rtcB

Functionⁱ

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, a step that requires GTP (PubMed:21224389, PubMed:22730297). Also acts as a DNA ligase in case of DNA damage by splicing 'dirty' DNA breaks, characterized by 3'-PO4 (or cyclic-PO4) and 5'-OH ends that cannot be sealed by classical DNA ligases (PubMed:24218597).6 Publications

Miscellaneous

In contrast to the vertebrate homolog, ligation does not seem to require ATP, while GTP stimulates activity.1 Publication

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 (PubMed:22474365). Acts as a DNA ligase by attaching a GMP nucleotide to the DNA 3'-PO4 end to activate it for nucleophilic attack by the 5'-OH (PubMed:24218597).2 Publications

Cofactorⁱ

Mn²⁺2 PublicationsNote: Binds 2 manganese ions per subunit.2 Publications

Sites

Feature key	Position(s)	DescriptionActions	Length
Metal bindingⁱ	75	Manganese 1By similarity	1
Metal bindingⁱ	78	Manganese 1By similarity	1
Metal bindingⁱ	78	Manganese 2By similarity	1
Metal bindingⁱ	168	Manganese 1By similarity	1
Binding siteⁱ	171	GMPBy similarity	1
Metal bindingⁱ	185	Manganese 2By similarity	1
Metal bindingⁱ	281	Manganese 2By similarity	1
Binding siteⁱ	320	GMPBy similarity	1
Active siteⁱ	337	GMP-histidine intermediate1 Publication	1
Binding siteⁱ	407	GMPBy similarity	1

Regions

Feature key	Position(s)	DescriptionActions	Length
Nucleotide bindingⁱ	281 – 282	GMPBy similarity	2
Nucleotide bindingⁱ	311 – 314	GMPBy similarity	4
Nucleotide bindingⁱ	337 – 340	GMPBy similarity	4

GO - Molecular functionⁱ

DNA ligase activity
Source: EcoCyc
Inferred from direct assayⁱ
- 24218597
manganese ion binding
Source: UniProtKB
Inferred from direct assayⁱ
- 24218597
RNA ligase activity
Source: EcoCyc
Inferred from direct assayⁱ
- 21224389

View the complete GO annotation on QuickGO ...

GO - Biological processⁱ

cellular response to DNA damage stimulus
Source: UniProtKB
Inferred from direct assayⁱ
- 24218597
DNA repair
Source: UniProtKB
Inferred from direct assayⁱ
- 24218597
RNA processing
Source: UniProtKB
Inferred from direct assayⁱ
- 21224389
RNA repair
Source: EcoCyc
Inferred from experimentⁱ
- 21757685

View the complete GO annotation on QuickGO ...

Keywordsⁱ

Molecular function	Ligase
Biological process	DNA damage, DNA repair
Ligand	Manganese, Metal-binding

Enzyme and pathway databases

BioCycⁱ	EcoCyc:G7751-MONOMER MetaCyc:G7751-MONOMER
BRENDAⁱ	6.5.1.4 2026

Names & Taxonomyⁱ

Protein namesⁱ	Recommended name: RNA-splicing ligase RtcB (EC:6.5.1.-)
Gene namesⁱ	Name:rtcB Synonyms:yhgL Ordered Locus Names:b3421, JW3384
Organismⁱ	Escherichia coli (strain K12)
Taxonomic identifierⁱ	83333 [NCBI]
Taxonomic lineageⁱ	cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › Escherichia coli
Proteomesⁱ	UP000000318 Componentⁱ: Chromosome UP000000625 Componentⁱ: Chromosome

Organism-specific databases

EcoGeneⁱ	EG12939 rtcB

EcoGeneⁱ

EG12939 rtcB

Pathology & Biotechⁱ

Mutagenesis

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Mutagenesisⁱ	337	H → A, N or Q: Loss of function. Abolishes formation of guanylylated RtcB intermediate. 1 Publication		1

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Graphical view	Length
ChainⁱPRO_0000215109	1 – 408	RNA-splicing ligase RtcBAdd BLAST		408

