RBN_ECOLI
ID RBN_ECOLI Reviewed; 305 AA.
AC P0A8V0; P77449; Q47012;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=Ribonuclease BN {ECO:0000255|HAMAP-Rule:MF_01818};
DE Short=RNase BN {ECO:0000255|HAMAP-Rule:MF_01818};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_01818};
DE AltName: Full=Ribonuclease Z homolog {ECO:0000255|HAMAP-Rule:MF_01818};
DE Short=RNase Z homolog {ECO:0000255|HAMAP-Rule:MF_01818};
GN Name=rbn; Synonyms=elaC, rnz; OrderedLocusNames=b2268, JW2263;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RA Huisman G.W.;
RL Submitted (JUN-1996) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
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 FUNCTION, DIMERIZATION, AND COFACTOR.
RC STRAIN=K12 / DH5-alpha;
RX PubMed=12029081; DOI=10.1074/jbc.m112047200;
RA Vogel A., Schilling O., Niecke M., Bettmer J., Meyer-Klaucke W.;
RT "ElaC encodes a novel binuclear zinc phosphodiesterase.";
RL J. Biol. Chem. 277:29078-29085(2002).
RN [6]
RP IDENTIFICATION AS RNASE BN, FUNCTION, ACTIVITY REGULATION, SUBUNIT, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=15764599; DOI=10.1074/jbc.c500098200;
RA Ezraty B., Dahlgren B., Deutscher M.P.;
RT "The RNase Z homologue encoded by Escherichia coli elaC gene is RNase BN.";
RL J. Biol. Chem. 280:16542-16545(2005).
RN [7]
RP FUNCTION IN MRNA DECAY.
RC STRAIN=K12;
RX PubMed=16629673; DOI=10.1111/j.1365-2958.2006.05124.x;
RA Perwez T., Kushner S.R.;
RT "RNase Z in Escherichia coli plays a significant role in mRNA decay.";
RL Mol. Microbiol. 60:723-737(2006).
RN [8]
RP FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=19366704; DOI=10.1074/jbc.m109.005462;
RA Dutta T., Deutscher M.P.;
RT "Catalytic properties of RNase BN/RNase Z from Escherichia coli: RNase BN
RT is both an exo- and endoribonuclease.";
RL J. Biol. Chem. 284:15425-15431(2009).
RN [9]
RP FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=20489203; DOI=10.1074/jbc.m110.141101;
RA Dutta T., Deutscher M.P.;
RT "Mode of action of RNase BN/RNase Z on tRNA precursors: RNase BN does not
RT remove the CCA sequence from tRNA.";
RL J. Biol. Chem. 285:22874-22881(2010).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 3-305 IN COMPLEX WITH ZINC IONS,
RP AND SUBUNIT.
RX PubMed=16452444; DOI=10.1128/jb.188.4.1607-1614.2006;
RA Kostelecky B., Pohl E., Vogel A., Schilling O., Meyer-Klaucke W.;
RT "The crystal structure of the zinc phosphodiesterase from Escherichia coli
RT provides insight into function and cooperativity of tRNase Z-family
RT proteins.";
RL J. Bacteriol. 188:1607-1614(2006).
CC -!- FUNCTION: Zinc phosphodiesterase, which has both exoribonuclease and
CC endoribonuclease activities, depending on the nature of the substrate
CC and of the added divalent cation, and on its 3'-terminal structure. Can
CC process the 3' termini of both CCA-less and CCA-containing tRNA
CC precursors. CCA-less tRNAs are cleaved endonucleolytically after the
CC discriminator base, whereas residues following the CCA sequence can be
CC removed exonucleolytically or endonucleolytically in CCA-containing
CC molecules. Does not remove the CCA sequence. May also be involved in
CC the degradation of mRNAs. In vitro, hydrolyzes bis(p-
CC nitrophenyl)phosphate and thymidine-5'-p-nitrophenyl phosphate.
CC {ECO:0000269|PubMed:12029081, ECO:0000269|PubMed:15764599,
CC ECO:0000269|PubMed:16629673, ECO:0000269|PubMed:19366704,
CC ECO:0000269|PubMed:20489203}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:12029081};
CC Note=Binds 2 Zn(2+) ions. {ECO:0000269|PubMed:12029081};
CC -!- ACTIVITY REGULATION: Activated by cobalt and manganese. Strongly
CC inhibited by the presence of a 3'-CCA sequence or a 3'-phosphoryl
CC group. {ECO:0000269|PubMed:15764599, ECO:0000269|PubMed:19366704,
CC ECO:0000269|PubMed:20489203}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15764599,
CC ECO:0000269|PubMed:16452444}.
CC -!- DISRUPTION PHENOTYPE: Mutants are unaffected in growth.
CC {ECO:0000269|PubMed:15764599}.
CC -!- SIMILARITY: Belongs to the RNase Z family. RNase BN subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01818, ECO:0000305}.
CC -!- CAUTION: Was initially thought to be an arylsulfatase, given its
CC similarity with the AtsA family. PubMed:12029081 however showed that it
CC is a zinc phosphodiesterase. {ECO:0000305}.
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DR EMBL; U58768; AAB02732.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75328.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA16095.2; -; Genomic_DNA.
DR PIR; B64998; B64998.
DR RefSeq; NP_416771.4; NC_000913.3.
DR RefSeq; WP_001300687.1; NZ_STEB01000008.1.
DR PDB; 2CBN; X-ray; 2.90 A; A=1-305.
