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Protein

Ribonuclease U2

Gene

RNU2

Organism
Ustilago sphaerogena (Smut fungus)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

Two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in A-P or G-P with 2',3'-cyclic phosphate intermediates.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi29 – 291Calcium 11 Publication
Metal bindingi29 – 291Calcium 21 Publication
Metal bindingi30 – 301Calcium 1; via carbonyl oxygen1 Publication
Metal bindingi31 – 311Calcium 2; via carbonyl oxygen1 Publication
Metal bindingi32 – 321Calcium 11 Publication
Metal bindingi32 – 321Calcium 21 Publication
Metal bindingi37 – 371Calcium 11 Publication
Metal bindingi39 – 391Calcium 2; via carbonyl oxygen1 Publication
Active sitei41 – 4111 Publication
Active sitei62 – 621Proton acceptor1 Publication
Sitei62 – 621Methylation inactivates enzyme1 Publication
Binding sitei85 – 851Substrate
Active sitei101 – 1011Proton donor1 Publication

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. ribonuclease U2 activity Source: UniProtKB-EC
  3. RNA binding Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BRENDAi3.1.27.4. 6588.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease U2 (EC:3.1.27.4)
Short name:
RNase U2
Gene namesi
Name:RNU2
OrganismiUstilago sphaerogena (Smut fungus)
Taxonomic identifieri5271 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaBasidiomycotaUstilaginomycotinaUstilaginomycetesUstilaginalesUstilaginaceaeUstilago

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 114114Ribonuclease U2PRO_0000137379Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi1 ↔ 541 Publication
Disulfide bondi9 ↔ 1131 Publication
Disulfide bondi55 ↔ 961 Publication

Keywords - PTMi

Disulfide bond

Structurei

Secondary structure

1
114
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 95Combined sources
Beta strandi12 – 154Combined sources
Helixi16 – 3116Combined sources
Helixi36 – 383Combined sources
Beta strandi41 – 433Combined sources
Helixi47 – 493Combined sources
Beta strandi60 – 645Combined sources
Beta strandi75 – 773Combined sources
Beta strandi83 – 897Combined sources
Turni90 – 923Combined sources
Beta strandi95 – 1017Combined sources
Beta strandi105 – 1095Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RTUX-ray1.80A1-114[»]
3AGNX-ray0.96A1-114[»]
3AGOX-ray0.99A1-114[»]
3AHSX-ray1.32A/B/C1-114[»]
3AHWX-ray1.03A1-114[»]
ProteinModelPortaliP00654.
SMRiP00654. Positions 1-114.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00654.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni39 – 4911Substrate bindingAdd
BLAST
Regioni108 – 1103Substrate binding

Sequence similaritiesi

Belongs to the ribonuclease U2 family.Curated

Family and domain databases

Gene3Di3.10.450.30. 1 hit.
InterProiIPR000026. Gua-sp_ribonuclease_N1/T1.
IPR016191. Ribonuclease/ribotoxin.
[Graphical view]
PfamiPF00545. Ribonuclease. 1 hit.
[Graphical view]
SUPFAMiSSF53933. SSF53933. 1 hit.

Sequencei

Sequence statusi: Complete.

P00654-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
CDIPQSTNCG GNVYSNDDIN TAIQGALDDV ANGDRPDNYP HQYYDEASED
60 70 80 90 100
ITLCCGSGPW SEFPLVYNGP YYSSRDNYVS PGPDRVIYQT NTGEFCATVT
110
HTGAASYDGF TQCS
Length:114
Mass (Da):12,387
Last modified:December 15, 1998 - v4
Checksum:i96D32CB2E23AAB98
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ004827 Genomic DNA. Translation: CAC04098.1.
PIRiPC4081. NRUSU2.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ004827 Genomic DNA. Translation: CAC04098.1.
PIRiPC4081. NRUSU2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RTUX-ray1.80A1-114[»]
3AGNX-ray0.96A1-114[»]
3AGOX-ray0.99A1-114[»]
3AHSX-ray1.32A/B/C1-114[»]
3AHWX-ray1.03A1-114[»]
ProteinModelPortaliP00654.
SMRiP00654. Positions 1-114.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.1.27.4. 6588.

Miscellaneous databases

EvolutionaryTraceiP00654.
PROiP00654.

Family and domain databases

Gene3Di3.10.450.30. 1 hit.
InterProiIPR000026. Gua-sp_ribonuclease_N1/T1.
IPR016191. Ribonuclease/ribotoxin.
[Graphical view]
PfamiPF00545. Ribonuclease. 1 hit.
[Graphical view]
SUPFAMiSSF53933. SSF53933. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "The amino acid sequence of ribonuclease U2 from Ustilago sphaerogena."
    Sato S., Uchida T.
    Biochem. J. 145:353-360(1975) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE.
  2. "Ribonuclease U2: cloning, production in Pichia pastoris and affinity chromatography purification of the active recombinant protein."
    Martinez-Ruiz A., Garcia-Ortega L., Kao R., Onaderra M., Mancheno J.M., Davies J., Martinez del Pozo A., Gavilanes J.G.
    FEMS Microbiol. Lett. 189:165-169(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 15-106.
    Strain: ATCC 12421 / CBS 534.71 / IMI 61828 / 50-135.
  3. "Revised sequence of ribonuclease U2 in the substrate-binding region."
    Kanaya S., Uchida T.
    J. Biochem. 118:681-682(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 44-53, SEQUENCE REVISION.
  4. "The disulfide bridges of ribonuclease U2 from Ustilago sphaerogena."
    Sato S., Uchida T.
    J. Biochem. 77:1171-1176(1975) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISULFIDE BONDS.
  5. Uchida T., Sato S.
    (In) Zelinka J., Balan J. (eds.); Ribosomes and RNA metabolism, pp.453-472, Publ. House Slovak Acad. Sci., Bratislava (1973)
    Cited for: ACTIVE SITE.
  6. "Crystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8-A resolution."
    Noguchi S., Satow Y., Uchida T., Sasaki C., Matsuzaki T.
    Biochemistry 34:15583-15591(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), SEQUENCE REVISION.
  7. "Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate."
    Noguchi S.
    Acta Crystallogr. D 66:843-849(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (0.96 ANGSTROMS) IN COMPLEX WITH CALCIUM IONS AND ADENOSINE 3'-MONOPHOSPHATE, FORMATION OF ISOASPARTATE, DISULFIDE BONDS.
  8. "Structural changes induced by the deamidation and isomerization of asparagine revealed by the crystal structure of Ustilago sphaerogena ribonuclease U2B."
    Noguchi S.
    Biopolymers 93:1003-1010(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.32 ANGSTROMS).
  9. "Conformational variation revealed by the crystal structure of RNase U2A complexed with Ca ion and 2'-adenylic acid at 1.03 A resolution."
    Noguchi S.
    Protein Pept. Lett. 17:1559-1561(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.03 ANGSTROMS) IN COMPLEX WITH CALCIUM AND ADENOSINE 2'-PHOSPHATE.

Entry informationi

Entry nameiRNU2_USTSP
AccessioniPrimary (citable) accession number: P00654
Secondary accession number(s): Q9HGK7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: December 15, 1998
Last modified: November 26, 2014
This is version 88 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

After treatment by base Asn-32 and Asp-45 partially isomerise by succinimide rearrangement to form iosaspartyl peptides.

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.