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Protein

tRNA-splicing endonuclease

Gene

endA

Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Status
Reviewed-Annotation score: -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.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)DescriptionActionsGraphical viewLength
Active sitei125UniRule annotation1
Active sitei133UniRule annotation1
Active sitei164UniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLyase
Biological processtRNA processing

Enzyme and pathway databases

BRENDAi4.6.1.16 171

Names & Taxonomyi

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001094691 – 186tRNA-splicing endonucleaseAdd BLAST186

Proteomic databases

PRIDEiQ9YBF1

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.UniRule annotation

Protein-protein interaction databases

STRINGi272557.APE_1646.1

Structurei

Secondary structure

1186
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 15Combined sources6
Beta strandi18 – 21Combined sources4
Helixi24 – 32Combined sources9
Beta strandi37 – 41Combined sources5
Beta strandi54 – 57Combined sources4
Helixi58 – 66Combined sources9
Beta strandi69 – 73Combined sources5
Helixi82 – 90Combined sources9
Helixi93 – 107Combined sources15
Beta strandi111 – 114Combined sources4
Helixi116 – 118Combined sources3
Beta strandi120 – 127Combined sources8
Turni129 – 131Combined sources3
Beta strandi132 – 134Combined sources3
Beta strandi136 – 141Combined sources6
Helixi150 – 159Combined sources10
Turni160 – 162Combined sources3
Beta strandi164 – 172Combined sources9
Beta strandi175 – 183Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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
SMRiQ9YBF1
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9YBF1

Family & Domainsi

Sequence similaritiesi

Belongs to the tRNA-intron endonuclease family. Archaeal short subfamily.UniRule annotation

Phylogenomic databases

eggNOGiarCOG01701 Archaea
COG1676 LUCA
HOGENOMiHOG000107823
KOiK01170
OrthoDBiPOG093Z0DMC

Family and domain databases

Gene3Di3.40.1350.10, 1 hit
HAMAPiMF_01833 EndA_short, 1 hit
InterProiView protein in InterPro
IPR011856 tRNA_endonuc-like_dom_sf
IPR036167 tRNA_intron_Endo_cat-like_sf
IPR006677 tRNA_intron_Endonuc_cat-like
IPR006678 tRNA_intron_Endonuc_N
IPR036740 tRNA_intron_Endonuc_N_sf
IPR006676 tRNA_splic
IPR016442 tRNA_splic_arch_short
PANTHERiPTHR21227 PTHR21227, 2 hits
PfamiView protein in Pfam
PF01974 tRNA_int_endo, 1 hit
PF02778 tRNA_int_endo_N, 1 hit
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

        10         20         30         40         50
MGDRCAPIKA SGVLIGDSVL VTDVEQARSL YSCGYYGQPL DVEKPRGADF
60 70 80 90 100
EGPLRLSLIE SLYLAEKGVL EVAKPDGSSV GVEDLRTAVR GNPRFSMLYN
110 120 130 140 150
IYRDLRERGF VVRSGLKFGS DFAVYRLGPG IDHAPFIVHA YSPEDNIDPV
160 170 180
EIVRAGRLSH SVRKKFVFAV TRGGDVSYLM IDWFRP
Length:186
Mass (Da):20,602
Last modified:June 26, 2007 - v2
Checksum:i3377457A91F479B9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA Translation: BAA80647.2
PIRiB72545

Genome annotation databases

EnsemblBacteriaiBAA80647; BAA80647; APE_1646.1
KEGGiape:APE_1646.1
PATRICifig|272557.25.peg.1110

Entry informationi

Entry nameiENDA_AERPE
AccessioniPrimary (citable) accession number: Q9YBF1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: June 26, 2007
Last modified: May 23, 2018
This is version 88 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

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