RND_ECOLI
ID RND_ECOLI Reviewed; 375 AA.
AC P09155;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1989, sequence version 1.
DT 03-AUG-2022, entry version 164.
DE RecName: Full=Ribonuclease D {ECO:0000255|HAMAP-Rule:MF_01899};
DE Short=RNase D {ECO:0000255|HAMAP-Rule:MF_01899};
DE EC=3.1.13.5 {ECO:0000255|HAMAP-Rule:MF_01899};
GN Name=rnd {ECO:0000255|HAMAP-Rule:MF_01899};
GN OrderedLocusNames=b1804, JW1793;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-6, AND FUNCTION.
RX PubMed=3041371; DOI=10.1093/nar/16.14.6265;
RA Zhang J., Deutscher M.P.;
RT "Escherichia coli RNase D: sequencing of the rnd structural gene and
RT purification of the overexpressed protein.";
RL Nucleic Acids Res. 16:6265-6278(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097040; DOI=10.1093/dnares/3.6.379;
RA Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
RA Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
RA Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
RA Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
RA Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y.,
RA Horiuchi T.;
RT "A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 40.1-50.0 min region on the linkage map.";
RL DNA Res. 3:379-392(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-38.
RC STRAIN=K12;
RX PubMed=8107670; DOI=10.1007/bf00280412;
RA Fulda M., Heinz E., Wolter F.P.;
RT "The fadD gene of Escherichia coli K12 is located close to rnd at 39.6 min
RT of the chromosomal map and is a new member of the AMP-binding protein
RT family.";
RL Mol. Gen. Genet. 242:241-249(1994).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, AND COFACTOR.
RX PubMed=6263886; DOI=10.1016/s0021-9258(19)69251-3;
RA Cudny H., Zaniewski R., Deutscher M.P.;
RT "Escherichia coli RNase D. Catalytic properties and substrate
RT specificity.";
RL J. Biol. Chem. 256:5633-5637(1981).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
RX PubMed=16004870; DOI=10.1016/j.str.2005.04.015;
RA Zuo Y., Wang Y., Malhotra A.;
RT "Crystal structure of Escherichia coli RNase D, an exoribonuclease involved
RT in structured RNA processing.";
RL Structure 13:973-984(2005).
CC -!- FUNCTION: Exonuclease involved in the 3' processing of various
CC precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA
CC molecule and releases 5'-mononucleotides. {ECO:0000255|HAMAP-
CC Rule:MF_01899, ECO:0000269|PubMed:3041371, ECO:0000269|PubMed:6263886}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage that removes extra residues from the
CC 3'-terminus of tRNA to produce 5'-mononucleotides.; EC=3.1.13.5;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01899,
CC ECO:0000269|PubMed:6263886};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01899,
CC ECO:0000269|PubMed:6263886};
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the RNase D family. {ECO:0000255|HAMAP-
CC Rule:MF_01899}.
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DR EMBL; X07055; CAA30098.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74874.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15599.1; -; Genomic_DNA.
DR EMBL; X70994; CAA50322.1; -; Genomic_DNA.
DR PIR; S01223; NRECD.
DR RefSeq; NP_416318.1; NC_000913.3.
DR PDB; 1YT3; X-ray; 1.60 A; A=1-375.
DR PDBsum; 1YT3; -.
DR AlphaFoldDB; P09155; -.
DR SMR; P09155; -.
DR BioGRID; 4260338; 55.
DR IntAct; P09155; 1.
DR STRING; 511145.b1804; -.
DR jPOST; P09155; -.
DR PaxDb; P09155; -.
DR PRIDE; P09155; -.
DR DNASU; 946328; -.
DR EnsemblBacteria; AAC74874; AAC74874; b1804.
DR EnsemblBacteria; BAA15599; BAA15599; BAA15599.
DR GeneID; 946328; -.
DR KEGG; ecj:JW1793; -.
DR KEGG; eco:b1804; -.
DR PATRIC; fig|511145.12.peg.1880; -.
DR EchoBASE; EB0851; -.
