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Protein

tRNA-splicing ligase RtcB

Gene

rtcB

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

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 an RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity).By similarity

Cofactori

Mn2+By similarityNote: Binds 2 manganese ions per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi95Manganese 1By similarity1
Metal bindingi98Manganese 1By similarity1
Metal bindingi98Manganese 2By similarity1
Metal bindingi639Manganese 1By similarity1
Binding sitei642GMPBy similarity1
Metal bindingi670Manganese 2By similarity1
Metal bindingi764Manganese 2By similarity1
Binding sitei820GMPBy similarity1
Active sitei839GMP-histidine intermediateBy similarity1
Binding sitei915GMPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi764 – 765GMPBy similarity2
Nucleotide bindingi811 – 814GMPBy similarity4
Nucleotide bindingi839 – 842GMPBy similarity4

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Ligase, Nuclease

Keywords - Biological processi

Intron homing, tRNA processing

Keywords - Ligandi

DNA-binding, Manganese, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-splicing ligase RtcB (EC:6.5.1.-)
Cleaved into the following chain:
Gene namesi
Name:rtcB
Ordered Locus Names:PYRAB05600
ORF Names:PAB0383
OrganismiPyrococcus abyssi (strain GE5 / Orsay)
Taxonomic identifieri272844 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000810 Componenti: Chromosome
  • UP000009139 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002325291 – 97tRNA-splicing ligase RtcB, 1st partSequence analysisAdd BLAST97
ChainiPRO_000023253098 – 533Pab hyp2 inteinSequence analysisAdd BLAST436
ChainiPRO_0000232531534 – 916tRNA-splicing ligase RtcB, 2nd partSequence analysisAdd BLAST383

Post-translational modificationi

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.Curated

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

STRINGi272844.PAB0383.

Structurei

3D structure databases

ProteinModelPortaliQ9V168.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini248 – 409DOD-type homing endonucleasePROSITE-ProRule annotationAdd BLAST162

Sequence similaritiesi

Belongs to the RtcB family.Curated
Contains 1 DOD-type homing endonuclease domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiarCOG03158. Archaea.
arCOG04246. Archaea.
ENOG4102TCK. Archaea.
COG1372. LUCA.
COG1690. LUCA.
HOGENOMiHOG000296282.
KOiK14415.
OMAiVHNCGVR.

