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Q9YBF1

- ENDA_AERPE

UniProt

Q9YBF1 - ENDA_AERPE

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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: 2 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.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 – 1251UniRule annotation
Active sitei133 – 1331UniRule annotation
Active sitei164 – 1641UniRule annotation

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 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
ProteomesiUP000002518: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 186186tRNA-splicing endonucleasePRO_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.UniRule annotation

Protein-protein interaction databases

STRINGi272557.APE_1646.1.

Structurei

Secondary structure

1
186
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 156Combined sources
Beta strandi18 – 214Combined sources
Helixi24 – 329Combined sources
Beta strandi37 – 415Combined sources
Beta strandi54 – 574Combined sources
Helixi58 – 669Combined sources
Beta strandi69 – 735Combined sources
Helixi82 – 909Combined sources
Helixi93 – 10715Combined sources
Beta strandi111 – 1144Combined sources
Helixi116 – 1183Combined sources
Beta strandi120 – 1278Combined sources
Turni129 – 1313Combined sources
Beta strandi132 – 1343Combined sources
Beta strandi136 – 1416Combined sources
Helixi150 – 15910Combined sources
Turni160 – 1623Combined sources
Beta strandi164 – 1729Combined sources
Beta strandi175 – 1839Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9YBF1.

Family & Domainsi

Sequence similaritiesi

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

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

        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.
RefSeqiNP_148074.2. NC_000854.2.
WP_010866506.1. NC_000854.2.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA. Translation: BAA80647.2 .
PIRi B72545.
RefSeqi NP_148074.2. NC_000854.2.
WP_010866506.1. NC_000854.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 74 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, Reference 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