NOB1_PYRHO
ID NOB1_PYRHO Reviewed; 161 AA.
AC O58440;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Endoribonuclease Nob1;
DE Short=RNase Nob1;
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_00265};
DE AltName: Full=Endonuclease VapC6;
DE AltName: Full=Putative toxin VapC6 {ECO:0000255|HAMAP-Rule:MF_00265};
GN Name=nob1; Synonyms=vapC6; OrderedLocusNames=PH0709;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP POSSIBLE FUNCTION.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=15718296; DOI=10.1093/nar/gki201;
RA Pandey D.P., Gerdes K.;
RT "Toxin-antitoxin loci are highly abundant in free-living but lost from
RT host-associated prokaryotes.";
RL Nucleic Acids Res. 33:966-976(2005).
RN [3]
RP STRUCTURE BY NMR, FUNCTION AS AN ENDORIBONUCLEASE, COFACTOR, RNA-BINDING,
RP DOMAIN, AND MUTAGENESIS OF ASP-12; SER-79; ASP-100 AND ARG-115.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=22156373; DOI=10.1093/nar/gkr1186;
RA Veith T., Martin R., Wurm J.P., Weis B.L., Duchardt-Ferner E.,
RA Safferthal C., Hennig R., Mirus O., Bohnsack M.T., Wohnert J., Schleiff E.;
RT "Structural and functional analysis of the archaeal endonuclease Nob1.";
RL Nucleic Acids Res. 40:3259-3274(2012).
CC -!- FUNCTION: Toxic component of a type II toxin-antitoxin (TA) system
CC (Potential). Processes pre-16S-rRNA at its 3' end (the D-site) to yield
CC the mature 3' end. {ECO:0000269|PubMed:22156373, ECO:0000305}.
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:22156373};
CC Note=Manganese; magnesium does not support nuclease activity.
CC {ECO:0000269|PubMed:22156373};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:22156373};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:22156373};
CC -!- DOMAIN: Has 2 structurally independent domains; the N-terminal PINc
CC domain which binds Mn(2+), rRNA substrate and probably has
CC endoribonuclease activity, and the C-terminal zinc ribbon domain which
CC also binds rRNA substrate. {ECO:0000269|PubMed:22156373}.
CC -!- SIMILARITY: Belongs to the PINc/VapC protein family.
CC {ECO:0000255|HAMAP-Rule:MF_00265}.
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DR EMBL; BA000001; BAA29800.1; -; Genomic_DNA.
DR PIR; F71117; F71117.
DR RefSeq; WP_010884804.1; NC_000961.1.
DR PDB; 2LCQ; NMR; -; A=1-161.
DR PDBsum; 2LCQ; -.
DR AlphaFoldDB; O58440; -.
DR BMRB; O58440; -.
DR SMR; O58440; -.
DR STRING; 70601.3257117; -.
DR EnsemblBacteria; BAA29800; BAA29800; BAA29800.
DR GeneID; 1443039; -.
DR KEGG; pho:PH0709; -.
DR eggNOG; arCOG00721; Archaea.
DR OMA; GCGREFD; -.
DR OrthoDB; 102178at2157; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004540; F:ribonuclease activity; IEA:InterPro.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0042254; P:ribosome biogenesis; IEA:UniProtKB-KW.
DR CDD; cd09876; PIN_Nob1-like; 1.
DR HAMAP; MF_00265; VapC_Nob1; 1.
DR InterPro; IPR039907; NOB1.
DR InterPro; IPR029060; PIN-like_dom_sf.
DR InterPro; IPR002716; PIN_dom.
DR InterPro; IPR033411; Ribonuclease_PIN.
DR InterPro; IPR022907; VapC_family.
DR PANTHER; PTHR12814; PTHR12814; 2.
DR Pfam; PF17146; PIN_6; 1.
DR SMART; SM00670; PINc; 1.
DR SUPFAM; SSF88723; SSF88723; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Endonuclease; Hydrolase; Manganese; Metal-binding; Nuclease;
KW Ribosome biogenesis; RNA-binding; rRNA-binding; Toxin-antitoxin system;
KW Zinc.
FT CHAIN 1..161
FT /note="Endoribonuclease Nob1"
FT /id="PRO_0000156048"
FT DOMAIN 7..105
FT /note="PINc"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT REGION 120..125
FT /note="Flexible linker"
FT REGION 126..161
FT /note="Zinc ribbon"
FT BINDING 12
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000255"
FT BINDING 131
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 134
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 147
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 150
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT MUTAGEN 12
FT /note="D->N: No cleavage of pre-16S-rRNA."
FT /evidence="ECO:0000269|PubMed:22156373"
FT MUTAGEN 79
FT /note="S->A: Reduced cleavage of pre-16S-rRNA."
FT /evidence="ECO:0000269|PubMed:22156373"
FT MUTAGEN 100
FT /note="D->N: Non-specific cleavage pre-16S-rRNA, maybe due
FT to altered substrate-binding."
FT /evidence="ECO:0000269|PubMed:22156373"
FT MUTAGEN 115
FT /note="R->A: Non-specific cleavage pre-16S-rRNA, maybe due
FT to altered substrate-binding."
FT /evidence="ECO:0000269|PubMed:22156373"
FT HELIX 13..18
FT /evidence="ECO:0007829|PDB:2LCQ"
FT STRAND 24..26
FT /evidence="ECO:0007829|PDB:2LCQ"
FT HELIX 28..31
FT /evidence="ECO:0007829|PDB:2LCQ"
FT HELIX 38..48
FT /evidence="ECO:0007829|PDB:2LCQ"
FT STRAND 51..54
FT /evidence="ECO:0007829|PDB:2LCQ"
FT HELIX 59..72
FT /evidence="ECO:0007829|PDB:2LCQ"
FT HELIX 80..92
FT /evidence="ECO:0007829|PDB:2LCQ"
FT HELIX 101..109
FT /evidence="ECO:0007829|PDB:2LCQ"
FT STRAND 129..134
FT /evidence="ECO:0007829|PDB:2LCQ"
FT STRAND 137..140
FT /evidence="ECO:0007829|PDB:2LCQ"
FT HELIX 143..145
FT /evidence="ECO:0007829|PDB:2LCQ"
FT TURN 148..150
FT /evidence="ECO:0007829|PDB:2LCQ"
FT STRAND 153..156
FT /evidence="ECO:0007829|PDB:2LCQ"
SQ SEQUENCE 161 AA; 17972 MW; BDB3A1AA59912AE3 CRC64;
MLRNLKKTLV LDSSVFIQGI DIEGYTTPSV VEEIKDRESK IFLESLISAG KVKIAEPSKE
SIDRIIQVAK ETGEVNELSK ADIEVLALAY ELKGEIFSDD YNVQNIASLL GLRFRTLKRG
IKKVIKWRYV CIGCGRKFST LPPGGVCPDC GSKVKLIPRK R