Family and domain databases

Gene3Di2.170.16.10. 3 hits.
3.10.28.10. 2 hits.
InterProiIPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR004860. LAGLIDADG_2.
IPR001233. RtcB.
[Graphical view]
PANTHERiPTHR11118. PTHR11118. 2 hits.
PfamiPF14528. LAGLIDADG_3. 1 hit.
PF01139. RtcB. 1 hit.
[Graphical view]
PRINTSiPR00379. INTEIN.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF103365. SSF103365. 2 hits.
SSF51294. SSF51294. 3 hits.
SSF55608. SSF55608. 1 hit.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9V168-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTVPLKRIDK IRWEIPKFDK RMRVPGRVYA DDVLLEKMKS DRTLEQAANV
60 70 80 90 100
AMLPGIYKYS IVMPDGHQGY GFPIGGVAAF DVNEGVISPG GIGYDINCLA
110 120 130 140 150
PGSKVLTEHG YWLKVEELPE KFKLQGVKVY NLDEGHNDTS NVAFVAEREV
160 170 180 190 200
ETGEMAVRVT TESGRIIEGS EDHPVLTPEG YVYLGNLKEG NLVIVYPFEG
210 220 230 240 250
VEYEERKGVI LDEDAFKDED PQVLSFLREK GLVPLRWDDP RIGTIARILG
260 270 280 290 300
FAFGDGYLGE MGGRLTLTFY GKEETLRELK KDLERLGISA NLYVRESIET
310 320 330 340 350
TSGHSEGKSL SIELRVTSRS FALFLEKLGM PRGKKTEKAY RVPGWILEAP
360 370 380 390 400
LWVKRNFLAG LFAADGSIVE FKGNTPLPIN LTQSKSDELA ENLVEFLGDV
410 420 430 440 450
AKLLAEFGIE TTLYEVKSKK GVTYRLSIVG EDSIRTFVER INYEYDPEKK
460 470 480 490 500
VKGLIAAAYL KLKERIVKEA HEAVKDDFPT FEEFAKERGY EGGFVAEKVV
510 520 530 540 550
KVERVKPEYT KFYDIGVYHE AHNFIANGIV VHNCGVRLIR TNLTEKDVRP
560 570 580 590 600
RIKQLVDTLF KNVPSGVGSQ GRVRLHWTQI DDVLVDGAKW AVDNGYGWEE
610 620 630 640 650
DLERLEEGGR MEGADPDAVS QRAKQRGAPQ LGSLGSGNHF LEVQVVDKIF
660 670 680 690 700
DPEVAKVYGL FEGQVVVMVH TGSRGLGHQV ASDYLRIMER AIRKYRIPWP
710 720 730 740 750
DRELVSVPFQ SEEGQRYFSA MKAAANFAWA NRQMITHWVR ESFQEVFRQD
760 770 780 790 800
PEDLGMSIVY DVAHNIGKVE EHEVDGKKVK VIVHRKGATR AFPPGHEAIP
810 820 830 840 850
KIYRDVGQPV LIPGSMGTAS YVLAGTEGAM KETFGSTCHG AGRVLSRKAA
860 870 880 890 900
TRQYRGDRIR QELLNRGIYV RAASMRVVAE EAPGAYKNVD NVVKVVSEAG
910
IAKLVARMRP IGVAKG
Length:916
Mass (Da):102,456
Last modified:May 1, 2000 - v1
Checksum:i32DB1F28BE85155A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248284 Genomic DNA. Translation: CAB49482.1.
HE613800 Genomic DNA. Translation: CCE69950.1.
PIRiC75175.
RefSeqiWP_010867684.1. NC_000868.1.

Genome annotation databases

EnsemblBacteriaiCAB49482; CAB49482; PAB0383.
GeneIDi1495463.
KEGGipab:PAB0383.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248284 Genomic DNA. Translation: CAB49482.1.
HE613800 Genomic DNA. Translation: CCE69950.1.
PIRiC75175.
RefSeqiWP_010867684.1. NC_000868.1.

3D structure databases

ProteinModelPortaliQ9V168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272844.PAB0383.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB49482; CAB49482; PAB0383.
GeneIDi1495463.
KEGGipab:PAB0383.

Phylogenomic databases

eggNOGiarCOG03158. Archaea.
arCOG04246. Archaea.
ENOG4102TCK. Archaea.
COG1372. LUCA.
COG1690. LUCA.
HOGENOMiHOG000296282.
KOiK14415.
OMAiVHNCGVR.

Family and domain databases

Gene3Di2.170.16.10. 3 hits.
3.10.28.10. 2 hits.
InterProiIPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR004860. LAGLIDADG_2.
IPR001233. RtcB.
[Graphical view]
PANTHERiPTHR11118. PTHR11118. 2 hits.
PfamiPF14528. LAGLIDADG_3. 1 hit.
PF01139. RtcB. 1 hit.
[Graphical view]
PRINTSiPR00379. INTEIN.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF103365. SSF103365. 2 hits.
SSF51294. SSF51294. 3 hits.
SSF55608. SSF55608. 1 hit.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRTCB_PYRAB
AccessioniPrimary (citable) accession number: Q9V168
Secondary accession number(s): G8ZJ23
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: May 1, 2000
Last modified: November 30, 2016
This is version 93 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Ligation proceeds through 3 nucleotidyl transfer steps, with 2',3'-cyclic phosphate termini being hydrolyzed to 3'-P termini in a step that precedes 3'-P activation with GMP. In the first nucleotidyl transfer step, RtcB reacts with GTP to form a covalent RtcB-histidine-GMP intermediate with release of PPi; in the second step, the GMP moiety is transferred to the RNA 3'-P; in the third step, the 5'-OH from the opposite RNA strand attacks the activated 3'-P to form a 3',5'-phosphodiester bond and release GMP (By similarity).By similarity

Keywords - Technical termi

Complete proteome

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.