RNY_STAA8
ID RNY_STAA8 Reviewed; 519 AA.
AC Q2FZ08; A9ZP05;
DT 10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 21-MAR-2006, sequence version 1.
DT 25-MAY-2022, entry version 109.
DE RecName: Full=Ribonuclease Y;
DE Short=RNase Y;
DE EC=3.1.-.-;
DE AltName: Full=Conserved virulence factor A;
GN Name=rny; Synonyms=cvfA; OrderedLocusNames=SAOUHSC_01263;
OS Staphylococcus aureus (strain NCTC 8325 / PS 47).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93061;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION AS A PHOSPHODIESTERASE,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, AND MUTAGENESIS OF
RP HIS-338; HIS-367; ASP-368; LYS-371 AND ASP-423.
RX PubMed=17951247; DOI=10.1074/jbc.m705309200;
RA Nagata M., Kaito C., Sekimizu K.;
RT "Phosphodiesterase activity of CvfA is required for virulence in
RT Staphylococcus aureus.";
RL J. Biol. Chem. 283:2176-2184(2008).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NCTC 8325 / PS 47;
RA Gillaspy A.F., Worrell V., Orvis J., Roe B.A., Dyer D.W., Iandolo J.J.;
RT "The Staphylococcus aureus NCTC 8325 genome.";
RL (In) Fischetti V., Novick R., Ferretti J., Portnoy D., Rood J. (eds.);
RL Gram positive pathogens, 2nd edition, pp.381-412, ASM Press, Washington
RL D.C. (2006).
RN [3]
RP FUNCTION IN EXOTOXIN PRODUCTION AND VIRULENCE, AGR EXPRESSION, AND
RP MUTAGENESIS OF GLY-229; ILE-232 AND ASP-423.
RX PubMed=15853881; DOI=10.1111/j.1365-2958.2005.04596.x;
RA Kaito C., Kurokawa K., Matsumoto Y., Terao Y., Kawabata S., Hamada S.,
RA Sekimizu K.;
RT "Silkworm pathogenic bacteria infection model for identification of novel
RT virulence genes.";
RL Mol. Microbiol. 56:934-944(2005).
RN [4]
RP FUNCTION IN SARZ EXPRESSION.
RX PubMed=17087772; DOI=10.1111/j.1365-2958.2006.05480.x;
RA Kaito C., Morishita D., Matsumoto Y., Kurokawa K., Sekimizu K.;
RT "Novel DNA binding protein SarZ contributes to virulence in Staphylococcus
RT aureus.";
RL Mol. Microbiol. 62:1601-1617(2006).
RN [5]
RP INTERACTION WITH CSHA AND ENO, AND SUBUNIT.
RC STRAIN=UAMS-1;
RX PubMed=21764917; DOI=10.1128/jb.05485-11;
RA Roux C.M., DeMuth J.P., Dunman P.M.;
RT "Characterization of components of the Staphylococcus aureus mRNA
RT degradosome holoenzyme-like complex.";
RL J. Bacteriol. 193:5520-5526(2011).
RN [6]
RP DISRUPTION PHENOTYPE.
RC STRAIN=SA564;
RX PubMed=22447609; DOI=10.1128/aem.00202-12;
RA Redder P., Linder P.;
RT "New range of vectors with a stringent 5-fluoroorotic acid-based
RT counterselection system for generating mutants by allelic replacement in
RT Staphylococcus aureus.";
RL Appl. Environ. Microbiol. 78:3846-3854(2012).
CC -!- FUNCTION: Endoribonuclease that initiates mRNA decay (By similarity).
CC In vitro, catalyzes the hydrolysis of both 2',3'-cyclic AMP and 2',3'-
CC cyclic GMP into 3'-AMP and 3'-GMP, respectively, at the 3'-terminal of
CC RNA. Activates sarZ and agr operon resulting in the expression of
CC virulence genes such as hemolysin, DNase and protease. Contributes to
CC virulence in both silkworm-infection model and mice. {ECO:0000250,
CC ECO:0000269|PubMed:15853881, ECO:0000269|PubMed:17087772,
CC ECO:0000269|PubMed:17951247}.
