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Protein

Endoribonuclease Nob1

Gene

nob1

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Toxic component of a toxin-antitoxin (TA) module (Potential). Processes pre-16S-rRNA at its 3' end (the D-site) to yield the mature 3' end.Curated1 Publication

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi12ManganeseSequence analysis1
Metal bindingi131Zinc1
Metal bindingi134Zinc1
Metal bindingi147Zinc1
Metal bindingi150Zinc1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease, Toxin

Keywords - Biological processi

Ribosome biogenesis

Keywords - Ligandi

Manganese, Metal-binding, RNA-binding, rRNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Endoribonuclease Nob1 (EC:3.1.-.-UniRule annotation)
Short name:
RNase Nob1
Alternative name(s):
Endonuclease VapC6
Putative toxin VapC6UniRule annotation
Gene namesi
Name:nob1
Synonyms:vapC6
Ordered Locus Names:PH0709
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi12D → N: No cleavage of pre-16S-rRNA. 1 Publication1
Mutagenesisi79S → A: Reduced cleavage of pre-16S-rRNA. 1 Publication1
Mutagenesisi100D → N: Non-specific cleavage pre-16S-rRNA, maybe due to altered substrate-binding. 1 Publication1
Mutagenesisi115R → A: Non-specific cleavage pre-16S-rRNA, maybe due to altered substrate-binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001560481 – 161Endoribonuclease Nob1Add BLAST161

Interactioni

Protein-protein interaction databases

STRINGi70601.PH0709.

Structurei

Secondary structure

1161
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi13 – 18Combined sources6
Beta strandi24 – 26Combined sources3
Helixi28 – 31Combined sources4
Helixi38 – 48Combined sources11
Beta strandi51 – 54Combined sources4
Helixi59 – 72Combined sources14
Helixi80 – 92Combined sources13
Helixi101 – 109Combined sources9
Beta strandi129 – 134Combined sources6
Beta strandi137 – 140Combined sources4
Helixi143 – 145Combined sources3
Turni148 – 150Combined sources3
Beta strandi153 – 156Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LCQNMR-A1-161[»]
ProteinModelPortaliO58440.
SMRiO58440.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini7 – 105PINcUniRule annotationAdd BLAST99

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni120 – 125Flexible linker6
Regioni126 – 161Zinc ribbonAdd BLAST36

Domaini

Has 2 structurally independent domains; the N-terminal PINc domain which binds Mn2+, rRNA substrate and probably has endoribonuclease activity, and the C-terminal zinc ribbon domain which also binds rRNA substrate.1 Publication

Sequence similaritiesi

Belongs to the PINc/VapC protein family.UniRule annotation
Contains 1 PINc domain.UniRule annotation

Phylogenomic databases

eggNOGiarCOG00721. Archaea.
COG1439. LUCA.
HOGENOMiHOG000223294.
KOiK07060.
OMAiMQNVAEK.

Family and domain databases

HAMAPiMF_00265. VapC_Nob1. 1 hit.
InterProiIPR002716. PIN_dom.
IPR029060. PIN_domain-like.
IPR033411. Ribonuclease_PIN.
IPR022907. VapC_family.
[Graphical view]
PfamiPF17146. PIN_6. 1 hit.
[Graphical view]
SMARTiSM00670. PINc. 1 hit.
[Graphical view]
SUPFAMiSSF88723. SSF88723. 1 hit.

Sequencei

Sequence statusi: Complete.

O58440-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLRNLKKTLV LDSSVFIQGI DIEGYTTPSV VEEIKDRESK IFLESLISAG
60 70 80 90 100
KVKIAEPSKE SIDRIIQVAK ETGEVNELSK ADIEVLALAY ELKGEIFSDD
110 120 130 140 150
YNVQNIASLL GLRFRTLKRG IKKVIKWRYV CIGCGRKFST LPPGGVCPDC
160
GSKVKLIPRK R
Length:161
Mass (Da):17,972
Last modified:August 1, 1998 - v1
Checksum:iBDB3A1AA59912AE3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29800.1.
PIRiF71117.
RefSeqiWP_010884804.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA29800; BAA29800; BAA29800.
GeneIDi1443039.
KEGGipho:PH0709.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29800.1.
PIRiF71117.
RefSeqiWP_010884804.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LCQNMR-A1-161[»]
ProteinModelPortaliO58440.
SMRiO58440.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH0709.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA29800; BAA29800; BAA29800.
GeneIDi1443039.
KEGGipho:PH0709.

Phylogenomic databases

eggNOGiarCOG00721. Archaea.
COG1439. LUCA.
HOGENOMiHOG000223294.
KOiK07060.
OMAiMQNVAEK.

Family and domain databases

HAMAPiMF_00265. VapC_Nob1. 1 hit.
InterProiIPR002716. PIN_dom.
IPR029060. PIN_domain-like.
IPR033411. Ribonuclease_PIN.
IPR022907. VapC_family.
[Graphical view]
PfamiPF17146. PIN_6. 1 hit.
[Graphical view]
SMARTiSM00670. PINc. 1 hit.
[Graphical view]
SUPFAMiSSF88723. SSF88723. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiNOB1_PYRHO
AccessioniPrimary (citable) accession number: O58440
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: August 1, 1998
Last modified: November 2, 2016
This is version 94 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.