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O29362

- ENDA_ARCFU

UniProt

O29362 - ENDA_ARCFU

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Protein

tRNA-splicing endonuclease

Gene

endA

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
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.

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 sitei246 – 2461UniRule annotation
Active sitei257 – 2571UniRule annotation
Active sitei287 – 2871UniRule 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

BioCyciAFUL224325:GJBC-922-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:AF_0900
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
ProteomesiUP000002199: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 305305tRNA-splicing endonucleasePRO_0000109484Add
BLAST

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

STRINGi224325.AF0900.

Structurei

Secondary structure

1
305
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 107
Helixi13 – 186
Beta strandi21 – 244
Beta strandi27 – 304
Helixi32 – 409
Helixi49 – 5911
Beta strandi60 – 623
Helixi63 – 7513
Beta strandi81 – 833
Beta strandi86 – 9712
Helixi104 – 1107
Turni111 – 1133
Beta strandi118 – 1225
Beta strandi128 – 1347
Beta strandi149 – 1546
Beta strandi157 – 1615
Helixi164 – 1674
Beta strandi172 – 1754
Beta strandi178 – 1814
Helixi183 – 1919
Beta strandi195 – 1973
Helixi202 – 21211
Helixi216 – 22813
Beta strandi232 – 2354
Helixi237 – 2393
Beta strandi241 – 2477
Helixi252 – 2576
Beta strandi259 – 2646
Helixi272 – 28413
Beta strandi288 – 2936
Beta strandi296 – 3038

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1R0VX-ray2.00A/B/C/D1-305[»]
1R11X-ray2.70A/B1-305[»]
1RLVX-ray3.00A/B1-305[»]
2GJWX-ray2.85A/B/C/D2-305[»]
3P1YX-ray2.05A/B/C/D1-305[»]
ProteinModelPortaliO29362.
SMRiO29362. Positions 2-305.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO29362.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1676.
KOiK01170.
OMAiRGFVVKT.

Family and domain databases

Gene3Di3.40.1350.10. 2 hits.
HAMAPiMF_01834. EndA_long.
InterProiIPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006678. tRNA_intron_Endonuc_N.
IPR006676. tRNA_splic.
IPR023516. tRNA_splic_arch_long.
[Graphical view]
PfamiPF01974. tRNA_int_endo. 1 hit.
PF02778. tRNA_int_endo_N. 1 hit.
[Graphical view]
SUPFAMiSSF53032. SSF53032. 2 hits.
SSF55267. SSF55267. 2 hits.
TIGRFAMsiTIGR00324. endA. 1 hit.

Sequencei

Sequence statusi: Complete.

O29362-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MIGGDFAVVK AKKSLERRGF GVKRGDKIYL HPLEVVYLQI KGIESFGELE
60 70 80 90 100
DVLSWAESRM EDFSTYYFVY EDLRDRGNKV KIQGEFLLTK KPYLPISERK
110 120 130 140 150
TIRMEEIAEK ARNFDELRLA VVDEESEITY FRVYEPDMMG EQKEELPEIA
160 170 180 190 200
GILSDEYVIT KQTEIFSRYF YGSEKGDLVT LSLIESLYLL DLGKLNLLNA
210 220 230 240 250
DREELVKRAR EVERNFDRRY EVYRNLKERG FVVKTGFKFG SEFRVYRKVE
260 270 280 290 300
SVDDLPHSEY LVDIADSREI RLIDLARAVR LAQNVRKRMV FAYGKNYLCF

ERVKV
Length:305
Mass (Da):35,959
Last modified:January 1, 1998 - v1
Checksum:iDC0B5A5DEBD99E35
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE000782 Genomic DNA. Translation: AAB90338.1.
PIRiD69362.
RefSeqiNP_069733.1. NC_000917.1.
WP_010878400.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90338; AAB90338; AF_0900.
GeneIDi1484123.
KEGGiafu:AF0900.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE000782 Genomic DNA. Translation: AAB90338.1 .
PIRi D69362.
RefSeqi NP_069733.1. NC_000917.1.
WP_010878400.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1R0V X-ray 2.00 A/B/C/D 1-305 [» ]
1R11 X-ray 2.70 A/B 1-305 [» ]
1RLV X-ray 3.00 A/B 1-305 [» ]
2GJW X-ray 2.85 A/B/C/D 2-305 [» ]
3P1Y X-ray 2.05 A/B/C/D 1-305 [» ]
ProteinModelPortali O29362.
SMRi O29362. Positions 2-305.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 224325.AF0900.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAB90338 ; AAB90338 ; AF_0900 .
GeneIDi 1484123.
KEGGi afu:AF0900.

Phylogenomic databases

eggNOGi COG1676.
KOi K01170.
OMAi RGFVVKT.

Enzyme and pathway databases

BioCyci AFUL224325:GJBC-922-MONOMER.

Miscellaneous databases

EvolutionaryTracei O29362.

Family and domain databases

Gene3Di 3.40.1350.10. 2 hits.
HAMAPi MF_01834. EndA_long.
InterProi IPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006678. tRNA_intron_Endonuc_N.
IPR006676. tRNA_splic.
IPR023516. tRNA_splic_arch_long.
[Graphical view ]
Pfami PF01974. tRNA_int_endo. 1 hit.
PF02778. tRNA_int_endo_N. 1 hit.
[Graphical view ]
SUPFAMi SSF53032. SSF53032. 2 hits.
SSF55267. SSF55267. 2 hits.
TIGRFAMsi TIGR00324. endA. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
    Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
    , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
    Nature 390:364-370(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
  2. "Crystal structure of a dimeric archaeal splicing endonuclease."
    Li H., Abelson J.
    J. Mol. Biol. 302:639-648(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).

Entry informationi

Entry nameiENDA_ARCFU
AccessioniPrimary (citable) accession number: O29362
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 1, 1998
Last modified: October 1, 2014
This is version 94 of the entry and version 1 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