Structure of PDB 2id0 Chain D

Receptor sequence

>2id0D (length=636) Species: 83333 (Escherichia coli K-12)

NPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKV
MHGDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHP
LLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFG
DDHFVPWWVTLARHNLEKEAPDGVATEMLDEGLVREDLTALDFVTIDSAS
TEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYL
PGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAAT
IESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNH
ALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVL
RDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRR
ELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGD
MINHRLLKAVIKGRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKA
GTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENG
TVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPVA

3D structure

• PDB: 2id0 Structural Basis for Processivity and Single-Strand Specificity of RNase II.
• Chain: D
• Resolution: 2.35 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D201 D207 D209 D210 Y313 R500
• Catalytic site (residue number reindexed from 1): D197 D203 D205 D206 Y309 R496
• 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	MN	D	D201 D209 D210	D197 D205 D206

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0004527 exonuclease activity
• GO:0004540 RNA nuclease activity
• GO:0005515 protein binding
• GO:0008408 3'-5' exonuclease activity
• GO:0008859 exoribonuclease II activity

Biological Process

• GO:0006401 RNA catabolic process
• GO:0006402 mRNA catabolic process
• GO:0016070 RNA metabolic process
• GO:0016078 tRNA decay

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:2id0, PDBe:2id0, PDBj:2id0
• PDBsum: 2id0
• PubMed: 16996291
• UniProt: P30850|RNB_ECOLI Exoribonuclease 2 (Gene Name=rnb)