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Protein

Ribonuclease Y

Gene

rny

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Endoribonuclease that initiates mRNA decay. Initiates the decay of all SAM-dependent riboswitches, such as yitJ riboswitch. Involved in processing of the gapA operon mRNA, it cleaves between cggR and gapA (PubMed:19193632). Is also the decay-initiating endonuclease for rpsO mRNA.5 Publications

Cofactori

Mg2+1 Publication, Mn2+1 Publication, Zn2+1 PublicationNote: Magnesium. Can also use manganese or zinc.1 Publication

Enzyme regulationi

Shows preference for transcripts carrying a monophosphate group at the 5' end.1 Publication

GO - Molecular functioni

  • endoribonuclease activity Source: UniProtKB-HAMAP
  • identical protein binding Source: IntAct
  • RNA binding Source: UniProtKB-HAMAP

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciBSUB:BSU16960-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease Y (EC:3.1.-.-)
Short name:
RNase Y
Gene namesi
Name:rny
Synonyms:ymdA
Ordered Locus Names:BSU16960
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 3ExtracellularSequence analysis3
Transmembranei4 – 24HelicalSequence analysisAdd BLAST21
Topological domaini25 – 520CytoplasmicSequence analysisAdd BLAST496

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

Essential; depletion mutants show a significant increase in global mRNA half-life (PubMed:19779461) a decrease in at least 1 specific mRNA processing event (PubMed:19193632); in a more severe depletion experiment alteration of about 26% of transcripts was seen (PubMed:22412379). Later shown not to be essential in 4 strains, with a doubled doubling time, cells are translucent, suggesting a possible cell surface defect. 168 trpC2 cells able to grow on minimal medium. Loss of competence for plasmid transformation, 1000-fold less sporulation. Increased sensitivity to a wide range of antibiotics. Thinner cells form long curved structures of 2-3 cell lengths, cell walls are altered with looser, considerably less dense peptidoglycan. Double pnp-rny mutants grow very slowly, while rnjA-rny mutants could not be isolated (PubMed:23504012).4 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1 – 26MTPIM…YFVRK → MEFVIGLLIVLLALFAAGYF F: Increased protein expression (replaces with transmembrane helix from EzrA). Add BLAST26
Mutagenesisi368H → A: Impairs cleavage of the yitJ riboswitch. 1 Publication1
Mutagenesisi369D → A: Impairs cleavage of the yitJ riboswitch. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001637651 – 520Ribonuclease YAdd BLAST520

Proteomic databases

PaxDbiO31774.
PRIDEiO31774.

Interactioni

Subunit structurei

Homodimer (Probable). Component of a possible RNA degradosome complex composed of rny, rnjA, rnjB, pnp, pfkA and eno (PubMed:19193632) (although rnjA and rnjB's presence is unclear). Interacts with RNA helicase CshA which may also be a member of the RNA degradosome complex (PubMed:20572937).Curated4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself4EBI-6415578,EBI-6415578
cshAP966142EBI-6415578,EBI-6415210
enoP378692EBI-6415578,EBI-6415666
pfkAO345292EBI-6415578,EBI-5250040
pnpP508492EBI-6415578,EBI-5254714
rnjAQ454932EBI-6415578,EBI-6415229

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

IntActiO31774. 6 interactors.
STRINGi224308.Bsubs1_010100009331.

Structurei

3D structure databases

ProteinModelPortaliO31774.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini210 – 273KHAdd BLAST64
Domaini337 – 428HDAdd BLAST92

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili29 – 141Sequence analysisAdd BLAST113

Domaini

Has 5 domains: N-terminal transmembrane, coiled-coil, KH, HD and an unnamed conserved C-terminal domain (residues 430-520). Both the N-terminal transmembrane helix and C-terminal domain are required for protein function in vivo.1 Publication

Sequence similaritiesi

Belongs to the RNase Y family.Curated
Contains 1 HD domain.Curated
Contains 1 KH domain.Curated

Keywords - Domaini

Coiled coil, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105E4Y. Bacteria.
COG1418. LUCA.
HOGENOMiHOG000221256.
InParanoidiO31774.
KOiK18682.
OMAiYYARGQA.
PhylomeDBiO31774.

