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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: -Experimental evidence at protein leveli

Functioni

Toxic component of a type II toxin-antitoxin (TA) system (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

Keywordsi

Molecular functionEndonuclease, Hydrolase, Nuclease, RNA-binding, rRNA-binding
Biological processRibosome biogenesis, Toxin-antitoxin system
LigandManganese, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciPHOR70601:G1G39-695-MONOMER

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[»]
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

Phylogenomic databases

eggNOGiarCOG00721 Archaea
COG1439 LUCA
HOGENOMiHOG000223294
KOiK07060
OMAiGCGREFD
OrthoDBiPOG093Z0IIX

Family and domain databases

HAMAPiMF_00265 VapC_Nob1, 1 hit
InterProiView protein in InterPro
IPR029060 PIN-like_dom_sf
IPR002716 PIN_dom
IPR033411 Ribonuclease_PIN
IPR022907 VapC_family
PfamiView protein in Pfam
PF17146 PIN_6, 1 hit
SMARTiView protein in SMART
SM00670 PINc, 1 hit
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

Similar proteinsi

Entry informationi

Entry nameiNOB1_PYRHO
AccessioniPrimary (citable) accession number: O58440
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: August 1, 1998
Last modified: April 25, 2018
This is version 103 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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