DR eggNOG; COG0349; Bacteria.
DR HOGENOM; CLU_042387_0_1_6; -.
DR InParanoid; P09155; -.
DR OMA; FMRVDTF; -.
DR PhylomeDB; P09155; -.
DR BioCyc; EcoCyc:EG10858-MON; -.
DR BioCyc; MetaCyc:EG10858-MON; -.
DR EvolutionaryTrace; P09155; -.
DR PRO; PR:P09155; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IDA:EcoCyc.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0033890; F:ribonuclease D activity; IDA:EcoCyc.
DR GO; GO:0042780; P:tRNA 3'-end processing; IEA:UniProtKB-UniRule.
DR Gene3D; 1.10.150.80; -; 2.
DR Gene3D; 3.30.420.10; -; 1.
DR HAMAP; MF_01899; RNase_D; 1.
DR InterPro; IPR002562; 3'-5'_exonuclease_dom.
DR InterPro; IPR010997; HRDC-like_sf.
DR InterPro; IPR002121; HRDC_dom.
DR InterPro; IPR044876; HRDC_dom_sf.
DR InterPro; IPR006292; RNase_D.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF01612; DNA_pol_A_exo1; 1.
DR Pfam; PF00570; HRDC; 1.
DR SMART; SM00474; 35EXOc; 1.
DR SMART; SM00341; HRDC; 1.
DR SUPFAM; SSF47819; SSF47819; 2.
DR SUPFAM; SSF53098; SSF53098; 1.
DR TIGRFAMs; TIGR01388; rnd; 1.
DR PROSITE; PS50967; HRDC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Exonuclease; Hydrolase;
KW Nuclease; Reference proteome; tRNA processing.
FT CHAIN 1..375
FT /note="Ribonuclease D"
FT /id="PRO_0000097368"
FT DOMAIN 3..169
FT /note="3'-5' exonuclease"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT DOMAIN 210..289
FT /note="HRDC"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01899"
FT STRAND 4..6
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 9..19
FT /evidence="ECO:0007829|PDB:1YT3"
FT STRAND 22..32
FT /evidence="ECO:0007829|PDB:1YT3"
FT STRAND 40..47
FT /evidence="ECO:0007829|PDB:1YT3"
FT STRAND 52..55
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 57..59
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 64..71
FT /evidence="ECO:0007829|PDB:1YT3"
FT STRAND 75..81
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 83..93
FT /evidence="ECO:0007829|PDB:1YT3"
FT STRAND 98..102
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 103..109
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 118..126
FT /evidence="ECO:0007829|PDB:1YT3"
FT TURN 133..136
FT /evidence="ECO:0007829|PDB:1YT3"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 146..157
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 159..172
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 176..191
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 196..202
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 206..208
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 211..231
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 241..250
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 255..260
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 265..284
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 287..289
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 297..299
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 303..321
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 325..328
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 331..341
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 352..354
FT /evidence="ECO:0007829|PDB:1YT3"
FT HELIX 356..370
FT /evidence="ECO:0007829|PDB:1YT3"
SQ SEQUENCE 375 AA; 42734 MW; AC0E6D3883712BAE CRC64;
MNYQMITTDD ALASLCEAVR AFPAIALDTE FVRTRTYYPQ LGLIQLFDGE HLALIDPLGI
TDWSPLKAIL RDPSITKFLH AGSEDLEVFL NVFGELPQPL IDTQILAAFC GRPMSWGFAS
MVEEYSGVTL DKSESRTDWL ARPLTERQCE YAAADVWYLL PITAKLMVET EASGWLPAAL
DECRLMQMRR QEVVAPEDAW RDITNAWQLR TRQLACLQLL ADWRLRKARE RDLAVNFVVR
EEHLWSVARY MPGSLGELDS LGLSGSEIRF HGKTLLALVE KAQTLPEDAL PQPMLNLMDM
PGYRKAFKAI KSLITDVSET HKISAELLAS RRQINQLLNW HWKLKPQNNL PELISGWRGE
LMAEALHNLL QEYPQ
