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Q9V168

- RTCB_PYRAB

UniProt

Q9V168 - RTCB_PYRAB

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Protein

tRNA-splicing ligase RtcB

Gene

rtcB

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed - 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi95 – 951Manganese 1By similarity
Metal bindingi98 – 981Manganese 1By similarity
Metal bindingi98 – 981Manganese 2By similarity
Metal bindingi639 – 6391Manganese 1By similarity
Binding sitei642 – 6421GMPBy similarity
Metal bindingi670 – 6701Manganese 2By similarity
Metal bindingi764 – 7641Manganese 2By similarity
Binding sitei820 – 8201GMPBy similarity
Active sitei839 – 8391GMP-histidine intermediateBy similarity
Binding sitei915 – 9151GMPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi764 – 7652GMPBy similarity
Nucleotide bindingi811 – 8144GMPBy similarity
Nucleotide bindingi839 – 8424GMPBy 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: InterPro

GO - Biological processi

  1. intein-mediated protein splicing Source: InterPro
  2. intron homing Source: UniProtKB-KW
  3. tRNA processing Source: UniProtKB-KW
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
ProteomesiUP000000810: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 9797tRNA-splicing ligase RtcB, 1st partSequence AnalysisPRO_0000232529Add
BLAST
Chaini98 – 533436Pab hyp2 inteinSequence AnalysisPRO_0000232530Add
BLAST
Chaini534 – 916383tRNA-splicing ligase RtcB, 2nd partSequence AnalysisPRO_0000232531Add
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.By similarity

Protein-protein interaction databases

STRINGi272844.PAB0383.

Structurei

3D structure databases

ProteinModelPortaliQ9V168.
SMRiQ9V168. Positions 3-98, 533-916.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini248 – 409162DOD-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. 2 hits.
PF01139. RtcB. 2 hits.
[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.
RefSeqiNP_126251.1. NC_000868.1.
WP_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 .
PIRi C75175.
RefSeqi NP_126251.1. NC_000868.1.
WP_010867684.1. NC_000868.1.

3D structure databases

ProteinModelPortali Q9V168.
SMRi Q9V168. Positions 3-98, 533-916.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 272844.PAB0383.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CAB49482 ; CAB49482 ; PAB0383 .
GeneIDi 1495463.
KEGGi pab:PAB0383.

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. 2 hits.
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. 3 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.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. 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.

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 26, 2014
This is version 80 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

External Data

Dasty 3