tRNA-splicing ligase RtcB - Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Preferred order of sections

Names and origin

Protein names

Recommended name:
tRNA-splicing ligase RtcB
EC=6.5.1.-

Cleaved into the following chain:

Mja hyp2 intein
EC=3.1.-.-

Gene names

Name:	rtcB
Ordered Locus Names:	MJ0682

Organism

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)

Taxonomic identifier

243232 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus

Protein attributes

Sequence length	968 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

General annotation (Comments)

Function	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 a RNA ligase with broad substrate specificity, and may function toward other RNAs By similarity.
Subunit structure	Monomer By similarity.
Post-translational modification	This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation Potential.
Sequence similarities	Belongs to the RtcB family. Contains 1 DOD-type homing endonuclease domain.

Ontologies

Keywords
Biological process	Intron homing tRNA processing
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Endonuclease Hydrolase Ligase Nuclease
PTM	Autocatalytic cleavage Protein splicing
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	intein-mediated protein splicing Inferred from electronic annotation. Source: InterPro intron homing Inferred from electronic annotation. Source: UniProtKB-KW tRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW ligase activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 97

97

tRNA-splicing ligase RtcB, 1st part Potential

PRO_0000036183

Chain

98 – 585

488

Mja hyp2 intein Potential

PRO_0000036184

Chain

586 – 968

383

tRNA-splicing ligase RtcB, 2nd part Potential

PRO_0000036185

Regions

Domain

245 – 414

170

DOD-type homing endonuclease

Sites

Metal binding

586

1

Zinc Potential

Metal binding

691

1

Zinc Potential

Metal binding

722

1

Zinc Potential

Sequences

Sequence

Length

Mass (Da)

Tools

Q58095 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 39A2A66280466130
Show »

FASTA

968

110,206

        10         20         30         40         50         60 
MKDVLKRVSD VVWELPKDYK DCMRVPGRIY LNEILLDELE PEVLEQIANV ACLPGIYKYS 

        70         80         90        100        110        120 
IAMPDVHYGY GFAIGGVAAF DQREGVISPG GVGFDINCLT SNSKILTDDG YYIKLEKLKE 

       130        140        150        160        170        180 
KLDLHIKIYN TEEGEKSSNI LFVSERYADE KIIRIKTESG RVLEGSKDHP VLTLNGYVPM 

       190        200        210        220        230        240 
GMLKEGDDVI VYPYEGVEYE EPSDEIILDE DDFAEYDKQI IKYLKDRGLL PLRMDNKNIG 

       250        260        270        280        290        300 
IIARLLGFAF GDGSIVKENG DRERLYVAFY GKRETLIKIR EDLEKLGIKA SRIYSRKREV 

       310        320        330        340        350        360 
EIRNAYGDEY TSLCEDNSIK ITSKAFALFM HKLGMPIGKK TEQIYKIPEW IKKAPKWVKR 

       370        380        390        400        410        420 
NFLAGLFGAD GSRAVFKNYT PLPINLTMSK SEELKENILE FLNEIKLLLA EFDIESMIYE 

       430        440        450        460        470        480 
IKSLDGRVSY RLAIVGEESI KNFLGRINYE YSGEKKVIGL LAYEYLRRKD IAKEIRKKCI 

       490        500        510        520        530        540 
KRAKELYKKG VTVSEMLKMD EFRNEFISKR LIERAVYENL DEDDVRISTK FPKFEEFIEK 

       550        560        570        580        590        600 
YGVIGGFVID KIKEIEEISY DSKLYDVGIV SKEHNFIANS IVVHNCGVRL IRTNLTKEEV 

       610        620        630        640        650        660 
QSKIKELIKT LFKNVPSGLG SKGILKFSKS VMDDVLEEGV RWAVKEGYGW KEDLEFIEEH 

       670        680        690        700        710        720 
GCLKDADASY VSDKAKERGR VQLGSLGSGN HFLEVQYVEK VFDEEAAEIY GIEENQVVVL 

       730        740        750        760        770        780 
VHTGSRGLGH QICTDYLRIM EKAAKNYGIK LPDRQLACAP FESEEGQSYF KAMCCGANYA 

       790        800        810        820        830        840 
WANRQMITHW VRESFEEVFK IHAEDLEMNI VYDVAHNIAK KEEHIIDGRK VKVIVHRKGA 

       850        860        870        880        890        900 
TRAFPPKHEA IPKEYWSVGQ PVIIPGDMGT ASYLMRGTEI AMKETFGSTA HGAGRKLSRA 

       910        920        930        940        950        960 
KALKLWKGKE IQRRLAEMGI VAMSDSKAVM AEEAPEAYKS VDLVADTCHK AGISLKVARM 


RPLGVIKG

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References

[1]

"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii."
Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G.

Venter J.C.
Science 273:1058-1073(1996) [PubMed: 8688087] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.

Cross-references

Sequence databases
EMBL GenBank DDBJ	L77117 Genomic DNA. Translation: AAB98677.1.
PIR	B64385.
RefSeq	NP_247666.1. NC_000909.1.
3D structure databases
ProteinModelPortal	Q58095.
SMR	Q58095. Positions 5-98, 585-968.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1451548.
GenomeReviews	Gene locus MJ0682 in contig L77117_GR.
KEGG	mja:MJ_0682.
NMPDR	fig\|243232.1.peg.703.
TIGR	MJ0682.
Phylogenomic databases
HOGENOM	HBG539468.
OMA	VHNCGVR.
ProtClustDB	CLSK2749909.
Enzyme and pathway databases
BioCyc	MJAN243232:MJ_0682-MONOMER.
Family and domain databases
InterPro	IPR003586. Hedgehog_hint_C. IPR003587. Hedgehog_hint_N. IPR006142. INTEIN. IPR004042. Intein_endonuc. IPR006141. Intein_splice_site. IPR001233. UPF0027. [Graphical view]
KO	K14415.
PANTHER	PTHR11118. UPF0027. 1 hit.
Pfam	PF01139. UPF0027. 2 hits. [Graphical view]
PRINTS	PR00379. INTEIN.
SMART	SM00305. HintC. 1 hit. SM00306. HintN. 1 hit. [Graphical view]
SUPFAM	SSF103365. UPF0027. 2 hits.
TIGRFAMs	TIGR01443. Intein_Cterm. 1 hit. TIGR01445. Intein_Nterm. 1 hit.
PROSITE	PS50818. INTEIN_C_TER. 1 hit. PS50819. INTEIN_ENDONUCLEASE. 1 hit. PS50817. INTEIN_N_TER. 1 hit. PS01288. UPF0027. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RTCB_METJA

Accession

Primary (citable) accession number: Q58095

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	November 16, 2011
This is version 74 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Intein-containing proteins

List of intein-containing protein entries

Methanococcus jannaschii

Methanococcus jannaschii: entries and gene names

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Cleaved into the following chain:

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents