ID Q56BF0_9CAUD Unreviewed; 347 AA.
AC Q56BF0;
DT 10-MAY-2005, integrated into UniProtKB/TrEMBL.
DT 10-MAY-2005, sequence version 1.
DT 24-JAN-2024, entry version 70.
DE RecName: Full=RNA ligase 2 {ECO:0000256|HAMAP-Rule:MF_04150};
DE EC=6.5.1.3 {ECO:0000256|HAMAP-Rule:MF_04150};
DE AltName: Full=Rnl2 {ECO:0000256|HAMAP-Rule:MF_04150};
GN Name=rnlB {ECO:0000313|EMBL:AAX78771.1};
GN ORFNames=RB43ORF249w {ECO:0000313|EMBL:AAX78771.1};
OS Escherichia phage RB43.
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Straboviridae; Pseudotevenvirus; Pseudotevenvirus RB43.
OX NCBI_TaxID=2887182 {ECO:0000313|EMBL:AAX78771.1, ECO:0000313|Proteomes:UP000211040};
RN [1] {ECO:0000313|EMBL:AAX78771.1, ECO:0000313|Proteomes:UP000211040}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Petrov V.M., Nolan J.M., Chin D., Krisch H.M., Karam J.D.;
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Repairs 3'-OH/5'-PO4 nicks in duplex RNA or RNA:DNA hybrid in
CC which the broken 3'-OH strand is RNA. The nick ligation reaction
CC entails three nucleotidyl transfer steps. In the first step, the RNA
CC ligase reacts with ATP in the absence of nucleic acid to form a
CC covalent ligase-AMP intermediate and release pyrophosphate. In step 2,
CC the ligase-AMP binds to the nicked duplex nucleic acid and transfers
CC the adenylate to the 5'-PO4 terminus to form an adenylylated nicked
CC intermediate. In step 3, the RNA ligase directs the attack of the nick
CC 3'-OH on the 5'-phosphoanhydride linkage, resulting in a repaired 3'
CC - 5' phosphodiester and release of AMP. {ECO:0000256|HAMAP-
CC Rule:MF_04150}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate.;
CC EC=6.5.1.3; Evidence={ECO:0000256|ARBA:ARBA00034038,
CC ECO:0000256|HAMAP-Rule:MF_04150};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_04150};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_04150};
CC Note=Binds 2 magnesium ions that may perform the catalytic activity via
CC a two-metal mechanism. {ECO:0000256|HAMAP-Rule:MF_04150};
CC -!- DOMAIN: The adenylyltransferase domain in the N-terminus performs step
CC 1 and step 3 reactions. The C-terminus domain is required for step 2 of
CC the ligation pathway. {ECO:0000256|HAMAP-Rule:MF_04150}.
CC -!- SIMILARITY: Belongs to the RNA ligase 2 family. {ECO:0000256|HAMAP-
CC Rule:MF_04150}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_04150}.
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DR EMBL; AY967407; AAX78771.1; -; Genomic_DNA.
DR RefSeq; YP_239225.1; NC_007023.1.
DR GeneID; 3416267; -.
DR KEGG; vg:3416267; -.
DR OrthoDB; 15759at10239; -.
DR Proteomes; UP000211040; Genome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003972; F:RNA ligase (ATP) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0042245; P:RNA repair; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.1490.70; -; 1.
DR Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR Gene3D; 1.10.10.1810; RNA ligase; 1.
DR HAMAP; MF_04150; RNALIG2_T4; 1.
DR InterPro; IPR012647; RNA_lig_RNL2.
DR InterPro; IPR021122; RNA_ligase_dom_REL/Rnl2.
DR InterPro; IPR041948; Rnl1/2_C_sf.
DR InterPro; IPR040609; Rnl2_C.
DR InterPro; IPR044263; Rnl2_vir.
DR NCBIfam; TIGR02307; RNA_lig_RNL2; 1.
DR Pfam; PF09414; RNA_ligase; 1.
DR Pfam; PF18043; T4_Rnl2_C; 1.
DR SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_04150};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_04150};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_04150};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_04150};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_04150}; Reference proteome {ECO:0000313|Proteomes:UP000211040};
KW RNA repair {ECO:0000256|HAMAP-Rule:MF_04150}.
FT DOMAIN 30..232
FT /note="RNA ligase"
FT /evidence="ECO:0000259|Pfam:PF09414"
FT DOMAIN 259..318
FT /note="RNA ligase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF18043"
FT ACT_SITE 35
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 34
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 36
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 40
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 56
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 108
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 210
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 231
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 233
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
SQ SEQUENCE 347 AA; 38708 MW; 593579B17858FD41 CRC64;
MFVKYSSLTN HYEGKFINGV IMNGLTGGVW VAREKIHGAN FSLITSDGER VIPAKRSGEI
LPTEQFYGCE PVVARYAPAI RKLWDVINTA QQVSGIYVDS LVIQVYGEFA GRGVQKDVDY
GEKDFYVFDI RVNGKFLHDN IVAVYAKTVG LKMAPLLAYG TFDEIRALPI TFDSVVNLAN
SGAIPAHNGV EPEFKNFMTL KDGEGENIAE GFVMKPVHPA FMPNGERVAI KCKTTKFSEK
KNKQANRFNA PAELSENDKV KLDVFTCYLT ENRVKNVLSK IDSTNLTAKD FGRVMGLTVQ
DALEEIERNY GPFIEQFENP TLAKKTFTNE ASSLIRTNWG AILNNEF
//
