P46850 (RTCB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Gene names

Name:	rtcB
Synonyms:	yhgL
Ordered Locus Names:	b3421, JW3384

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	408 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	RNA ligase that mediates the joining of broken tRNA-like stem-loop structures in case of tRNA damage. Probably participates to tRNA restriction-repair by ligating broken tRNA-like stem-loop structures with 2',3'-cyclic phosphate and 5'-OH ends to form a splice junction with a 2'-OH, 3',5'-phosphodiester. Ref.4
Subunit structure	Monomer. Ref.4
Induction	Expression is repressed by RtcR. Ref.4
Miscellaneous	In contrast to the vertebrate homolog, ligation does not seem to require ATP, while GTP stimulates activity. The enzyme mechanism is still unclear and it is unknown whether reaction requires some NTP or whether it is mediated by a catalytic zinc (Ref.4).
Sequence similarities	Belongs to the RtcB family.

Ontologies

Keywords
Ligand	Metal-binding Zinc
Molecular function	Ligase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	RNA processing Inferred from direct assay Ref.4. Source: UniProtKB RNA repair Traceable author statement Ref.4. Source: UniProtKB
Molecular_function	RNA ligase activity Inferred from direct assay Ref.4. Source: EcoCyc manganese ion binding Inferred from direct assay Ref.4. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
cusB	P77239	1	EBI-1115171,EBI-1118842

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 408	408	RNA-splicing ligase RtcB		PRO_0000215109
Sites
	Metal binding	78	1	Zinc Potential
	Metal binding	168	1	Zinc Potential
	Metal binding	185	1	Zinc Potential
Experimental info
	Sequence conflict	84	1	R → G in AAA58219. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P46850 [UniParc]. Last modified July 15, 1998. Version 3. Checksum: C0C33BA04542185F	FASTA	408	45,222
	10 20 30 40 50 60 MNYELLTTEN APVKMWTKGV PVEADARQQL INTAKMPFIF KHIAVMPDVH LGKGSTIGSV 70 80 90 100 110 120 IPTKGAIIPA AVGVDIGCGM NALRTALTAE DLPENLAELR QAIETAVPHG RTTGRCKRDK 130 140 150 160 170 180 GAWENPPVNV DAKWAELEAG YQWLTQKYPR FLNTNNYKHL GTLGTGNHFI EICLDESDQV 190 200 210 220 230 240 WIMLHSGSRG IGNAIGTYFI DLAQKEMQET LETLPSRDLA YFMEGTEYFD DYLKAVAWAQ 250 260 270 280 290 300 LFASLNRDAM MENVVTALQS ITQKTVRQPQ TLAMEEINCH HNYVQKEQHF GEEIYVTRKG 310 320 330 340 350 360 AVSARAGQYG IIPGSMGAKS FIVRGLGNEE SFCSCSHGAG RVMSRTKAKK LFSVEDQIRA 370 380 390 400 TAHVECRKDA EVIDEIPMAY KDIDAVMAAQ SDLVEVIYTL RQVVCVKG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon." Genschik P., Drabikowski K., Filipowicz W. J. Biol. Chem. 273:25516-25526(1998) [PubMed] [Europe PMC] [Abstract] Cited for: GENE NAME.
[4]	"RtcB is the RNA ligase component of an Escherichia coli RNA repair operon." Tanaka N., Shuman S. J. Biol. Chem. 286:7727-7731(2011) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBUNIT, INDUCTION. Strain: K12.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U18997 Genomic DNA. Translation: AAA58219.1. U00096 Genomic DNA. Translation: AAC76446.1. AP009048 Genomic DNA. Translation: BAE77871.1.
PIR	H65137.
RefSeq	NP_417879.1. NC_000913.2. YP_492012.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P46850.
SMR	P46850. Positions 28-408.
ModBase	Search...
Protein-protein interaction databases
IntAct	P46850. 20 interactions.
STRING	511145.b3421.
2D gel databases
SWISS-2DPAGE	P46850.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC76446; AAC76446; b3421. BAE77871; BAE77871; BAE77871.
GeneID	12932194. 947929.
KEGG	ecj:Y75_p3756. eco:b3421.
PATRIC	32122278. VBIEscCol129921_3516.
Organism-specific databases
EchoBASE	EB2774.
EcoGene	EG12939. rtcB.
Phylogenomic databases
eggNOG	COG1690.
HOGENOM	HOG000220066.
KO	K14415.
OMA	FKHLAVM.
ProtClustDB	CLSK880652.
Enzyme and pathway databases
BioCyc	EcoCyc:G7751-MONOMER. ECOL316407:JW3384-MONOMER. MetaCyc:G7751-MONOMER.
Gene expression databases
Genevestigator	P46850.
Family and domain databases
InterPro	IPR001233. RtcB_family. [Graphical view]
PANTHER	PTHR11118. PTHR11118. 1 hit.
Pfam	PF01139. UPF0027. 1 hit. [Graphical view]
SUPFAM	SSF103365. UPF0027. 1 hit.
PROSITE	PS01288. UPF0027. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RTCB_ECOLI

Accession

Primary (citable) accession number: P46850
Secondary accession number(s): P76690, Q2M785

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	July 15, 1998
Last modified:	May 1, 2013
This is version 79 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program