ID RLIG2_BPT4 Reviewed; 334 AA.
AC P32277;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 08-NOV-2023, entry version 109.
DE RecName: Full=RNA ligase 2 {ECO:0000255|HAMAP-Rule:MF_04150};
DE EC=6.5.1.3 {ECO:0000255|HAMAP-Rule:MF_04150, ECO:0000269|PubMed:12228725, ECO:0000269|PubMed:12611899, ECO:0000269|PubMed:16671895, ECO:0000269|PubMed:17018278, ECO:0000269|PubMed:24158792};
DE AltName: Full=Rnl2 {ECO:0000255|HAMAP-Rule:MF_04150};
GN Name=Y10A; Synonyms=24.1;
OS Enterobacteria phage T4 (Bacteriophage T4).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Straboviridae; Tevenvirinae; Tequatrovirus.
OX NCBI_TaxID=10665;
OH NCBI_TaxID=562; Escherichia coli.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Kaliman A.V., Khasanova M.A., Tanyashin V.I.;
RL Submitted (NOV-1992) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=12626685; DOI=10.1128/mmbr.67.1.86-156.2003;
RA Miller E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Ruger W.;
RT "Bacteriophage T4 genome.";
RL Microbiol. Mol. Biol. Rev. 67:86-156(2003).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF LYS-35; HIS-37; GLU-204;
RP LYS-225 AND LYS-227.
RX PubMed=12228725; DOI=10.1073/pnas.192184699;
RA Ho C.K., Shuman S.;
RT "Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases
RT found in all phylogenetic domains.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:12709-12714(2002).
RN [4]
RP MUTAGENESIS OF GLU-34; LYS-35; HIS-37; ASN-40; ARG-55; GLU-99; PHE-119;
RP ASP-120; LYS-189; LYS-209 AND LYS-227, CATALYTIC ACTIVITY, AND FUNCTION.
RX PubMed=12611899; DOI=10.1074/jbc.m300817200;
RA Yin S., Ho C.K., Shuman S.;
RT "Structure-function analysis of T4 RNA ligase 2.";
RL J. Biol. Chem. 278:17601-17608(2003).
RN [5]
RP FUNCTION.
RX PubMed=15494308; DOI=10.1016/j.molcel.2004.09.022;
RA Nandakumar J., Shuman S.;
RT "How an RNA ligase discriminates RNA versus DNA damage.";
RL Mol. Cell 16:211-221(2004).
RN [6]
RP COFACTOR.
RX PubMed=15084599; DOI=10.1074/jbc.m402394200;
RA Nandakumar J., Ho C.K., Lima C.D., Shuman S.;
RT "RNA substrate specificity and structure-guided mutational analysis of
RT bacteriophage T4 RNA ligase 2.";
RL J. Biol. Chem. 279:31337-31347(2004).
RN [7]
RP FUNCTION, AND COFACTOR.
RX PubMed=15851476; DOI=10.1074/jbc.m500831200;
RA Nandakumar J., Shuman S.;
RT "Dual mechanisms whereby a broken RNA end assists the catalysis of its
RT repair by T4 RNA ligase 2.";
RL J. Biol. Chem. 280:23484-23489(2005).
RN [8]
RP BIOPHYSICOCHEMICAL PROPERTIES, FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=16671895; DOI=10.1042/bj20060313;
RA Bullard D.R., Bowater R.P.;
RT "Direct comparison of nick-joining activity of the nucleic acid ligases
RT from bacteriophage T4.";
RL Biochem. J. 398:135-144(2006).
RN [9]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=24158792; DOI=10.1261/rna.041731.113;
RA Chauleau M., Shuman S.;
RT "Kinetic mechanism of nick sealing by T4 RNA ligase 2 and effects of 3'-OH
RT base mispairs and damaged base lesions.";
RL RNA 19:1840-1847(2013).
RN [10] {ECO:0007744|PDB:1S68}
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-249 IN COMPLEX WITH AMP, AND
RP DOMAIN.
RX PubMed=14962393; DOI=10.1016/j.str.2004.01.011;
RA Ho C.K., Wang L.K., Lima C.D., Shuman S.;
RT "Structure and mechanism of RNA ligase.";
RL Structure 12:327-339(2004).
