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Protein

tRNA-splicing ligase RtcB

Gene

rtcB

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed-Annotation score: -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

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 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

Keywordsi

Molecular functionDNA-binding, Endonuclease, Hydrolase, Ligase, Nuclease
Biological processIntron homing, tRNA processing
LigandManganese, Metal-binding

Enzyme and pathway databases

BioCyciPABY272844:G1GT8-610-MONOMER

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
SMRiQ9V168
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

Phylogenomic databases

eggNOGiarCOG03158 Archaea
arCOG04246 Archaea
ENOG4102TCK Archaea
COG1372 LUCA
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, 3 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

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
PATRICifig|272844.11.peg.596

Similar proteinsi

Entry informationi

Entry nameiRTCB_PYRAB
AccessioniPrimary (citable) accession number: Q9V168
Secondary accession number(s): G8ZJ23
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: May 1, 2000
Last modified: March 28, 2018
This is version 101 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

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