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Protein

Ribonuclease-like 3

Gene

rnasel3

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Ribonuclease. Angiogenic. Plays a role in host defense. Exhibits strong antibacterial activity against Gram-negative bacteria but mild antibacterial activity against Gram-positive bacteria. The RNase activity is not required for the bactericidal activity.4 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei38 – 381Proton acceptor1 Publication
Active sitei142 – 1421Proton donor1 Publication

GO - Molecular functioni

  • endonuclease activity Source: UniProtKB-KW
  • ribonuclease activity Source: ZFIN
  • RNA binding Source: ZFIN

GO - Biological processi

  • angiogenesis Source: UniProtKB-KW
  • cell differentiation Source: UniProtKB-KW
  • defense response to Gram-negative bacterium Source: ZFIN
  • defense response to Gram-positive bacterium Source: ZFIN
  • immune system process Source: UniProtKB-KW
  • RNA phosphodiester bond hydrolysis Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

Antibiotic, Antimicrobial, Developmental protein, Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Angiogenesis, Differentiation, Immunity

Enzyme and pathway databases

BRENDAi3.1.27.5. 928.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease-like 31 Publication (EC:3.1.27.-)
Short name:
RNase ZF-31 Publication
Short name:
RNase-like 31 Publication
Short name:
ZF-RNase-31 Publication
Alternative name(s):
Dr-RNase 11 Publication
Cleaved into the following 2 chains:
N-terminal peptide1 Publication
LF-ZF31 Publication
Gene namesi
Name:rnasel3Imported
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-050809-5. rnasel3.

Subcellular locationi

  • Secreted By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 22221 PublicationAdd
BLAST
Chaini23 – 149127Ribonuclease-like 3Sequence analysisPRO_0000394404Add
BLAST
Peptidei23 – 5533N-terminal peptide1 PublicationPRO_0000394405Add
BLAST
Peptidei56 – 14994LF-ZF31 PublicationPRO_0000394406Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei23 – 231Pyrrolidone carboxylic acidBy similarity
Disulfide bondi48 ↔ 1091 Publication
Disulfide bondi66 ↔ 1201 Publication
Disulfide bondi84 ↔ 1351 Publication

Post-translational modificationi

Cleavage between Arg-55 and Arg-56 is catalyzed by a membrane-localized Gram-negative bacterium protease (OmpT in E.coli). The excised fragment is then transported to the bacterium cytosol for cleavage of the disulfide bridge linking Cys-48 and Cys-109, thus separating the N-terminal and LF-ZF3. LF-ZF3 but not the N-terminal peptide possesses bactericidal activity.1 Publication

Keywords - PTMi

Disulfide bond, Pyrrolidone carboxylic acid

Proteomic databases

PaxDbiA5HAK0.

Expressioni

Tissue specificityi

Strongly expressed in the adult liver and gut, and weakly in the heart and testis.1 Publication

Developmental stagei

Only expressed in adults.1 Publication

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000123763.

Structurei

Secondary structure

1
149
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi28 – 3811Combined sources
Helixi48 – 547Combined sources
Beta strandi58 – 636Combined sources
Beta strandi68 – 758Combined sources
Helixi77 – 815Combined sources
Helixi82 – 843Combined sources
Beta strandi87 – 904Combined sources
Beta strandi92 – 943Combined sources
Beta strandi97 – 1026Combined sources
Beta strandi104 – 11310Combined sources
Beta strandi121 – 13616Combined sources
Beta strandi139 – 1479Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2VQ9X-ray1.85A23-149[»]
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiA5HAK0.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni67 – 715Substrate binding1 Publication

Sequence similaritiesi

Belongs to the pancreatic ribonuclease family.Sequence analysis

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410IZBW. Eukaryota.
ENOG410Y4FD. LUCA.
HOGENOMiHOG000276883.
HOVERGENiHBG008396.
InParanoidiA5HAK0.
KOiK16631.
PhylomeDBiA5HAK0.

Family and domain databases

Gene3Di3.10.130.10. 1 hit.
InterProiIPR001427. RNaseA.
IPR023411. RNaseA_AS.
IPR023412. RNaseA_domain.
[Graphical view]
PANTHERiPTHR11437. PTHR11437. 1 hit.
PfamiPF00074. RnaseA. 1 hit.
[Graphical view]
PRINTSiPR00794. RIBONUCLEASE.
SMARTiSM00092. RNAse_Pc. 1 hit.
[Graphical view]
SUPFAMiSSF54076. SSF54076. 1 hit.
PROSITEiPS00127. RNASE_PANCREATIC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

