSGFIRSLDDDKTVYYVHYSNLTGALDGDLVEFCKLDKPQ
FGDKFDAAVITILKRARILYAGNFLVDQNEFALEYKIVADNPRFYLTMIV
NPDSIPNNLASNTKIAFQIDEYDPDNNLCKVSVQQVLGNNDDPLINIKAI
MLDNSIVFETNDVVEQHANKLSFDTEEQHKAYRQDLTDLAFVTVDPTTSK
DLDDAIYVKTIPTGFVLYVAIADVAHYVNRNSEIDIEAKHKTSSIYLPGH
YVVPMLPEQLSNQLCSLNPAQKRYVVVCEISFDNQGRIKTNKLYPATIIS
KNRFSYDQVNKWLNNKSELNCDETVINSLKAAFTLSDLIQAQRQKRGTID
LSHKETEIVVDEHYFPIKINFLVHDKAETMIENLMVVANETVAWVLTNNK
IALPYRVHPRPSKKKLQSLIETVGELNITKPQFNLDTVTSSQIASWLNEN
KDNPSYEIFVILLLRTLGKAFYSVNPLMHFSIGSNHYTHFTSPIRRYIDL
TIHRLLWMHLFTPDQFTDNERDQLKQELEKIADTVNDTEIKIINCERNAN
DYLTTLLLSKQIGKTFSGFISAITSFGIFMRMDENNFDGLIKITTIPDDF
FIFEKEKMVLKGRKTNKVYKIGDRLEAKLSEIDFIQKRAILTLI

3D structure

• PDB: 7dcy Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation.
• Chain: A
• Resolution: 1.972 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D276 D282 D284 D285 Y387 R576
• Catalytic site (residue number reindexed from 1): D195 D201 D203 D204 Y306 R495
• 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	MG	A	D276 D285	D195 D204

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:7dcy, PDBe:7dcy, PDBj:7dcy
• PDBsum: 7dcy
• PubMed: 33788943
• UniProt: P47350|RNR_MYCGE Ribonuclease R (Gene Name=rnr)