ID K4I475_9CAUD Unreviewed; 335 AA.
AC K4I475;
DT 09-JAN-2013, integrated into UniProtKB/TrEMBL.
DT 09-JAN-2013, sequence version 1.
DT 27-MAR-2024, entry version 44.
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};
OS Salmonella phage STML-198.
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Straboviridae; Tevenvirinae; Gelderlandvirus; Gelderlandvirus stml198.
OX NCBI_TaxID=1204531 {ECO:0000313|EMBL:AFU64117.1, ECO:0000313|Proteomes:UP000006954};
RN [1] {ECO:0000313|EMBL:AFU64117.1, ECO:0000313|Proteomes:UP000006954}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=STML-198 {ECO:0000313|EMBL:AFU64117.1};
RA Woolston J., Parks A.R., Hanna L.F., Charbonneau D., Sulakvelidze A.;
RT "Bacteriophages quickly and effectively reduce contamination of various
RT foods with Salmonella.";
RL Submitted (JUN-2012) 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; JX181825; AFU64117.1; -; Genomic_DNA.
DR RefSeq; YP_009148159.1; NC_027344.1.
DR GeneID; 24629971; -.
DR KEGG; vg:24629971; -.
DR Proteomes; UP000006954; 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}; RNA repair {ECO:0000256|HAMAP-Rule:MF_04150}.
FT DOMAIN 30..226
FT /note="RNA ligase"
FT /evidence="ECO:0000259|Pfam:PF09414"
FT DOMAIN 249..320
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 55
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 102
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 205
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 226
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
FT BINDING 228
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04150"
SQ SEQUENCE 335 AA; 37948 MW; 48E6A724CBF99A7B CRC64;
MFKKYSSLEN HYNNKFISKI RFEGKDGGLW VAREKIHGTN FSIIVSKDLV SACKRSGPIL
PSESFYGHEI ILKNYDESIK TIQRCMNANE LGSVSSYQIF GEFAGQGIQK EVDYGEKDFY
VFDILVNTQN GNVLYMDDMM MTSFCNEFGF KMAPFIGCGS FDELIQLPNN FTSVIKAYNE
AAKDDLKEVN LCVFDPLVTD DNVAEGYVLK PVYPDFFNNG IRIAIKSKNS RFTEKKKSDK
PIKPKAVLTS NDSTVLANLC EYSTWNRVSN VISHIGEVKA KDFGKVMGLT MQDIFIEAKR
EGVEIVHADN PDLVKRELQT VVSTTIREKW LEIVS
//
