Q9V168 (RTCB_PYRAB) 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. Pab hyp2 intein
   EC=3.1.-.-

Gene names

Name:	rtcB
Ordered Locus Names:	PYRAB05600
ORF Names:	PAB0383

Organism

Pyrococcus abyssi (strain GE5 / Orsay) [Complete proteome] [HAMAP]

Taxonomic identifier

272844 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	916 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
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 – 97	97	tRNA-splicing ligase RtcB, 1st part Potential		PRO_0000232529
	Chain	98 – 533	436	Pab hyp2 intein Potential		PRO_0000232530
	Chain	534 – 916	383	tRNA-splicing ligase RtcB, 2nd part Potential		PRO_0000232531
Regions
	Domain	248 – 409	162	DOD-type homing endonuclease
Sites
	Metal binding	534	1	Zinc Potential
	Metal binding	639	1	Zinc Potential
	Metal binding	670	1	Zinc Potential

Sequences

	Sequence		Length	Mass (Da)
	Q9V168 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: 32DB1F28BE85155A	FASTA	916	102,456
	10 20 30 40 50 60 MTVPLKRIDK IRWEIPKFDK RMRVPGRVYA DDVLLEKMKS DRTLEQAANV AMLPGIYKYS 70 80 90 100 110 120 IVMPDGHQGY GFPIGGVAAF DVNEGVISPG GIGYDINCLA PGSKVLTEHG YWLKVEELPE 130 140 150 160 170 180 KFKLQGVKVY NLDEGHNDTS NVAFVAEREV ETGEMAVRVT TESGRIIEGS EDHPVLTPEG 190 200 210 220 230 240 YVYLGNLKEG NLVIVYPFEG VEYEERKGVI LDEDAFKDED PQVLSFLREK GLVPLRWDDP 250 260 270 280 290 300 RIGTIARILG FAFGDGYLGE MGGRLTLTFY GKEETLRELK KDLERLGISA NLYVRESIET 310 320 330 340 350 360 TSGHSEGKSL SIELRVTSRS FALFLEKLGM PRGKKTEKAY RVPGWILEAP LWVKRNFLAG 370 380 390 400 410 420 LFAADGSIVE FKGNTPLPIN LTQSKSDELA ENLVEFLGDV AKLLAEFGIE TTLYEVKSKK 430 440 450 460 470 480 GVTYRLSIVG EDSIRTFVER INYEYDPEKK VKGLIAAAYL KLKERIVKEA HEAVKDDFPT 490 500 510 520 530 540 FEEFAKERGY EGGFVAEKVV KVERVKPEYT KFYDIGVYHE AHNFIANGIV VHNCGVRLIR 550 560 570 580 590 600 TNLTEKDVRP RIKQLVDTLF KNVPSGVGSQ GRVRLHWTQI DDVLVDGAKW AVDNGYGWEE 610 620 630 640 650 660 DLERLEEGGR MEGADPDAVS QRAKQRGAPQ LGSLGSGNHF LEVQVVDKIF DPEVAKVYGL 670 680 690 700 710 720 FEGQVVVMVH TGSRGLGHQV ASDYLRIMER AIRKYRIPWP DRELVSVPFQ SEEGQRYFSA 730 740 750 760 770 780 MKAAANFAWA NRQMITHWVR ESFQEVFRQD PEDLGMSIVY DVAHNIGKVE EHEVDGKKVK 790 800 810 820 830 840 VIVHRKGATR AFPPGHEAIP KIYRDVGQPV LIPGSMGTAS YVLAGTEGAM KETFGSTCHG 850 860 870 880 890 900 AGRVLSRKAA TRQYRGDRIR QELLNRGIYV RAASMRVVAE EAPGAYKNVD NVVKVVSEAG 910 IAKLVARMRP IGVAKG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi." Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O., Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J., Weissenbach J., Zivanovic Y., Forterre P. Mol. Microbiol. 47:1495-1512(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: GE5 / Orsay.
[2]	"Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638." Gao J., Wang J. Curr. Microbiol. 64:118-129(2012) [PubMed] [Europe PMC] [Abstract] Cited for: GENOME REANNOTATION. Strain: GE5 / Orsay.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AJ248284 Genomic DNA. Translation: CAB49482.1. HE613800 Genomic DNA. Translation: CCE69950.1.
PIR	C75175.
RefSeq	NP_126251.1. NC_000868.1.
3D structure databases
ProteinModelPortal	Q9V168.
SMR	Q9V168. Positions 3-98, 533-916.
ModBase	Search...
Protein-protein interaction databases
STRING	272844.PAB0383.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	CAB49482; CAB49482; PAB0383.
GeneID	1495463.
KEGG	pab:PAB0383.
Organism-specific databases
CMR	Search...
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_PYRAB

Accession

Primary (citable) accession number: Q9V168
Secondary accession number(s): G8ZJ23

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 18, 2006
Last sequence update:	May 1, 2000
Last modified:	May 1, 2013
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program