Q8U0H4 (RTCB_PYRFU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA-splicing ligase RtcB
EC=6.5.1.-

Cleaved into the following chain:

1. Pfu hyp2 intein
   EC=3.1.-.-

Gene names

Name:	rtcB
Ordered Locus Names:	PF1615

Organism

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [Reference proteome] [HAMAP]

Taxonomic identifier

186497 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus › Pyrococcus furiosus

Protein attributes

Sequence length	970 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

General annotation (Comments)

Function	tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs By similarity.
Subunit structure	Monomer By similarity.
Post-translational modification	This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation Potential.
Sequence similarities	Belongs to the RtcB family. Contains 1 DOD-type homing endonuclease domain.

Ontologies

Keywords
Biological process	Intron homing tRNA processing
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Endonuclease Hydrolase Ligase Nuclease
PTM	Autocatalytic cleavage Protein splicing
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	intein-mediated protein splicing Inferred from electronic annotation. Source: InterPro intron homing Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC tRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW ligase activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 105	105	tRNA-splicing ligase RtcB, 1st part Potential		PRO_0000232532
	Chain	106 – 586	481	Pfu hyp2 intein Potential		PRO_0000232533
	Chain	587 – 970	384	tRNA-splicing ligase RtcB, 2nd part Potential		PRO_0000232534
Regions
	Domain	256 – 420	165	DOD-type homing endonuclease
Sites
	Metal binding	587	1	Zinc Potential
	Metal binding	692	1	Zinc Potential
	Metal binding	723	1	Zinc Potential

Sequences

	Sequence		Length	Mass (Da)
	Q8U0H4 [UniParc]. Last modified June 1, 2002. Version 1. Checksum: CC0AEE4573CFE7C2	FASTA	970	109,712
	10 20 30 40 50 60 MIILRVVNVA VPLKRIDKIR WEIPKFDKRM KVPGRVYADD VLIEKMRQDR TLEQAANVAM 70 80 90 100 110 120 LPGIYKYSIV MPDGHQGYGF PIGGVAAFDI KEGVISPGGI GYDINCLAPG TKVLTEHGYW 130 140 150 160 170 180 LKIEEMPEKF KLQRLRLYNI EEGHNDFSRV AFVAERNIEK DETAIRIVTE TGTLIEGSED 190 200 210 220 230 240 HPVLTPQGYV YLKNIKEGDY VIVYPFEGVP YEEKKGIIID ESAFEGEDPQ VIKFLKERNL 250 260 270 280 290 300 LPLRWEDPKI GTLARILGFA LGDGHLGEMG GRLVLAFYGR EETLRELKKD LESLGIKANL 310 320 330 340 350 360 YVREKNYRIK TESGEYSGKT VLAELRVSSR SFALLLEKLG MPRGEKTKKA YRIPVWIMEA 370 380 390 400 410 420 PLWVKRNFLA GFFGADGSIV EFKGTTPLPI HLTQAKDVAL EENLKEFLYD ISRILEEFGV 430 440 450 460 470 480 KTTIYKVNSK KSVTYRLSIV GEENIRNFLG KINYEYDPKK KAKGLIAYAY LKFKESVKKE 490 500 510 520 530 540 RRKAMEISKK IYEETGNIDR AYKAVKDIVN RRFVERTIYE GERNPRVPKN FLTFEEFAKE 550 560 570 580 590 600 RGYEGGFVAE KVVKVERIKP EYDRFYDIGV YHEAHNFIAN GIVVHNCGVR LIRTNLTEKD 610 620 630 640 650 660 VRPKIKQLVD TLFKNVPSGV GSQGKVRLHW TQIDDVLVDG AKWAVDQGYG WERDLERLEE 670 680 690 700 710 720 GGRMEGADPD AVSQRAKQRG APQLGSLGSG NHFLEVQVVD KIFDEEIAKA YGLFEGQVVV 730 740 750 760 770 780 MVHTGSRGLG HQVASDYLRI MERAIRKYGI PWPDRELVSV PFQSEEGQRY FSAMKAAANF 790 800 810 820 830 840 AWANRQMITH WVRESFQEVF RQDPEGDLGM EIVYDVAHNI GKVEEHEVDG KKVKVIVHRK 850 860 870 880 890 900 GATRAFPPGH EAIPKIYRDV GQPVLIPGSM GTASYVLAGT EGAMAETFGS TCHGAGRVLS 910 920 930 940 950 960 RAAATRQYRG DRIRDELLRR GIYVRAASMR VVAEEAPGAY KNVDNVVKVV SEAGIAKLVA 970 RMRPIGVAKG

References

[1]

"Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences." Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T. Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE009950 Genomic DNA. Translation: AAL81739.1.
RefSeq	NP_579344.1. NC_003413.1.
3D structure databases
ProteinModelPortal	Q8U0H4.
SMR	Q8U0H4. Positions 11-106, 586-970.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q8U0H4. 1 interaction.
STRING	186497.PF1615.
Proteomic databases
PRIDE	Q8U0H4.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAL81739; AAL81739; PF1615.
GeneID	1469492.
KEGG	pfu:PF1615.
Phylogenomic databases
eggNOG	COG1372.
HOGENOM	HOG000296282.
KO	K14415.
OMA	VHNCGVR.
ProtClustDB	CLSK785498.
Family and domain databases
InterPro	IPR003586. Hint_dom_C. IPR003587. Hint_dom_N. IPR006142. INTEIN. IPR004042. Intein_endonuc. IPR006141. Intein_splice_site. IPR001233. RtcB_family. [Graphical view]
PANTHER	PTHR11118. PTHR11118. 1 hit.
Pfam	PF01139. UPF0027. 2 hits. [Graphical view]
PRINTS	PR00379. INTEIN.
SMART	SM00305. HintC. 1 hit. SM00306. HintN. 1 hit. [Graphical view]
SUPFAM	SSF103365. UPF0027. 2 hits.
TIGRFAMs	TIGR01443. intein_Cterm. 1 hit. TIGR01445. intein_Nterm. 1 hit.
PROSITE	PS50818. INTEIN_C_TER. 1 hit. PS50819. INTEIN_ENDONUCLEASE. 1 hit. PS50817. INTEIN_N_TER. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RTCB_PYRFU

Accession

Primary (citable) accession number: Q8U0H4

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 18, 2006
Last sequence update:	June 1, 2002
Last modified:	May 1, 2013
This is version 63 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program