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EXRBN_MYCTU
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   03-AUG-2022, entry version 40.
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; Actinobacteria; Corynebacteriales; 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.m111.011627;
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; P9WJ73; -.
DR   GeneID; 45426155; -.
DR   GeneID; 887927; -.
DR   KEGG; mtu:Rv2179c; -.
DR   KEGG; mtv:RVBD_2179c; -.
DR   TubercuList; Rv2179c; -.
DR   eggNOG; ENOG5032SJD; Bacteria.
DR   OMA; CEFIEDG; -.
DR   PhylomeDB; P9WJ73; -.
DR   Proteomes; UP000001584; Chromosome.
DR   GO; GO:0008408; F:3'-5' exonuclease activity; IEA:InterPro.
DR   GO; GO:0004532; F:exoribonuclease activity; IEA:UniProtKB-UniRule.
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   Gene3D; 3.30.420.10; -; 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   Pfam; PF16473; DUF5051; 1.
DR   SUPFAM; SSF53098; SSF53098; 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
 
 
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