RNB_ECOLI
ID RNB_ECOLI Reviewed; 644 AA.
AC P30850; P78280;
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 3.
DT 03-AUG-2022, entry version 184.
DE RecName: Full=Exoribonuclease 2;
DE EC=3.1.13.1;
DE AltName: Full=Exoribonuclease II;
DE Short=RNase II;
DE Short=Ribonuclease II;
GN Name=rnb; OrderedLocusNames=b1286, JW1279;
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;
RX PubMed=8497196; DOI=10.1111/j.1365-2958.1993.tb01201.x;
RA Zilhao R., Camelo L., Arraiano C.M.;
RT "DNA sequencing and expression of the gene rnb encoding Escherichia coli
RT ribonuclease II.";
RL Mol. Microbiol. 8:43-51(1993).
RN [2]
RP SEQUENCE REVISION.
RA Zilhao R.;
RL Submitted (OCT-1994) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [4]
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 [5]
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 [6]
RP FUNCTION, COFACTOR, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=11948193; DOI=10.1074/jbc.m202942200;
RA Cheng Z.F., Deutscher M.P.;
RT "Purification and characterization of the Escherichia coli exoribonuclease
RT RNase R. Comparison with RNase II.";
RL J. Biol. Chem. 277:21624-21629(2002).
RN [7]
RP FUNCTION IN RIBOSOME DEGRADATION DURING STARVATION AND QUALITY CONTROL.
RC STRAIN=K12 / MG1655(Seq)*;
RX PubMed=21135037; DOI=10.1261/rna.2448911;
RA Basturea G.N., Zundel M.A., Deutscher M.P.;
RT "Degradation of ribosomal RNA during starvation: comparison to quality
RT control during steady-state growth and a role for RNase PH.";
RL RNA 17:338-345(2011).
RN [8]
RP ACETYLATION AT LYS-501, ACTIVITY REGULATION, AND MUTAGENESIS OF LYS-501.
RC STRAIN=K12;
RX PubMed=26847092; DOI=10.1093/nar/gkw053;
RA Song L., Wang G., Malhotra A., Deutscher M.P., Liang W.;
RT "Reversible acetylation on Lys501 regulates the activity of RNase II.";
RL Nucleic Acids Res. 44:1979-1988(2016).
RN [9]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655(Seq)*;
RX PubMed=28625967; DOI=10.1261/rna.060558.116;
RA Sulthana S., Quesada E., Deutscher M.P.;
RT "RNase II regulates RNase PH and is essential for cell survival during
RT starvation and stationary phase.";
RL RNA 23:1456-1464(2017).
CC -!- FUNCTION: Involved in mRNA degradation. Hydrolyzes single-stranded
CC polyribonucleotides processively in the 3' to 5' direction
CC (PubMed:11948193). RNases 2 and R (rnr) contribute to rRNA degradation
CC during starvation, while RNase R and PNPase (pnp) are the major
CC contributors to quality control of rRNA during steady state growth
CC (PubMed:21135037). This RNase is required to decrease expression of
CC RNase PH (rnp) at 42 degrees Celsius during starvation, which in turn
CC represses rRNA degradation (PubMed:28625967).
CC {ECO:0000269|PubMed:11948193, ECO:0000269|PubMed:21135037,
CC ECO:0000269|PubMed:28625967}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC nucleoside 5'-phosphates.; EC=3.1.13.1;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11948193};
CC -!- ACTIVITY REGULATION: Stimulated by the presence of a monovalent cation
CC (PubMed:11948193). Acetylation leads to decreased substrate binding and
CC decreased catalytic activity (PubMed:26847092).
CC {ECO:0000269|PubMed:11948193, ECO:0000269|PubMed:26847092}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Vmax=109800 nmol/min/mg enzyme with Poly(A) as substrate
CC {ECO:0000269|PubMed:11948193};
CC Vmax=160 nmol/min/mg enzyme with 23S rRNA as substrate
CC {ECO:0000269|PubMed:11948193};
CC Vmax=30 nmol/min/mg enzyme with 16S rRNA as substrate
CC {ECO:0000269|PubMed:11948193};
CC Vmax=20 nmol/min/mg enzyme with 5S rRNA as substrate
CC {ECO:0000269|PubMed:11948193};
CC pH dependence:
CC Optimum pH is 7.5-9.5. {ECO:0000269|PubMed:11948193};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius.