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=30 mM for bis-p-nitrophenyl phosphate (bis-pNPP)
CC {ECO:0000269|PubMed:17951247};
CC KM=17 mM for 2',3'-cAMP {ECO:0000269|PubMed:17951247};
CC KM=15 mM for 2',3'-cGMP {ECO:0000269|PubMed:17951247};
CC KM=1.1 uM for 2',3'-cGMP at the 3'-terminal of RNA
CC {ECO:0000269|PubMed:17951247};
CC Vmax=0.75 umol/min/mg enzyme with bis-p-nitrophenyl phosphate (bis-
CC pNPP) as substrate {ECO:0000269|PubMed:17951247};
CC Vmax=0.93 umol/min/mg enzyme with 2',3'-cAMP as substrate
CC {ECO:0000269|PubMed:17951247};
CC Vmax=0.38 umol/min/mg enzyme with 2',3'-cGMP as substrate
CC {ECO:0000269|PubMed:17951247};
CC Vmax=0.0015 umol/min/mg enzyme with 2',3'-cGMP at the 3'-terminal of
CC RNA as substrate {ECO:0000269|PubMed:17951247};
CC pH dependence:
CC Optimum pH is 9.0. {ECO:0000269|PubMed:17951247};
CC -!- SUBUNIT: Homodimer (Probable). Component of a possible RNA degradosome
CC complex composed of cshA, eno, pfkA, pnp, rnjA, rnjB, rnpA and rny.
CC Interacts specifically with RNA helicase CshA and enolase.
CC {ECO:0000269|PubMed:21764917, ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:17951247};
CC Single-pass membrane protein {ECO:0000269|PubMed:17951247}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype.
CC {ECO:0000269|PubMed:22447609}.
CC -!- SIMILARITY: Belongs to the RNase Y family. {ECO:0000305}.
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DR EMBL; AB325528; BAF96735.1; -; Genomic_DNA.
DR EMBL; CP000253; ABD30364.1; -; Genomic_DNA.
DR RefSeq; WP_001050913.1; NZ_LS483365.1.
DR RefSeq; YP_499796.1; NC_007795.1.
DR AlphaFoldDB; Q2FZ08; -.
DR SMR; Q2FZ08; -.
DR STRING; 1280.SAXN108_1291; -.
DR EnsemblBacteria; ABD30364; ABD30364; SAOUHSC_01263.
DR GeneID; 3919916; -.
DR KEGG; sao:SAOUHSC_01263; -.
DR PATRIC; fig|93061.5.peg.1157; -.
DR eggNOG; COG1418; Bacteria.
DR HOGENOM; CLU_028328_1_0_9; -.
DR OMA; PHAILGM; -.
DR SABIO-RK; Q2FZ08; -.
DR PHI-base; PHI:2965; -.
DR PHI-base; PHI:6427; -.
DR PHI-base; PHI:8891; -.
DR PRO; PR:Q2FZ08; -.
DR Proteomes; UP000008816; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0004521; F:endoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006402; P:mRNA catabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd00077; HDc; 1.
DR Gene3D; 3.30.1370.10; -; 1.
DR HAMAP; MF_00335; RNase_Y; 1.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR006674; HD_domain.
DR InterPro; IPR006675; HDIG_dom.
DR InterPro; IPR004087; KH_dom.
DR InterPro; IPR004088; KH_dom_type_1.
DR InterPro; IPR036612; KH_dom_type_1_sf.
DR InterPro; IPR017705; Ribonuclease_Y.
DR InterPro; IPR022711; RNase_Y_N.
DR PANTHER; PTHR12826:SF15; PTHR12826:SF15; 1.
DR Pfam; PF01966; HD; 1.
