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Protein

Probable tRNA-splicing endonuclease subunit Sen2

Gene

Os06g0530700

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Constitutes one of the two catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3'-cyclic phosphate and 5'-OH termini. There are no conserved sequences at the splice sites, but the intron is invariably located at the same site in the gene, placing the splice sites an invariant distance from the constant structural features of the tRNA body. Probably carries the active site for 5'-splice site cleavage (By similarity).By similarity

Catalytic activityi

PretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei157 – 1571By similarity
Active sitei165 – 1651By similarity
Active sitei204 – 2041By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

mRNA processing, tRNA processing

Names & Taxonomyi

Protein namesi
Recommended name:
Probable tRNA-splicing endonuclease subunit Sen2 (EC:4.6.1.16)
Alternative name(s):
tRNA-intron endonuclease Sen2
Gene namesi
Ordered Locus Names:Os06g0530700, LOC_Os06g33980
ORF Names:P0410C01.17, P0438E12.38
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryza
Proteomesi
  • UP000059680 Componenti: Chromosome 6

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei267 – 28721HelicalSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 293293Probable tRNA-splicing endonuclease subunit Sen2PRO_0000109458Add
BLAST

Proteomic databases

PaxDbiQ5Z6B1.

Expressioni

Gene expression databases

ExpressionAtlasiQ5Z6B1. baseline and differential.
GenevisibleiQ5Z6B1. OS.

Interactioni

Subunit structurei

tRNA splicing endonuclease is a heterotetramer composed of SEN2, SEN15, SEN34/LENG5 and SEN54.By similarity

Protein-protein interaction databases

STRINGi39947.LOC_Os06g33980.1.

Structurei

3D structure databases

ProteinModelPortaliQ5Z6B1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi170 – 1734Poly-Val
Compositional biasi212 – 2154Poly-Ser

Sequence similaritiesi

Belongs to the tRNA-intron endonuclease family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG4685. Eukaryota.
COG1676. LUCA.
InParanoidiQ5Z6B1.
KOiK15322.

Family and domain databases

Gene3Di3.40.1350.10. 1 hit.
InterProiIPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006678. tRNA_intron_Endonuc_N.
IPR006676. tRNA_splic.
[Graphical view]
PANTHERiPTHR21227. PTHR21227. 1 hit.
PfamiPF01974. tRNA_int_endo. 1 hit.
PF02778. tRNA_int_endo_N. 1 hit.
[Graphical view]
SUPFAMiSSF53032. SSF53032. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5Z6B1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDLPGPRWKK GKDGKDFASL AAANPMSAIV SELKASFISS KPVAILSGPG
60 70 80 90 100
GSAVLGVGPE QAVILNRAAF GHAIENATAQ KHWFQLSPEE VFYLCHALNC
110 120 130 140 150
IRVDSLDNKQ MSEIELWDYF RSGSESFPEM YKAYAHLRLK NWVVRSGLQY
160 170 180 190 200
GADFVAYRHH PALVHSEFAV VVVPEGAEFG NRCGRLEVWS DLLCALRASG
210 220 230 240 250
SVAKTLLVLT ISSSSKCELS SPDCLEQLVV HERTITRWIL QQCREQRCEP
260 270 280 290
SRDEVNREEL IIEKESVVFN HWGVILGFTV LSGLLVYRLK FRQ
Length:293
Mass (Da):32,737
Last modified:November 23, 2004 - v1
Checksum:i673DE4101F5408C1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP004749 Genomic DNA. Translation: BAD54220.1.
AP005450 Genomic DNA. Translation: BAD54480.1.
AP008212 Genomic DNA. Translation: BAF19695.1.
AP014962 Genomic DNA. Translation: BAS98061.1.
AK059057 mRNA. Translation: BAG86882.1.
AK102915 mRNA. Translation: BAG95781.1.
RefSeqiXP_015641868.1. XM_015786382.1.
XP_015641869.1. XM_015786383.1.
XP_015641870.1. XM_015786384.1.
XP_015641871.1. XM_015786385.1.
UniGeneiOs.24713.

Genome annotation databases

EnsemblPlantsiOS06T0530700-02; OS06T0530700-02; OS06G0530700.
GeneIDi4341203.
GrameneiOS06T0530700-02; OS06T0530700-02; OS06G0530700.
KEGGiosa:4341203.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP004749 Genomic DNA. Translation: BAD54220.1.
AP005450 Genomic DNA. Translation: BAD54480.1.
AP008212 Genomic DNA. Translation: BAF19695.1.
AP014962 Genomic DNA. Translation: BAS98061.1.
AK059057 mRNA. Translation: BAG86882.1.
AK102915 mRNA. Translation: BAG95781.1.
RefSeqiXP_015641868.1. XM_015786382.1.
XP_015641869.1. XM_015786383.1.
XP_015641870.1. XM_015786384.1.
XP_015641871.1. XM_015786385.1.
UniGeneiOs.24713.

3D structure databases

ProteinModelPortaliQ5Z6B1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os06g33980.1.

Proteomic databases

PaxDbiQ5Z6B1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiOS06T0530700-02; OS06T0530700-02; OS06G0530700.
GeneIDi4341203.
GrameneiOS06T0530700-02; OS06T0530700-02; OS06G0530700.
KEGGiosa:4341203.

Phylogenomic databases

eggNOGiKOG4685. Eukaryota.
COG1676. LUCA.
InParanoidiQ5Z6B1.
KOiK15322.

Gene expression databases

ExpressionAtlasiQ5Z6B1. baseline and differential.
GenevisibleiQ5Z6B1. OS.

Family and domain databases

Gene3Di3.40.1350.10. 1 hit.
InterProiIPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006678. tRNA_intron_Endonuc_N.
IPR006676. tRNA_splic.
[Graphical view]
PANTHERiPTHR21227. PTHR21227. 1 hit.
PfamiPF01974. tRNA_int_endo. 1 hit.
PF02778. tRNA_int_endo_N. 1 hit.
[Graphical view]
SUPFAMiSSF53032. SSF53032. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  2. "The rice annotation project database (RAP-DB): 2008 update."
    The rice annotation project (RAP)
    Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  3. Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  4. "Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice."
    The rice full-length cDNA consortium
    Science 301:376-379(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Nipponbare.

Entry informationi

Entry nameiSEN2_ORYSJ
AccessioniPrimary (citable) accession number: Q5Z6B1
Secondary accession number(s): Q0DBS8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: November 23, 2004
Last modified: July 6, 2016
This is version 70 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  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.