CC {ECO:0000269|PubMed:11948193};
CC -!- INTERACTION:
CC P30850; P0A7Y0: rnc; NbExp=2; IntAct=EBI-557325, EBI-557336;
CC P30850; P0A7W1: rpsE; NbExp=3; IntAct=EBI-557325, EBI-543949;
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- PTM: Acetylated at Lys-501 by PatZ. Deacetylated by CobB.
CC {ECO:0000269|PubMed:26847092}.
CC -!- DISRUPTION PHENOTYPE: In the presence of wild-type RNase PH (rph) 80-
CC 90% reduction in viability in stationary phase (96 hours of growth) at
CC 31 and 42 degrees Celsius or when cells are rapidly starved at 42
CC degrees Celsius; if rph is also absent there is no visible phenotype
CC under these 3 growth conditions (PubMed:28625967). Its absence leads to
CC extensive degradation of rRNA (PubMed:28625967).
CC {ECO:0000269|PubMed:28625967}.
CC -!- MISCELLANEOUS: In K12 strains that are derived from W1485 (including
CC MG1655 and W3110) the rph gene has a frameshift that leads to loss of
CC its ribonuclease PH activity. In strain K12 / MG1655(Seq)* the wild-
CC type Rph protein has been restored (PubMed:28625967).
CC {ECO:0000269|PubMed:28625967}.
CC -!- SIMILARITY: Belongs to the RNR ribonuclease family. RNase II subfamily.
CC {ECO:0000305}.
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DR EMBL; X67913; CAA48112.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74368.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA14840.1; -; Genomic_DNA.
DR PIR; A64877; A64877.
DR RefSeq; NP_415802.1; NC_000913.3.
DR RefSeq; WP_000484984.1; NZ_SSZK01000012.1.
DR PDB; 2ID0; X-ray; 2.35 A; A/B/C/D=1-644.
DR PDB; 2IX0; X-ray; 2.44 A; A=6-644.
DR PDB; 2IX1; X-ray; 2.74 A; A=6-644.
DR PDBsum; 2ID0; -.
DR PDBsum; 2IX0; -.
DR PDBsum; 2IX1; -.
DR AlphaFoldDB; P30850; -.
DR SMR; P30850; -.
DR BioGRID; 4263341; 45.
DR BioGRID; 850231; 1.
DR DIP; DIP-10724N; -.
DR IntAct; P30850; 10.
DR STRING; 511145.b1286; -.
DR iPTMnet; P30850; -.
DR jPOST; P30850; -.
DR PaxDb; P30850; -.
DR PRIDE; P30850; -.
DR EnsemblBacteria; AAC74368; AAC74368; b1286.
DR EnsemblBacteria; BAA14840; BAA14840; BAA14840.
DR GeneID; 66674887; -.
DR GeneID; 945864; -.
DR KEGG; ecj:JW1279; -.
DR KEGG; eco:b1286; -.
DR PATRIC; fig|1411691.4.peg.993; -.
DR EchoBASE; EB1577; -.
DR eggNOG; COG4776; Bacteria.
DR HOGENOM; CLU_002333_7_3_6; -.
DR InParanoid; P30850; -.
DR OMA; CFTNYLP; -.
DR PhylomeDB; P30850; -.
DR BioCyc; EcoCyc:EG11620-MON; -.
DR BioCyc; MetaCyc:EG11620-MON; -.
DR BRENDA; 3.1.13.1; 2026.
DR EvolutionaryTrace; P30850; -.
DR PRO; PR:P30850; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IDA:EcoCyc.
DR GO; GO:0008859; F:exoribonuclease II activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006402; P:mRNA catabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 2.40.50.140; -; 2.
DR HAMAP; MF_01036; RNase_II; 1.
DR InterPro; IPR011129; CSD.
DR InterPro; IPR040476; CSD2.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR013223; RNase_B_OB_dom.
DR InterPro; IPR011804; RNase_II.
DR InterPro; IPR001900; RNase_II/R.
DR InterPro; IPR022966; RNase_II/R_CS.
DR InterPro; IPR004476; RNase_II/RNase_R.
DR InterPro; IPR003029; S1_domain.
DR Pfam; PF17876; CSD2; 1.
DR Pfam; PF08206; OB_RNB; 1.
DR Pfam; PF00773; RNB; 1.
DR Pfam; PF00575; S1; 1.
DR SMART; SM00357; CSP; 1.
DR SMART; SM00955; RNB; 1.
DR SUPFAM; SSF50249; SSF50249; 4.
DR TIGRFAMs; TIGR00358; 3_prime_RNase; 1.
DR TIGRFAMs; TIGR02062; RNase_B; 1.