Proteomic databases

PaxDbⁱ	P46850
PRIDEⁱ	P46850

2D gel databases

SWISS-2DPAGEⁱ	P46850

SWISS-2DPAGEⁱ

P46850

Expressionⁱ

Inductionⁱ

Expression is repressed by RtcR.1 Publication

Interactionⁱ

Subunit structureⁱ

Monomer.1 Publication

Protein-protein interaction databases

BioGridⁱ	4261188, 7 interactors
IntActⁱ	P46850, 20 interactors
STRINGⁱ	316385.ECDH10B_3595

Structureⁱ

3D structure databases

ProteinModelPortalⁱ	P46850
SMRⁱ	P46850
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Family & Domainsⁱ

Sequence similaritiesⁱ

Belongs to the RtcB family.Curated

Phylogenomic databases

eggNOGⁱ	ENOG4105E0Y Bacteria COG1690 LUCA
HOGENOMⁱ	HOG000220066
InParanoidⁱ	P46850
KEGG Orthology (KO) More...KOⁱ	K14415
OMAⁱ	YDVAHNV
PhylomeDBⁱ	P46850

Family and domain databases

Gene3Dⁱ	3.90.1860.10, 1 hit
InterProⁱ	View protein in InterPro IPR001233 RtcB IPR036025 RtcB-like_sf
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF01139 RtcB, 1 hit
SUPFAMⁱ	SSF103365 SSF103365, 1 hit
PROSITEⁱ	View protein in PROSITE PS01288 UPF0027, 1 hit

Sequenceⁱ

Sequence statusⁱ: Complete.

P46850-1 [UniParc]FASTA Add to basket

« Hide

        10         20         30         40         50
MNYELLTTEN APVKMWTKGV PVEADARQQL INTAKMPFIF KHIAVMPDVH 
        60         70         80         90        100
LGKGSTIGSV IPTKGAIIPA AVGVDIGCGM NALRTALTAE DLPENLAELR 
       110        120        130        140        150
QAIETAVPHG RTTGRCKRDK GAWENPPVNV DAKWAELEAG YQWLTQKYPR 
       160        170        180        190        200
FLNTNNYKHL GTLGTGNHFI EICLDESDQV WIMLHSGSRG IGNAIGTYFI 
       210        220        230        240        250
DLAQKEMQET LETLPSRDLA YFMEGTEYFD DYLKAVAWAQ LFASLNRDAM 
       260        270        280        290        300
MENVVTALQS ITQKTVRQPQ TLAMEEINCH HNYVQKEQHF GEEIYVTRKG 
       310        320        330        340        350
AVSARAGQYG IIPGSMGAKS FIVRGLGNEE SFCSCSHGAG RVMSRTKAKK 
       360        370        380        390        400
LFSVEDQIRA TAHVECRKDA EVIDEIPMAY KDIDAVMAAQ SDLVEVIYTL 

RQVVCVKG

Length:408

Mass (Da):45,222

Last modified:July 15, 1998 - v3

Checksum:ⁱC0C33BA04542185F

GO

Experimental Info

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Sequence conflictⁱ	84	R → G in AAA58219 (PubMed:9278503).Curated		1

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	U18997 Genomic DNA Translation: AAA58219.1 U00096 Genomic DNA Translation: AAC76446.1 AP009048 Genomic DNA Translation: BAE77871.1
PIRⁱ	H65137
NCBI Reference Sequences More...RefSeqⁱ	NP_417879.1, NC_000913.3 WP_001105504.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaⁱ	AAC76446; AAC76446; b3421 BAE77871; BAE77871; BAE77871
GeneIDⁱ	947929
KEGGⁱ	ecj:JW3384 eco:b3421
PATRICⁱ	fig\|511145.12.peg.3516

Protein	Similar proteins		Species	Score	Length	Source
P46850	Protein rtcB		ECOLX		408	UniRef100_P46850
Protein RtcB		Escherichia coli MS 145-7		408
RNA-splicing ligase RtcB		SHIBO		408
Protein RtcB		Escherichia coli MS 117-3		408
RNA-splicing ligase RtcB		SHIDY		408
+22

Protein	Similar proteins		Species	Score	Length	Source
P46850	Protein rtcB		ECOLX		408	UniRef90_P46850
Protein RtcB		Escherichia coli MS 145-7		408
RNA-splicing ligase RtcB		SHIBO		408
Protein RtcB		Escherichia coli MS 117-3		408
RNA-splicing ligase RtcB		SHIDY		408
+763

