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Protein

tRNA-splicing ligase RtcB

Gene

rtcB

Organism
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

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 (Probable).1 Publication

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

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi98Manganese 1By similarity1
Metal bindingi101Manganese 1By similarity1
Metal bindingi101Manganese 2By similarity1
Metal bindingi700Manganese 1By similarity1
Binding sitei703GMPBy similarity1
Metal bindingi732Manganese 2By similarity1
Metal bindingi833Manganese 2By similarity1
Binding sitei892GMPBy similarity1
Active sitei911GMP-histidine intermediateBy similarity1
Binding sitei987GMPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi833 – 834GMPBy similarity2
Nucleotide bindingi883 – 886GMPBy similarity4
Nucleotide bindingi911 – 914GMPBy similarity4

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • endonuclease activity Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • RNA ligase activity Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Endonuclease, Hydrolase, Ligase, Nuclease
Biological processIntron homing, tRNA processing
LigandManganese, 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:MK1682
OrganismiMethanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Taxonomic identifieri190192 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanopyriMethanopyralesMethanopyraceaeMethanopyrus
Proteomesi
  • UP000001826 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002325261 – 100tRNA-splicing ligase RtcB, 1st partSequence analysisAdd BLAST100
ChainiPRO_0000232527101 – 582Mka hyp2 inteinSequence analysisAdd BLAST482
ChainiPRO_0000232528583 – 988tRNA-splicing ligase RtcB, 2nd partSequence analysisAdd BLAST406

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

Proteomic databases

PRIDEiQ8TUS2

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi190192.MK1682

Structurei

3D structure databases

ProteinModelPortaliQ8TUS2
SMRiQ8TUS2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini251 – 415DOD-type homing endonucleasePROSITE-ProRule annotationAdd BLAST165

Sequence similaritiesi

Belongs to the RtcB family.Curated

Phylogenomic databases

eggNOGiarCOG03158 Archaea
arCOG04246 Archaea
COG1690 LUCA
HOGENOMiHOG000296282
KOiK14415
OMAiVHNCGVR
OrthoDBiPOG093Z01O0

Family and domain databases

Gene3Di3.10.28.10, 1 hit
3.90.1860.10, 2 hits
InterProiView protein in InterPro
IPR003586 Hint_dom_C
IPR003587 Hint_dom_N
IPR036844 Hint_dom_sf
IPR027434 Homing_endonucl
IPR006142 INTEIN
IPR030934 Intein_C
IPR004042 Intein_endonuc
IPR006141 Intein_N
IPR004860 LAGLIDADG_2
IPR001233 RtcB
IPR036025 RtcB-like_sf
PANTHERiPTHR11118 PTHR11118, 1 hit
PfamiView protein in Pfam
PF14528 LAGLIDADG_3, 1 hit
PF01139 RtcB, 1 hit
PRINTSiPR00379 INTEIN
SMARTiView protein in SMART
SM00305 HintC, 1 hit
SM00306 HintN, 1 hit
SUPFAMiSSF103365 SSF103365, 2 hits
SSF51294 SSF51294, 2 hits
SSF55608 SSF55608, 1 hit
TIGRFAMsiTIGR01443 intein_Cterm, 1 hit
TIGR01445 intein_Nterm, 1 hit
PROSITEiView protein in PROSITE
PS50818 INTEIN_C_TER, 1 hit
PS50819 INTEIN_ENDONUCLEASE, 1 hit
PS50817 INTEIN_N_TER, 1 hit
PS01288 UPF0027, 1 hit

Sequencei

Sequence statusi: Complete.

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

Q8TUS2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPKSMLKHI RNNVVWELPE DYKGCMKVPG RIYATEKLID GMEKGVFDQV
60 70 80 90 100
ANVACLPGIY GYSIALPDAH YGYGFPIGGV AAFDVEEGVV SPGGVGYDIN
110 120 130 140 150
CLAPGTKILT EHGCWVKVED LPKMLTDQKL KVYDVDEGRE DDSEIKFVME
160 170 180 190 200
RGIEEDERAV VLVTESGLTI EGSEDHPVLT PEGYVELGEI EEGDLVVVYP
210 220 230 240 250
FEGVEYEEKE GTILDESDFE DVDPQVLRYL EERDLIPLRW SDPKVGTLAR
260 270 280 290 300
ILGFAMGDGH LGEQAGRLTL SFYGDERTLR ELKRDLESLG VKANLHVRKR
310 320 330 340 350
RYEIETASGR YEGEATSVEL RVASRSFALL MEKLGMPRGR KVETPYKVPD
360 370 380 390 400
WIKEAPLWVK RNFLAGLFAA DGSVVKFKRY TPLPINLTQA KVEELEENLR
410 420 430 440 450
EFMNDVAKLL REFGIETTLY EVKSKKNVVY KLAIVGEENI KRFLGKVGYE
460 470 480 490 500
YDPEKKVEGL AAYAYLKLKE RVKKDRKEAA ETAAEVYEET GSITKAHEAV
510 520 530 540 550
ADVVNRRFVE RVVYDGGISS VRVPEDFPTF ERFKEERVLA GGFVIEEVVE
560 570 580 590 600
VKGVEPEYDR FYDIGVCHGA HNFIADGVVV HNCGVRVMKT DLTEDDVRPK
610 620 630 640 650
LRELLETIFR NVPAGLGSRH RRVRLSTQEL RQVMLYGAEW AVEEGFGFDE
660 670 680 690 700
DLDHIESRGN MTHAYETIGW EEYGPRDDVA SKRAIERGRP QLGTLGSGNH
710 720 730 740 750
FLEVQVVDEI YDKEAAEKMG IREEGQVTIM VHTGSRGFGH QVCSDHLRIM
760 770 780 790 800
ERSMRDVERR FGVRIPDRQL ACAAMGTDEA KRYFNAMNAA ANYAFANRQM
810 820 830 840 850
ISHWTRESFV EVFGDEYGDA DDMGIEVIYD IAHNMAKIEK HPVDGEERWL
860 870 880 890 900
VVHRKGATRA FSEEALKKHG EPVPFEGLPQ PVLIPGDMGT GSYILIGTEK
910 920 930 940 950
AMEETWGSTC HGAGRTMSRA AAKRKFWGED VARELERQGI LVKAASMPVV
960 970 980
AEEAPPAYKD VDEVVRAVAE AGISDPVVRL RPIGVVKG
Length:988
Mass (Da):110,989
Last modified:June 1, 2002 - v1
Checksum:iC24DAC047EAC3132
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009439 Genomic DNA Translation: AAM02895.1

Genome annotation databases

EnsemblBacteriaiAAM02895; AAM02895; MK1682
KEGGimka:MK1682
PATRICifig|190192.8.peg.1847

Similar proteinsi

Entry informationi

Entry nameiRTCB_METKA
AccessioniPrimary (citable) accession number: Q8TUS2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: June 1, 2002
Last modified: March 28, 2018
This is version 93 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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