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Q8TUS2

- RTCB_METKA

UniProt

Q8TUS2 - RTCB_METKA

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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: 4 out of 5- 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

Cofactori

Binds 2 manganese ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi98 – 981Manganese 1By similarity
Metal bindingi101 – 1011Manganese 1By similarity
Metal bindingi101 – 1011Manganese 2By similarity
Metal bindingi700 – 7001Manganese 1By similarity
Binding sitei703 – 7031GMPBy similarity
Metal bindingi732 – 7321Manganese 2By similarity
Metal bindingi833 – 8331Manganese 2By similarity
Binding sitei892 – 8921GMPBy similarity
Active sitei911 – 9111GMP-histidine intermediateBy similarity
Binding sitei987 – 9871GMPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi833 – 8342GMPBy similarity
Nucleotide bindingi883 – 8864GMPBy similarity
Nucleotide bindingi911 – 9144GMPBy similarity

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. endonuclease activity Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW
  4. RNA ligase activity Source: UniProtKB

GO - Biological processi

  1. intein-mediated protein splicing Source: InterPro
  2. intron homing Source: UniProtKB-KW
  3. tRNA splicing, via endonucleolytic cleavage and ligation Source: UniProtKB
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:MK1682
OrganismiMethanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Taxonomic identifieri190192 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanopyriMethanopyralesMethanopyraceaeMethanopyrus
ProteomesiUP000001826: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 100100tRNA-splicing ligase RtcB, 1st partSequence AnalysisPRO_0000232526Add
BLAST
Chaini101 – 582482Mka hyp2 inteinSequence AnalysisPRO_0000232527Add
BLAST
Chaini583 – 988406tRNA-splicing ligase RtcB, 2nd partSequence AnalysisPRO_0000232528Add
BLAST

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.1 Publication

Protein-protein interaction databases

STRINGi190192.MK1682.

Structurei

3D structure databases

ProteinModelPortaliQ8TUS2.
SMRiQ8TUS2. Positions 7-101, 582-988.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini251 – 415165DOD-type homing endonucleasePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1372.
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.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR001233. RtcB.
[Graphical view]
PANTHERiPTHR11118. PTHR11118. 1 hit.
PfamiPF14528. LAGLIDADG_3. 1 hit.
PF01139. RtcB. 2 hits.
[Graphical view]
PRINTSiPR00379. INTEIN.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF103365. SSF103365. 2 hits.
SSF51294. SSF51294. 2 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.
PS01288. UPF0027. 1 hit.
[Graphical view]

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:
EMBL
GenBank
DDBJ
Links Updated
AE009439 Genomic DNA. Translation: AAM02895.1.
RefSeqiNP_614965.1. NC_003551.1.
WP_011020050.1. NC_003551.1.

Genome annotation databases

EnsemblBacteriaiAAM02895; AAM02895; MK1682.
GeneIDi1478277.
KEGGimka:MK1682.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE009439 Genomic DNA. Translation: AAM02895.1 .
RefSeqi NP_614965.1. NC_003551.1.
WP_011020050.1. NC_003551.1.

3D structure databases

ProteinModelPortali Q8TUS2.
SMRi Q8TUS2. Positions 7-101, 582-988.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 190192.MK1682.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAM02895 ; AAM02895 ; MK1682 .
GeneIDi 1478277.
KEGGi mka:MK1682.

Phylogenomic databases

eggNOGi COG1372.
HOGENOMi HOG000296282.
KOi K14415.
OMAi VHNCGVR.

Family and domain databases

Gene3Di 2.170.16.10. 3 hits.
3.10.28.10. 2 hits.
InterProi IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR001233. RtcB.
[Graphical view ]
PANTHERi PTHR11118. PTHR11118. 1 hit.
Pfami PF14528. LAGLIDADG_3. 1 hit.
PF01139. RtcB. 2 hits.
[Graphical view ]
PRINTSi PR00379. INTEIN.
SMARTi SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view ]
SUPFAMi SSF103365. SSF103365. 2 hits.
SSF51294. SSF51294. 2 hits.
SSF55608. SSF55608. 1 hit.
TIGRFAMsi TIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEi PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS01288. UPF0027. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938.
  2. "Archaeal 3'-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation."
    Englert M., Sheppard K., Aslanian A., Yates J.R. III, Soll D.
    Proc. Natl. Acad. Sci. U.S.A. 108:1290-1295(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, SUBUNIT.
    Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938.

Entry informationi

Entry nameiRTCB_METKA
AccessioniPrimary (citable) accession number: Q8TUS2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: June 1, 2002
Last modified: October 29, 2014
This is version 74 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, Reference proteome

Documents

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

External Data

Dasty 3