_EC 3.1.13.1 exoribonuclease Ii. 24 PDB entries  
EC 3.-.-.- Hydrolases. [52,127 PDB entries]
EC 3.1.-.- Acting on ester bonds. [12,902 PDB entries]
EC 3.1.13.- Exoribonucleases producing 5'-phosphomonoesters. [1,717 PDB entries]
EC 3.1.13.1 exoribonuclease Ii. [24 PDB entries]
1vk0

Reaction: Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.
Other name(s): ribonuclease Ii.
Comments: Preference for single-stranded Rna. The enzyme processes 3'-terminal extra-nucleotides of monomeric tRNA precursors, following the action of Ec 3.1.26.5. Similar enzymes: RNase Q, RNase bn, RNase piii, RNase y. Formerly Ec 3.1.4.20.
Links:   [IntEnz]   [ExPASy]   [KEGG]  

There are 24 PDB entries in enzyme class E.C.3.1.13.1

  PDB code Protein
1vk0
X-ray structure of gene product from arabidopsis thaliana at5g06450
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: at5g06450. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B, C, D, E, F (200 residues) CATH domain: 3.30.420.10
1w0h
Crystallographic structure of the nuclease domain of 3'hexo, a deddh family member, bound to ramp
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: synthetic gene
Chain: A (200 residues) CATH domain: 3.30.420.10
1wlj
Human isg20
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (168 residues) CATH domain: 3.30.420.10
1zbh
3'-end specific recognition of histone mRNA stem-loop by 3'- exonuclease
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: eri1, 3'exo. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Chains: A, B, C, D (289 residues) CATH domains: 1.10.720.30 3.30.420.10
1zbu
Crystal structure of full-length 3'-exonuclease
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: eri1, 3'exo. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (225 residues) CATH domain: 3.30.420.10
2id0
Escherichia coli rnase ii
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: rnb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Chains: A, B, C, D (636 residues) CATH domains: 2.40.50.140 2.40.50.640 Unassigned 2.40.50.140
2ix0
Rnase ii
Source: Escherichia coli. Organism_taxid: 562. Strain: c600. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Chain: A (637 residues) CATH domains: 2.40.50.140 2.40.50.640 Unassigned 2.40.50.140
2ix1
Rnase ii d209n mutant
Source: Escherichia coli. Organism_taxid: 562. Strain: c600. Expressed in: escherichia coli. Expression_system_taxid: 469008. Escherichia coli bl21(de3). Organism_taxid: 469008
Chain: A (643 residues) CATH domains: 2.40.50.140 2.40.50.640 Unassigned 2.40.50.140
2q3s
Ensemble refinement of the protein crystal structure of gene product from arabidopsis thaliana at5g06450
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Strain: cv. Columbia. Gene: at5g06450, mhf15.3. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D, E, F (200 residues) CATH domain: 3.30.420.10
4l8r
Structure of mRNA stem-loop, human stem-loop binding protein and 3'hexo ternary complex
Source: Synthetic: yes. Other_details: synthesized by idt. Homo sapiens. Human. Organism_taxid: 9606. Gene: 3'exo, eri1, thex1. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: hbp, slbp.
Chains: B, E (276 residues) CATH domains: Unassigned 3.30.420.10
4qoz
Crystal structure of the histone mRNA stem-loop, stem-loop binding protein (phosphorylated), and 3'hexo ternary complex
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: eri1, 3'exo, thex1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: slbp, hbp. Expressed in: spodoptera frugiperda.
Chains: B, E (277 residues) CATH domains: Unassigned 3.30.420.10
5v5f
Crystal structure of rice1 (pnt2)
Source: Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Gene: f26k24.6, at3g11770, axx17_at3g11710. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B, C (200 residues)
7dcy
Apo form of mycoplasma genitalium rnase r
Source: Mycoplasma genitalium g37. Organism_taxid: 243273. Strain: g-37. Gene: rnr, vacb, mg104. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333.
Chain: A (644 residues)
7dic
Mycoplasma genitalium rnase r in complex with single-stranded RNA
Source: Mycoplasma genitalium g37. Organism_taxid: 243273. Strain: g-37. Gene: rnr, vacb, mg104. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333. Synthetic: yes. Organism_taxid: 243273
Chain: A (646 residues)
7did
Mycoplasma genitalium rnase r in complex with ribose methylated single-stranded RNA
Source: Mycoplasma genitalium g37. Organism_taxid: 243273. Strain: g-37. Gene: rnr, vacb, mg104. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333. Synthetic: yes. Organism_taxid: 243273
Chain: A (644 residues)
7dol
Mycoplasma genitalium rnase r in complex with double-stranded RNA
Source: Mycoplasma genitalium g37. Organism_taxid: 243273. Strain: g-37. Gene: rnr, vacb, mg104. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333. Synthetic: yes. Organism_taxid: 243273
Chain: A (565 residues)
7ugb
Crystal structure of rat erk2 complexed with docking peptide from isg20
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: mapk1, erk2, mapk, prkm1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Homo sapiens. Human.
Chain: I (15 residues)
8cdu
Rnase r bound to a 30s degradation intermediate (main state)
Source: Bacillus subtilis subsp. Subtilis str. 168. Organism_taxid: 224308. Organism_taxid: 224308
Chain: C (708 residues)
8cdv
Rnase r bound to a 30s degradation intermediate (state ii)
Source: Bacillus subtilis subsp. Subtilis str. 168. Organism_taxid: 224308. Organism_taxid: 224308
Chain: C (457 residues)
8cec
Rnase r bound to a 30s degradation intermediate (state i - head- turning)
Source: Bacillus subtilis subsp. Subtilis str. 168. Organism_taxid: 224308. Organism_taxid: 224308
Chain: C (708 residues)
8ced
Rnase r bound to a 30s degradation intermediate (state i - head- turning)
Source: Bacillus subtilis subsp. Subtilis str. 168. Organism_taxid: 224308. Organism_taxid: 224308
Chain: C (708 residues)
8cee
Rnase r bound to a 30s degradation intermediate (state i - head- turning)
Source: Bacillus subtilis subsp. Subtilis str. 168. Organism_taxid: 224308. Organism_taxid: 224308
Chain: C (708 residues)
9g8n
80s-bound human ski2-exosome complex
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: exosc4, rrp41, ski6. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: exosc8, oip2, rrp43. Gene: exosc5, cml28, rrp46. Gene: exosc7, kiaa0116, rrp42.
Chain: M (975 residues)
9g8p
40s-bound human ski2-exosome complex
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: exosc8, oip2, rrp43. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: exosc5, cml28, rrp46. Gene: exosc7, kiaa0116, rrp42. Gene: exosc3, rrp40, cgi-102.
Chain: M (975 residues)