RN [11] {ECO:0007744|PDB:2HVQ, ECO:0007744|PDB:2HVR, ECO:0007744|PDB:2HVS}
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH AMP; MAGNESIUM; ATP
RP AND RNA SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF THR-39;
RP PHE-65 AND PHE-66, ACTIVE SITE, COFACTOR, AND DOMAIN.
RX PubMed=17018278; DOI=10.1016/j.cell.2006.08.038;
RA Nandakumar J., Shuman S., Lima C.D.;
RT "RNA ligase structures reveal the basis for RNA specificity and
RT conformational changes that drive ligation forward.";
RL Cell 127:71-84(2006).
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 (Probable) (PubMed:12611899,
CC PubMed:24158792, PubMed:15494308, PubMed:16671895, PubMed:15851476).
CC The nick ligation reaction entails three nucleotidyl transfer steps
CC (PubMed:24158792, PubMed:15851476). In the first step, the RNA ligase
CC reacts with ATP in the absence of nucleic acid to form a covalent
CC ligase-AMP intermediate and release pyrophosphate (PubMed:24158792,
CC PubMed:15851476). In step 2, the ligase-AMP binds to the nicked duplex
CC nucleic acid and transfers the adenylate to the 5'-PO4 terminus to form
CC an adenylylated nicked intermediate (PubMed:24158792, PubMed:15851476).
CC In step 3, the RNA ligase directs the attack of the nick 3'-OH on the
CC 5'-phosphoanhydride linkage, resulting in a repaired 3' - 5'
CC phosphodiester and release of AMP (PubMed:24158792, PubMed:15851476).
CC {ECO:0000255|HAMAP-Rule:MF_04150, ECO:0000269|PubMed:12611899,
CC ECO:0000269|PubMed:15494308, ECO:0000269|PubMed:15851476,
CC ECO:0000269|PubMed:16671895, ECO:0000269|PubMed:24158792,
CC ECO:0000305|PubMed:12228725, ECO:0000305|PubMed:17018278}.
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:0000255|HAMAP-Rule:MF_04150,
CC ECO:0000269|PubMed:12228725, ECO:0000269|PubMed:12611899,
CC ECO:0000269|PubMed:16671895, ECO:0000269|PubMed:17018278,
CC ECO:0000269|PubMed:24158792};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_04150,
CC ECO:0000269|PubMed:15084599, ECO:0000269|PubMed:15851476,
CC ECO:0000269|PubMed:17018278};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_04150,
CC ECO:0000269|PubMed:15084599};
CC Note=Binds 2 magnesium ions that may perform the catalytic activity via
CC a two-metal mechanism. {ECO:0000255|HAMAP-Rule:MF_04150,
CC ECO:0000305|PubMed:17018278};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7. {ECO:0000269|PubMed:16671895};
CC -!- DOMAIN: The adenylyltransferase domain in the N-terminus performs step
CC 1 and step 3 reactions (PubMed:14962393). The C-terminus domain is
CC required for step 2 of the ligation pathway (PubMed:14962393,
CC PubMed:17018278). {ECO:0000255|HAMAP-Rule:MF_04150,
CC ECO:0000269|PubMed:14962393, ECO:0000269|PubMed:17018278}.
CC -!- SIMILARITY: Belongs to the RNA ligase 2 family. {ECO:0000255|HAMAP-
CC Rule:MF_04150}.
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DR EMBL; X69459; CAA49218.1; -; Genomic_DNA.
DR EMBL; AF158101; AAD42430.1; -; Genomic_DNA.
DR PIR; S28563; S28563.
DR RefSeq; NP_049790.1; NC_000866.4.
DR PDB; 1S68; X-ray; 1.90 A; A=1-249.
DR PDB; 2HVQ; X-ray; 2.40 A; A=1-334.
DR PDB; 2HVR; X-ray; 2.45 A; A/B=1-334.
DR PDB; 2HVS; X-ray; 2.50 A; A/B=1-334.
DR PDBsum; 1S68; -.
DR PDBsum; 2HVQ; -.
DR PDBsum; 2HVR; -.
DR PDBsum; 2HVS; -.
DR SMR; P32277; -.
DR GeneID; 1258563; -.
DR KEGG; vg:1258563; -.