DR Pfam; PF00013; KH_1; 1.
DR Pfam; PF12072; RNase_Y_N; 1.
DR SMART; SM00471; HDc; 1.
DR SMART; SM00322; KH; 1.
DR SUPFAM; SSF54791; SSF54791; 1.
DR TIGRFAMs; TIGR00277; HDIG; 1.
DR TIGRFAMs; TIGR03319; RNase_Y; 1.
DR PROSITE; PS51831; HD; 1.
DR PROSITE; PS50084; KH_TYPE_1; 1.
PE 1: Evidence at protein level;
KW Cell membrane; Endonuclease; Hydrolase; Membrane; Nuclease;
KW Reference proteome; RNA-binding; Transmembrane; Transmembrane helix;
KW Virulence.
FT CHAIN 1..519
FT /note="Ribonuclease Y"
FT /id="PRO_0000294066"
FT TRANSMEM 3..23
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 209..269
FT /note="KH"
FT DOMAIN 335..428
FT /note="HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT MUTAGEN 229
FT /note="G->A: Decrease in hemolysin and DNase production and
FT virulence in silkworm-infection model."
FT /evidence="ECO:0000269|PubMed:15853881"
FT MUTAGEN 232
FT /note="I->N: Decrease in hemolysin and DNase production and
FT virulence in silkworm-infection model."
FT /evidence="ECO:0000269|PubMed:15853881"
FT MUTAGEN 338
FT /note="H->A: Decrease in phosphodiesterase activity,
FT hemolysin production and virulence in silkworm-infection
FT model."
FT /evidence="ECO:0000269|PubMed:17951247"
FT MUTAGEN 367
FT /note="H->A: Decrease in phosphodiesterase activity,
FT hemolysin production and virulence in silkworm-infection
FT model."
FT /evidence="ECO:0000269|PubMed:17951247"
FT MUTAGEN 368
FT /note="D->A: Decrease in phosphodiesterase activity,
FT hemolysin production and virulence in silkworm-infection
FT model."
FT /evidence="ECO:0000269|PubMed:17951247"
FT MUTAGEN 371
FT /note="K->A: Decrease in phosphodiesterase activity,
FT hemolysin production and virulence in silkworm-infection
FT model."
FT /evidence="ECO:0000269|PubMed:17951247"
FT MUTAGEN 423
FT /note="D->A: Decrease in phosphodiesterase activity,
FT hemolysin and DNase production and virulence in silkworm-
FT infection model."
FT /evidence="ECO:0000269|PubMed:15853881,
FT ECO:0000269|PubMed:17951247"
SQ SEQUENCE 519 AA; 58512 MW; 076DE375A553FFA3 CRC64;
MNLLSLLLIL LGIILGVVGG YVVARNLLLQ KQSQARQTAE DIVNQAHKEA DNIKKEKLLE
AKEENQILRE QTEAELRERR SELQRQETRL LQKEENLERK SDLLDKKDEI LEQKESKIEE
KQQQVDAKES SVQTLIMKHE QELERISGLT QEEAINEQLQ RVEEELSQDI AVLVKEKEKE
AKEKVDKTAK ELLATAVQRL AADHTSESTV SVVNLPNDEM KGRIIGREGR NIRTLETLTG
IDLIIDDTPE AVILSGFDPI RREIARTALV NLVSDGRIHP GRIEDMVEKA RKEVDDIIRE
AGEQATFEVN AHNMHPDLVK IVGRLNYRTS YGQNVLKHSI EVAHLASMLA AELGEDETLA
KRAGLLHDVG KAIDHEVEGS HVEIGVELAK KYGENETVIN AIHSHHGDVE PTSIISILVA
AADALSAARP GARKETLENY IRRLERLETL SESYDGVEKA FAIQAGREIR VIVSPEEIDD
LKSYRLARDI KNQIEDELQY PGHIKVTVVR ETRAVEYAK