A5HAK0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGIHQCTAVV LLLLCASLST YGQPAEIRRR YEHFLTQHVY GGITEQTCDR
60 70 80 90 100
VMRQRRITRF PTGNDCKEVN TFIQANGNHV RTVCTGGGTR QTDNRDLYMS
110 120 130 140
NNQFTVITCT LRSGERHPNC RYRGKESSRK IVVACEGEWP THYEKGVIV
Length:149
Mass (Da):17,011
Last modified:June 15, 2010 - v2
Checksum:i096E21A32D5B6479
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti25 – 251A → M no nucleotide entry (PubMed:16861230).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti5 – 51Q → R in allele ZF-3d and allele ZF-3e. 1 Publication
Natural varianti56 – 561R → G in allele ZF-3a and allele ZF-3c. 2 Publications
Natural varianti93 – 931D → E in allele ZF-3c. 1 Publication
Natural varianti102 – 1021N → D in allele ZF-3e. 1 Publication
Natural varianti137 – 1371G → S in allele ZF-3c. 1 Publication
Natural varianti141 – 1411T → A in allele ZF-3e. 1 Publication
Natural varianti145 – 1451K → R in allele ZF-3d and allele ZF-3e. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF382669 mRNA. Translation: ABQ23783.1.
BX465197 Genomic DNA. No translation available.
RefSeqiNP_001092923.1. NM_001099453.1.
UniGeneiDr.134029.

Genome annotation databases

GeneIDi798787.
KEGGidre:798787.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF382669 mRNA. Translation: ABQ23783.1.
BX465197 Genomic DNA. No translation available.
RefSeqiNP_001092923.1. NM_001099453.1.
UniGeneiDr.134029.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2VQ9X-ray1.85A23-149[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000123763.

Proteomic databases

PaxDbiA5HAK0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi798787.
KEGGidre:798787.

Organism-specific databases

CTDi798787.
ZFINiZDB-GENE-050809-5. rnasel3.

Phylogenomic databases

eggNOGiENOG410IZBW. Eukaryota.
ENOG410Y4FD. LUCA.
HOGENOMiHOG000276883.
HOVERGENiHBG008396.
InParanoidiA5HAK0.
KOiK16631.
PhylomeDBiA5HAK0.

Enzyme and pathway databases

BRENDAi3.1.27.5. 928.

Miscellaneous databases

EvolutionaryTraceiA5HAK0.
PROiA5HAK0.

Family and domain databases

Gene3Di3.10.130.10. 1 hit.
InterProiIPR001427. RNaseA.
IPR023411. RNaseA_AS.
IPR023412. RNaseA_domain.
[Graphical view]
PANTHERiPTHR11437. PTHR11437. 1 hit.
PfamiPF00074. RnaseA. 1 hit.
[Graphical view]
PRINTSiPR00794. RIBONUCLEASE.
SMARTiSM00092. RNAse_Pc. 1 hit.
[Graphical view]
SUPFAMiSSF54076. SSF54076. 1 hit.
PROSITEiPS00127. RNASE_PANCREATIC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Zebrafish ribonucleases are bactericidal: implications for the origin of the vertebrate RNase A superfamily."
    Cho S., Zhang J.
    Mol. Biol. Evol. 24:1259-1268(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ALLELE ZF-3C), FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, VARIANTS GLY-56; GLU-93 AND SER-137.
    Strain: AB1 Publication.
  2. "Ribonuclease A homologues of the zebrafish: polymorphism, crystal structures of two representatives and their evolutionary implications."
    Kazakou K., Holloway D.E., Prior S.H., Subramanian V., Acharya K.R.
    J. Mol. Biol. 380:206-222(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ALLELES ZF-3D AND ZF-3E), FUNCTION, X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 23-149 (ALLELE ZF-3E), VARIANTS ARG-5; ASP-102; ALA-141 AND ARG-145.
  3. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (ALLELE ZF-3A), VARIANT GLY-56.
    Strain: Tuebingen.
  4. Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 25-148 (ALLELE ZF-3B), FUNCTION.
  5. "The bactericidal action on Escherichia coli of ZF-RNase-3 is triggered by the suicidal action of the bacterium OmpT protease."
    Zanfardino A., Pizzo E., Di Maro A., Varcamonti M., D'Alessio G.
    FEBS J. 277:1921-1928(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 56-63 (ALLELE ZF-3B), FUNCTION, CLEAVAGE AT ARG-56.
  6. "The success of the RNase scaffold in the advance of biosciences and in evolution."
    Pizzo E., D'Alessio G.
    Gene 406:8-12(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.

Entry informationi

Entry nameiRNSL3_DANRE
AccessioniPrimary (citable) accession number: A5HAK0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 15, 2010
Last sequence update: June 15, 2010
Last modified: June 8, 2016
This is version 60 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

Although the OmpT protease is absent in Gram-positive bacteria, LF-ZF3 generated by a Gram-negative bacterium can penetrate a Gram-positive bacterium and exert its cytotoxicity.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.