ID EXRBN_MYCTU Reviewed; 168 AA.
AC P9WJ73; F2GJZ2; I6Y8M5; L7N5T0; O53513; Q7D7E6;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 27-MAR-2024, entry version 47.
DE RecName: Full=3'-5' exoribonuclease Rv2179c {ECO:0000255|HAMAP-Rule:MF_00977};
DE EC=3.1.13.- {ECO:0000255|HAMAP-Rule:MF_00977};
GN OrderedLocusNames=Rv2179c, RVBD_2179c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RG The Broad Institute Genome Sequencing Platform;
RA Galagan J., Kreiswirth B., Dobos K., Fortune S., Fitzgerald M., Young S.K.,
RA Zeng Q., Gargeya S., Abouelleil A., Alvarado L., Berlin A.M., Chapman S.B.,
RA Gainer-Dewar J., Goldberg J., Gnerre S., Griggs A., Gujja S., Hansen M.,
RA Howarth C., Imamovic A., Larimer J., McCowan C., Murphy C., Pearson M.,
RA Poon T., Priest M., Roberts A., Saif S., Shea T., Sykes S., Wortman J.,
RA Nusbaum C., Birren B.;
RT "The genome sequence of Mycobacterium tuberculosis H37Rv.";
RL Submitted (NOV-2013) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011445;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH AMP AND MAGNESIUM
RP IONS, FUNCTION, COFACTOR, ACTIVITY REGULATION, MUTAGENESIS OF ASP-145, AND
RP SUBUNIT.
RX PubMed=24311791; DOI=10.1074/jbc.m113.525683;
RA Abendroth J., Ollodart A., Andrews E.S., Myler P.J., Staker B.L.,
RA Edwards T.E., Arcus V.L., Grundner C.;
RT "Mycobacterium tuberculosis Rv2179c establishes a new exoribonuclease
RT family with broad phylogenetic distribution.";
RL J. Biol. Chem. 289:2139-2147(2014).
CC -!- FUNCTION: Exonuclease that cleaves single-stranded 3' overhangs of
CC double-stranded RNA. Has no activity with 5' overhangs. Has negligible
CC endonuclease activity. Can bind ATP, dATP and AMP (in vitro); the
CC nucleotide occupies the predicted substrate binding site.
CC {ECO:0000255|HAMAP-Rule:MF_00977, ECO:0000269|PubMed:24311791}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00977,
CC ECO:0000269|PubMed:24311791};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00977,
CC ECO:0000269|PubMed:24311791};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA. {ECO:0000269|PubMed:24311791}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00977,
CC ECO:0000269|PubMed:24311791}.
CC -!- INTERACTION:
CC P9WJ73; P9WJ73: RVBD_2179c; NbExp=3; IntAct=EBI-16099288, EBI-16099288;
CC -!- MISCELLANEOUS: Member of the DEDD group of RNAses that are
CC characterized by the presence of four acidic residues in the active
CC site. These residues are conserved even when the proteins have highly
CC divergent sequences. Has high structural similarity to RNase T despite
CC very low sequence identity.
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DR EMBL; AL123456; CCP44956.1; -; Genomic_DNA.
DR EMBL; CP003248; AFN50127.1; -; Genomic_DNA.
DR PIR; E70936; E70936.
DR RefSeq; NP_216695.1; NC_000962.3.
DR RefSeq; WP_003411331.1; NZ_NVQJ01000008.1.
DR PDB; 4HEC; X-ray; 1.80 A; A/B=2-168.
DR PDB; 4HVJ; X-ray; 2.10 A; A/B=2-168.
DR PDBsum; 4HEC; -.
DR PDBsum; 4HVJ; -.
DR AlphaFoldDB; P9WJ73; -.
DR SMR; P9WJ73; -.
DR STRING; 83332.Rv2179c; -.
DR PaxDb; 83332-Rv2179c; -.
DR GeneID; 45426155; -.
DR GeneID; 887927; -.
DR KEGG; mtu:Rv2179c; -.
DR KEGG; mtv:RVBD_2179c; -.
DR TubercuList; Rv2179c; -.
DR eggNOG; ENOG5032SJD; Bacteria.
DR InParanoid; P9WJ73; -.
DR OrthoDB; 4640719at2; -.
DR PhylomeDB; P9WJ73; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IEA:InterPro.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0004532; F:RNA exonuclease activity; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 1.
DR HAMAP; MF_00977; 3_5_Exoribonuc_actinobact; 1.
DR InterPro; IPR030853; 3_5_Exoribonuc_actinobac.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR033390; Rv2179c-like.
DR NCBIfam; NF033638; RNase_AS; 1.
DR Pfam; PF16473; Rv2179c-like; 1.
DR SUPFAM; SSF53098; Ribonuclease H-like; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Reference proteome.
FT CHAIN 1..168
FT /note="3'-5' exoribonuclease Rv2179c"
FT /id="PRO_0000424958"
FT REGION 6..9
FT /note="RNA binding"
FT /evidence="ECO:0000305|PubMed:24311791"
FT BINDING 6
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24311791"
FT MUTAGEN 145
FT /note="D->A: Strongly reduces enzyme activity."
FT /evidence="ECO:0000269|PubMed:24311791"
FT STRAND 2..11
FT /evidence="ECO:0007829|PDB:4HEC"
FT STRAND 16..25
FT /evidence="ECO:0007829|PDB:4HEC"
FT STRAND 30..35
FT /evidence="ECO:0007829|PDB:4HEC"
FT HELIX 40..42
FT /evidence="ECO:0007829|PDB:4HEC"
FT HELIX 45..50
FT /evidence="ECO:0007829|PDB:4HEC"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:4HEC"
FT HELIX 66..76
FT /evidence="ECO:0007829|PDB:4HEC"
FT TURN 77..80
FT /evidence="ECO:0007829|PDB:4HEC"
FT STRAND 84..91
FT /evidence="ECO:0007829|PDB:4HEC"
FT HELIX 93..100
FT /evidence="ECO:0007829|PDB:4HEC"
FT TURN 101..103
FT /evidence="ECO:0007829|PDB:4HEC"
FT HELIX 106..108
FT /evidence="ECO:0007829|PDB:4HEC"
FT HELIX 120..126
FT /evidence="ECO:0007829|PDB:4HEC"
FT TURN 137..139
FT /evidence="ECO:0007829|PDB:4HEC"
FT HELIX 142..157
FT /evidence="ECO:0007829|PDB:4HEC"
SQ SEQUENCE 168 AA; 19520 MW; D6CE7EF4D2FB7FA1 CRC64;
MRYFYDTEFI EDGHTIELIS IGVVAEDGRE YYAVSTEFDP ERAGSWVRTH VLPKLPPPAS
QLWRSRQQIR LDLEEFLRID GTDSIELWAW VGAYDHVALC QLWGPMTALP PTVPRFTREL
RQLWEDRGCP RMPPRPRDVH DALVDARDQL RRFRLITSTD DAGRGAAR
//
