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Q9YBF1

- ENDA_AERPE

UniProt

Q9YBF1 - ENDA_AERPE

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Protein
tRNA-splicing endonuclease
Gene
endA, APE_1646.1
Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Status
Reviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

Functioni

Endonuclease that removes tRNA introns. 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. Recognizes a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp By similarity.UniRule annotation

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.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei125 – 1251 By similarity
Active sitei133 – 1331 By similarity
Active sitei164 – 1641 By similarity

GO - Molecular functioni

  1. lyase activity Source: UniProtKB-KW
  2. nucleic acid binding Source: InterPro
  3. tRNA-intron endonuclease activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. tRNA splicing, via endonucleolytic cleavage and ligation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

tRNA processing

Enzyme and pathway databases

BioCyciAPER272557:GJD6-1118-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-splicing endonuclease (EC:4.6.1.16)
Alternative name(s):
tRNA-intron endonuclease
Gene namesi
Name:endA
Ordered Locus Names:APE_1646.1
OrganismiAeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Taxonomic identifieri272557 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeAeropyrum
ProteomesiUP000002518: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 186186tRNA-splicing endonucleaseUniRule annotation
PRO_0000109469Add
BLAST

Interactioni

Subunit structurei

Homotetramer; although the tetramer contains four active sites, only two participate in the cleavage. Therefore, it should be considered as a dimer of dimers By similarity.

Protein-protein interaction databases

STRINGi272557.APE_1646.1.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 156
Beta strandi18 – 214
Helixi24 – 329
Beta strandi37 – 415
Beta strandi54 – 574
Helixi58 – 669
Beta strandi69 – 735
Helixi82 – 909
Helixi93 – 10715
Beta strandi111 – 1144
Helixi116 – 1183
Beta strandi120 – 1278
Turni129 – 1313
Beta strandi132 – 1343
Beta strandi136 – 1416
Helixi150 – 15910
Turni160 – 1623
Beta strandi164 – 1729
Beta strandi175 – 1839

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3AJVX-ray1.70B/D1-186[»]
3P1YX-ray2.05A/B/C/D39-53[»]
3P1ZX-ray2.80B/D/F/H/J/L1-186[»]
ProteinModelPortaliQ9YBF1.

Miscellaneous databases

EvolutionaryTraceiQ9YBF1.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1676.
HOGENOMiHOG000107823.
KOiK01170.

Family and domain databases

Gene3Di3.40.1350.10. 1 hit.
HAMAPiMF_01833. EndA_short.
InterProiIPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006678. tRNA_intron_Endonuc_N.
IPR006676. tRNA_splic.
IPR016442. tRNA_splic_arch_short.
[Graphical view]
PfamiPF01974. tRNA_int_endo. 1 hit.
PF02778. tRNA_int_endo_N. 1 hit.
[Graphical view]
PIRSFiPIRSF005285. tRNA_splic_archaea. 1 hit.
SUPFAMiSSF53032. SSF53032. 1 hit.
SSF55267. SSF55267. 1 hit.
TIGRFAMsiTIGR00324. endA. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9YBF1-1 [UniParc]FASTAAdd to Basket

« Hide

MGDRCAPIKA SGVLIGDSVL VTDVEQARSL YSCGYYGQPL DVEKPRGADF    50
EGPLRLSLIE SLYLAEKGVL EVAKPDGSSV GVEDLRTAVR GNPRFSMLYN 100
IYRDLRERGF VVRSGLKFGS DFAVYRLGPG IDHAPFIVHA YSPEDNIDPV 150
EIVRAGRLSH SVRKKFVFAV TRGGDVSYLM IDWFRP 186
Length:186
Mass (Da):20,602
Last modified:June 26, 2007 - v2
Checksum:i3377457A91F479B9
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000002 Genomic DNA. Translation: BAA80647.2.
PIRiB72545.
RefSeqiNP_148074.2. NC_000854.2.

Genome annotation databases

EnsemblBacteriaiBAA80647; BAA80647; APE_1646.1.
GeneIDi1446148.
KEGGiape:APE_1646.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000002 Genomic DNA. Translation: BAA80647.2 .
PIRi B72545.
RefSeqi NP_148074.2. NC_000854.2.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3AJV X-ray 1.70 B/D 1-186 [» ]
3P1Y X-ray 2.05 A/B/C/D 39-53 [» ]
3P1Z X-ray 2.80 B/D/F/H/J/L 1-186 [» ]
ProteinModelPortali Q9YBF1.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 272557.APE_1646.1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAA80647 ; BAA80647 ; APE_1646.1 .
GeneIDi 1446148.
KEGGi ape:APE_1646.1.

Phylogenomic databases

eggNOGi COG1676.
HOGENOMi HOG000107823.
KOi K01170.

Enzyme and pathway databases

BioCyci APER272557:GJD6-1118-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q9YBF1.

Family and domain databases

Gene3Di 3.40.1350.10. 1 hit.
HAMAPi MF_01833. EndA_short.
InterProi IPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006678. tRNA_intron_Endonuc_N.
IPR006676. tRNA_splic.
IPR016442. tRNA_splic_arch_short.
[Graphical view ]
Pfami PF01974. tRNA_int_endo. 1 hit.
PF02778. tRNA_int_endo_N. 1 hit.
[Graphical view ]
PIRSFi PIRSF005285. tRNA_splic_archaea. 1 hit.
SUPFAMi SSF53032. SSF53032. 1 hit.
SSF55267. SSF55267. 1 hit.
TIGRFAMsi TIGR00324. endA. 1 hit.
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1.

Entry informationi

Entry nameiENDA_AERPE
AccessioniPrimary (citable) accession number: Q9YBF1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: June 26, 2007
Last modified: June 11, 2014
This is version 72 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

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

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