DR PDBsum; 2CBN; -.
DR AlphaFoldDB; P0A8V0; -.
DR SMR; P0A8V0; -.
DR BioGRID; 4263118; 36.
DR BioGRID; 851101; 1.
DR DIP; DIP-9498N; -.
DR IntAct; P0A8V0; 7.
DR STRING; 511145.b2268; -.
DR jPOST; P0A8V0; -.
DR PaxDb; P0A8V0; -.
DR PRIDE; P0A8V0; -.
DR EnsemblBacteria; AAC75328; AAC75328; b2268.
DR EnsemblBacteria; BAA16095; BAA16095; BAA16095.
DR GeneID; 66673845; -.
DR GeneID; 946760; -.
DR KEGG; ecj:JW2263; -.
DR KEGG; eco:b2268; -.
DR PATRIC; fig|1411691.4.peg.4468; -.
DR EchoBASE; EB4008; -.
DR eggNOG; COG1234; Bacteria.
DR HOGENOM; CLU_031317_2_0_6; -.
DR InParanoid; P0A8V0; -.
DR OMA; GTQRQMM; -.
DR PhylomeDB; P0A8V0; -.
DR BioCyc; EcoCyc:G7175-MON; -.
DR BioCyc; MetaCyc:G7175-MON; -.
DR BRENDA; 3.1.26.11; 2026.
DR SABIO-RK; P0A8V0; -.
DR EvolutionaryTrace; P0A8V0; -.
DR PRO; PR:P0A8V0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0042781; F:3'-tRNA processing endoribonuclease activity; IDA:EcoCyc.
DR GO; GO:0016891; F:endoribonuclease activity, producing 5'-phosphomonoesters; IDA:EcoCyc.
DR GO; GO:0004532; F:exoribonuclease activity; IDA:EcoliWiki.
DR GO; GO:0016896; F:exoribonuclease activity, producing 5'-phosphomonoesters; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IDA:EcoCyc.
DR GO; GO:0004518; F:nuclease activity; IDA:EcoliWiki.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042779; P:tRNA 3'-trailer cleavage; IBA:GO_Central.
DR GO; GO:0008033; P:tRNA processing; IDA:EcoliWiki.
DR CDD; cd07717; RNaseZ_ZiPD-like_MBL-fold; 1.
DR Gene3D; 3.60.15.10; -; 1.
DR HAMAP; MF_01818; RNase_Z_BN; 1.
DR InterPro; IPR001279; Metallo-B-lactamas.
DR InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR InterPro; IPR013469; Rnase_BN.
DR InterPro; IPR013471; RNase_Z/BN.
DR Pfam; PF12706; Lactamase_B_2; 2.
DR SMART; SM00849; Lactamase_B; 1.
DR SUPFAM; SSF56281; SSF56281; 1.
DR TIGRFAMs; TIGR02651; RNase_Z; 1.
DR TIGRFAMs; TIGR02649; true_RNase_BN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Endonuclease; Exonuclease; Hydrolase; Metal-binding;
KW Nuclease; Reference proteome; tRNA processing; Zinc.
FT CHAIN 1..305
FT /note="Ribonuclease BN"
FT /id="PRO_0000155863"
FT ACT_SITE 68
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818"
FT BINDING 64
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:16452444"
FT BINDING 66
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:16452444"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:16452444"
FT BINDING 69
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:16452444"
FT BINDING 141
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:16452444"
FT BINDING 212
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:16452444"
FT BINDING 212
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:16452444"
FT BINDING 270
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01818,
FT ECO:0000269|PubMed:16452444"
FT CONFLICT 154
FT /note="D -> Y (in Ref. 1; AAB02732)"
FT /evidence="ECO:0000305"
FT CONFLICT 217
FT /note="D -> N (in Ref. 1; AAB02732)"
FT /evidence="ECO:0000305"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 9..12
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 21..25
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 34..37
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 43..48
FT /evidence="ECO:0007829|PDB:2CBN"
FT TURN 54..56
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 57..61
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 67..70
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 73..82
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 89..94
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 97..107
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 116..120
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 123..128
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 130..138
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 140..143
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 146..152
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 161..166
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 173..180
FT /evidence="ECO:0007829|PDB:2CBN"
FT TURN 187..189
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 219..223
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 227..232
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 237..239
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 240..245
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 251..261
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 264..269
FT /evidence="ECO:0007829|PDB:2CBN"
FT HELIX 277..288
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 294..296
FT /evidence="ECO:0007829|PDB:2CBN"
FT STRAND 302..304
FT /evidence="ECO:0007829|PDB:2CBN"
SQ SEQUENCE 305 AA; 32930 MW; 69A55EAE8BDDEF68 CRC64;
MELIFLGTSA GVPTRTRNVT AILLNLQHPT QSGLWLFDCG EGTQHQLLHT AFNPGKLDKI
FISHLHGDHL FGLPGLLCSR SMSGIIQPLT IYGPQGIREF VETALRISGS WTDYPLEIVE
IGAGEILDDG LRKVTAYPLE HPLECYGYRI EEHDKPGALN AQALKAAGVP PGPLFQELKA
GKTITLEDGR QINGADYLAA PVPGKALAIF GDTGPCDAAL DLAKGVDVMV HEATLDITME
AKANSRGHSS TRQAATLARE AGVGKLIITH VSSRYDDKGC QHLLRECRSI FPATELANDF
TVFNV