Protein	Similar proteins		Species	Score	Length	Source
P46850	Protein rtcB		ECOLX		408	UniRef50_P46850
Protein RtcB		Escherichia coli MS 145-7		408
RNA-splicing ligase RtcB		SHIBO		408
Protein RtcB		Escherichia coli MS 117-3		408
RNA-splicing ligase RtcB		SHIDY		408
+5346

Cross-referencesⁱ

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	U18997 Genomic DNA Translation: AAA58219.1 U00096 Genomic DNA Translation: AAC76446.1 AP009048 Genomic DNA Translation: BAE77871.1
PIRⁱ	H65137
RefSeqⁱ	NP_417879.1, NC_000913.3 WP_001105504.1, NZ_LN832404.1

3D structure databases

ProteinModelPortalⁱ	P46850
SMRⁱ	P46850
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Protein-protein interaction databases

BioGridⁱ	4261188, 7 interactors
IntActⁱ	P46850, 20 interactors
STRINGⁱ	316385.ECDH10B_3595

2D gel databases

SWISS-2DPAGEⁱ	P46850

SWISS-2DPAGEⁱ

P46850

Proteomic databases

PaxDbⁱ	P46850
PRIDEⁱ	P46850

Protocols and materials databases

Structural Biology Knowledgebase	Search...

Structural Biology Knowledgebase

Search...

Genome annotation databases

EnsemblBacteriaⁱ	AAC76446; AAC76446; b3421 BAE77871; BAE77871; BAE77871
GeneIDⁱ	947929
KEGGⁱ	ecj:JW3384 eco:b3421
PATRICⁱ	fig\|511145.12.peg.3516

Organism-specific databases

EchoBASEⁱ	EB2774
EcoGeneⁱ	EG12939 rtcB

Phylogenomic databases

eggNOGⁱ	ENOG4105E0Y Bacteria COG1690 LUCA
HOGENOMⁱ	HOG000220066
InParanoidⁱ	P46850
KOⁱ	K14415
OMAⁱ	YDVAHNV
PhylomeDBⁱ	P46850

Enzyme and pathway databases

BioCycⁱ	EcoCyc:G7751-MONOMER MetaCyc:G7751-MONOMER
BRENDAⁱ	6.5.1.4 2026

Miscellaneous databases

Protein Ontology More...PROⁱ	PR:P46850

PROⁱ

PR:P46850

Family and domain databases

Gene3Dⁱ	3.90.1860.10, 1 hit
InterProⁱ	View protein in InterPro IPR001233 RtcB IPR036025 RtcB-like_sf
Pfamⁱ	View protein in Pfam PF01139 RtcB, 1 hit
SUPFAMⁱ	SSF103365 SSF103365, 1 hit
PROSITEⁱ	View protein in PROSITE PS01288 UPF0027, 1 hit
ProtoNetⁱ	Search...

Entry informationⁱ

Entry nameⁱ	RTCB_ECOLI
Accessionⁱ	P46850Primary (citable) accession number: P46850 Secondary accession number(s): P76690, Q2M785
Entry historyⁱ	Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
	Last sequence update:	July 15, 1998
	Last modified:	March 28, 2018
	This is version 107 of the entry and version 3 of the sequence. See complete history.
Entry statusⁱ	Reviewed (UniProtKB/Swiss-Prot)
Annotation program	Prokaryotic Protein Annotation Program

Miscellaneousⁱ

Keywords - Technical termⁱ

Complete proteome, Reference proteome

Documents

SIMILARITY comments
Index of protein domains and families
Escherichia coli
Escherichia coli (strain K12): entries and cross-references to EcoGene

UniProtKB

UniParc

Help

UniRef

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UniProtKB - P46850 (RTCB_ECOLI)

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RNA-splicing ligase RtcB

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<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

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Enzyme and pathway databases

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

Organism-specific databases

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Mutagenesis

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Proteomic databases

2D gel databases

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

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Experimental Info

Sequence databases

Genome annotation databases

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Sequence databases

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Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

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Enzyme and pathway databases

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Functionⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Pathology & Biotechⁱ

PTM / Processingⁱ

Expressionⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ

Keywords - Technical termⁱ