DR PROSITE; PS01175; RIBONUCLEASE_II; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cytoplasm; Exonuclease; Hydrolase; Nuclease;
KW Reference proteome; RNA-binding.
FT CHAIN 1..644
FT /note="Exoribonuclease 2"
FT /id="PRO_0000166380"
FT DOMAIN 561..643
FT /note="S1 motif"
FT MOD_RES 501
FT /note="N6-acetyllysine; by PatZ"
FT /evidence="ECO:0000269|PubMed:26847092"
FT MUTAGEN 501
FT /note="K->Q,R: Strong decrease in acetylation."
FT /evidence="ECO:0000269|PubMed:26847092"
FT CONFLICT 384
FT /note="I -> N (in Ref. 1; CAA48112)"
FT /evidence="ECO:0000305"
FT CONFLICT 399
FT /note="C -> G (in Ref. 1; CAA48112)"
FT /evidence="ECO:0000305"
FT CONFLICT 513
FT /note="A -> R (in Ref. 1; CAA48112)"
FT /evidence="ECO:0000305"
FT HELIX 6..17
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 21..27
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 34..37
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 39..41
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 43..46
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 48..51
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 59..65
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 68..70
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 72..80
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 84..93
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 96..103
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 110..114
FT /evidence="ECO:0007829|PDB:2IX0"
FT STRAND 127..134
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 136..138
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 144..152
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 159..167
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 198..201
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 210..214
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 218..220
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 222..229
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 231..233
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 240..248
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 257..259
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 264..267
FT /evidence="ECO:0007829|PDB:2ID0"
FT TURN 268..270
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 278..288
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 300..306
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 310..312
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 313..319
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 331..354
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 364..368
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 374..379
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 384..407
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 413..416
FT /evidence="ECO:0007829|PDB:2ID0"
FT TURN 421..423
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 424..434
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 440..443
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 446..457
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 459..462
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 463..468
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 469..471
FT /evidence="ECO:0007829|PDB:2IX1"
FT STRAND 476..480
FT /evidence="ECO:0007829|PDB:2ID0"
FT TURN 485..488
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 489..491
FT /evidence="ECO:0007829|PDB:2ID0"
FT TURN 498..500
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 502..514
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 527..554
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 555..557
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 564..572
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 575..580
FT /evidence="ECO:0007829|PDB:2ID0"
FT TURN 581..583
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 586..590
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 591..593
FT /evidence="ECO:0007829|PDB:2ID0"
FT HELIX 598..600
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 601..604
FT /evidence="ECO:0007829|PDB:2ID0"
FT TURN 605..608
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 609..612
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 615..619
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 623..632
FT /evidence="ECO:0007829|PDB:2ID0"
FT TURN 633..636
FT /evidence="ECO:0007829|PDB:2ID0"
FT STRAND 637..642
FT /evidence="ECO:0007829|PDB:2ID0"
SQ SEQUENCE 644 AA; 72491 MW; 36B16712CDF14394 CRC64;
MFQDNPLLAQ LKQQLHSQTP RAEGVVKATE KGFGFLEVDA QKSYFIPPPQ MKKVMHGDRI
IAVIHSEKER ESAEPEELVE PFLTRFVGKV QGKNDRLAIV PDHPLLKDAI PCRAARGLNH
EFKEGDWAVA EMRRHPLKGD RSFYAELTQY ITFGDDHFVP WWVTLARHNL EKEAPDGVAT
EMLDEGLVRE DLTALDFVTI DSASTEDMDD ALFAKALPDD KLQLIVAIAD PTAWIAEGSK
LDKAAKIRAF TNYLPGFNIP MLPRELSDDL CSLRANEVRP VLACRMTLSA DGTIEDNIEF
FAATIESKAK LVYDQVSDWL ENTGDWQPES EAIAEQVRLL AQICQRRGEW RHNHALVFKD
RPDYRFILGE KGEVLDIVAE PRRIANRIVE EAMIAANICA ARVLRDKLGF GIYNVHMGFD
PANADALAAL LKTHGLHVDA EEVLTLDGFC KLRRELDAQP TGFLDSRIRR FQSFAEISTE
PGPHFGLGLE AYATWTSPIR KYGDMINHRL LKAVIKGETA TRPQDEITVQ MAERRRLNRM
AERDVGDWLY ARFLKDKAGT DTRFAAEIVD ISRGGMRVRL VDNGAIAFIP APFLHAVRDE
LVCSQENGTV QIKGETVYKV TDVIDVTIAE VRMETRSIIA RPVA