Family and domain databases

Gene3Di1.10.3210.10. 1 hit.
3.30.1370.10. 1 hit.
HAMAPiMF_00335. RNase_Y. 1 hit.
InterProiIPR003607. HD/PDEase_dom.
IPR006674. HD_domain.
IPR006675. HDIG_dom.
IPR004087. KH_dom.
IPR004088. KH_dom_type_1.
IPR017705. Ribonuclease_Y.
IPR022711. RNase_Y_N.
[Graphical view]
PfamiPF12072. DUF3552. 1 hit.
PF01966. HD. 1 hit.
PF00013. KH_1. 1 hit.
[Graphical view]
SMARTiSM00471. HDc. 1 hit.
SM00322. KH. 1 hit.
[Graphical view]
SUPFAMiSSF54791. SSF54791. 1 hit.
TIGRFAMsiTIGR00277. HDIG. 1 hit.
TIGR03319. RNase_Y. 1 hit.
PROSITEiPS50084. KH_TYPE_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O31774-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTPIMMVLIS ILLILLGLVV GYFVRKTIAE AKIAGARGAA EQILEDAKRD
60 70 80 90 100
AEALKKEALL EAKDEIHKLR IDAEQEVRER RNELQKQENR LLQKEENLDR
110 120 130 140 150
KHEGIDKREA MLEKKDHSLN ERQQHIEEME SKVDEMIRMQ QSELERISSL
160 170 180 190 200
TRDEAKQIIL ERVENELSHD IAIMTKETEN RAKEEADKKA KNILSLALQR
210 220 230 240 250
CAADHVAETT VSVVNLPNDE MKGRIIGREG RNIRTLETLT GIDLIIDDTP
260 270 280 290 300
EAVILSGFDP IRRETARIAL DKLVQDGRIH PARIEEMVEK SRREVDDYIR
310 320 330 340 350
EMGEQTTFEV GVHGLHPDLI KILGRLKFRT SYGQNVLKHS MEVAFLAGLM
360 370 380 390 400
ASELGEDAKL AKRAGLLHDI GKAIDHEVEG SHVEIGVELA TKYKEHPVVI
410 420 430 440 450
NSIASHHGDE EPTSIIAVLV AAADALSAAR PGARSETLEN YIRRLEKLEE
460 470 480 490 500
ISESYEGVEK SFAIQAGREV RIMVKPDSIN DLEAHRLARD IRKRIEDELD
510 520
YPGHIKVTVI RETRAVEYAK
Length:520
Mass (Da):58,919
Last modified:January 1, 1998 - v1
Checksum:iC137937C7665C58C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL009126 Genomic DNA. Translation: CAB13569.1.
PIRiF69884.
RefSeqiNP_389578.1. NC_000964.3.
WP_003221010.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB13569; CAB13569; BSU16960.
GeneIDi11239548.
939680.
KEGGibsu:BSU16960.
PATRICi18975199. VBIBacSub10457_1791.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL009126 Genomic DNA. Translation: CAB13569.1.
PIRiF69884.
RefSeqiNP_389578.1. NC_000964.3.
WP_003221010.1. NZ_JNCM01000035.1.

3D structure databases

ProteinModelPortaliO31774.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO31774. 6 interactors.
STRINGi224308.Bsubs1_010100009331.

Proteomic databases

PaxDbiO31774.
PRIDEiO31774.

Protocols and materials databases

DNASUi939680.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13569; CAB13569; BSU16960.
GeneIDi11239548.
939680.
KEGGibsu:BSU16960.
PATRICi18975199. VBIBacSub10457_1791.

Phylogenomic databases

eggNOGiENOG4105E4Y. Bacteria.
COG1418. LUCA.
HOGENOMiHOG000221256.
InParanoidiO31774.
KOiK18682.
OMAiYYARGQA.
PhylomeDBiO31774.

Enzyme and pathway databases

BioCyciBSUB:BSU16960-MONOMER.

Family and domain databases

Gene3Di1.10.3210.10. 1 hit.
3.30.1370.10. 1 hit.
HAMAPiMF_00335. RNase_Y. 1 hit.
InterProiIPR003607. HD/PDEase_dom.
IPR006674. HD_domain.
IPR006675. HDIG_dom.
IPR004087. KH_dom.
IPR004088. KH_dom_type_1.
IPR017705. Ribonuclease_Y.
IPR022711. RNase_Y_N.
[Graphical view]
PfamiPF12072. DUF3552. 1 hit.
PF01966. HD. 1 hit.
PF00013. KH_1. 1 hit.
[Graphical view]
SMARTiSM00471. HDc. 1 hit.
SM00322. KH. 1 hit.
[Graphical view]
SUPFAMiSSF54791. SSF54791. 1 hit.
TIGRFAMsiTIGR00277. HDIG. 1 hit.
TIGR03319. RNase_Y. 1 hit.
PROSITEiPS50084. KH_TYPE_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRNY_BACSU
AccessioniPrimary (citable) accession number: O31774
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: January 1, 1998
Last modified: October 5, 2016
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.