DR OrthoDB; 15759at10239; -.
DR BioCyc; MetaCyc:MONOMER-19918; -.
DR BRENDA; 6.5.1.3; 732.
DR EvolutionaryTrace; P32277; -.
DR Proteomes; UP000009087; Segment.
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 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Ligase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; RNA repair.
FT CHAIN 1..334
FT /note="RNA ligase 2"
FT /id="PRO_0000165156"
FT REGION 1..234
FT /note="Adenylyltransferase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150"
FT ACT_SITE 35
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:17018278"
FT BINDING 34
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:14962393, ECO:0000269|PubMed:17018278"
FT BINDING 35
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:14962393,
FT ECO:0000269|PubMed:17018278"
FT BINDING 36
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:14962393, ECO:0000269|PubMed:17018278"
FT BINDING 40
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:14962393, ECO:0000269|PubMed:17018278"
FT BINDING 55
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:14962393"
FT BINDING 99
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:14962393, ECO:0000269|PubMed:17018278"
FT BINDING 162
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:17018278"
FT BINDING 164
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:17018278"
FT BINDING 166
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:17018278"
FT BINDING 204
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:17018278"
FT BINDING 206
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:17018278"
FT BINDING 225
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:14962393, ECO:0000269|PubMed:17018278"
FT BINDING 227
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150,
FT ECO:0000269|PubMed:14962393, ECO:0000269|PubMed:17018278"
FT SITE 218
FT /note="Interaction with RNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150"
FT SITE 314
FT /note="Interaction with RNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04150"
FT MUTAGEN 34
FT /note="E->A,D: Complete loss of adenylyltransferase
FT activity and RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 34
FT /note="E->Q: Almost complete loss of adenylyltransferase
FT activity and RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 35
FT /note="K->A: Complete loss of RNA ligase activity in vitro.
FT Complete loss of ligase-AMP formation and RNA-adenylate
FT intermediate."
FT /evidence="ECO:0000269|PubMed:12228725,
FT ECO:0000269|PubMed:12611899"
FT MUTAGEN 37
FT /note="H->D: No effect on RNA ligase activity in vitro."
FT /evidence="ECO:0000269|PubMed:12228725,
FT ECO:0000269|PubMed:12611899"
FT MUTAGEN 39
FT /note="T->A: No effect on RNA ligase activity."
FT /evidence="ECO:0000269|PubMed:17018278"
FT MUTAGEN 40
FT /note="N->A: 85% loss of adenylyltransferase activity."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 40
FT /note="N->D: No effect on adenylyltransferase activity and
FT RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 40
FT /note="N->Q: 80% loss of adenylyltransferase activity and
FT RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 40
FT /note="N->R: Complete loss of adenylyltransferase activity
FT and RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 55
FT /note="R->A,Q: Almost complete loss of adenylyltransferase
FT activity and RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 65
FT /note="F->A: Strongly reduced RNA ligase activity."
FT /evidence="ECO:0000269|PubMed:17018278"
FT MUTAGEN 66
FT /note="F->A: Strongly reduced RNA ligase activity."
FT /evidence="ECO:0000269|PubMed:17018278"
FT MUTAGEN 99
FT /note="E->A,D,Q: Complete loss of adenylyltransferase
FT activity and RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 119
FT /note="F->A: Complete loss of adenylyltransferase activity
FT and RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 119
FT /note="F->L: Complete loss of adenylyltransferase activity.
FT Partial loss of RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 120
FT /note="D->A,N: Complete loss of adenylyltransferase
FT activity and RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 120
FT /note="D->E: 88% loss of adenylyltransferase activity.
FT Partial loss of RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 189
FT /note="K->A: 30% loss of adenylyltransferase activity. No
FT effect on RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 204
FT /note="E->A: Complete loss of RNA ligase activity in
FT vitro."
FT /evidence="ECO:0000269|PubMed:12228725"
FT MUTAGEN 209
FT /note="K->A: Almost complete loss of adenylyltransferase
FT activity."
FT /evidence="ECO:0000269|PubMed:12611899"
FT MUTAGEN 225
FT /note="K->A: Complete loss of RNA ligase activity in
FT vitro."
FT /evidence="ECO:0000269|PubMed:12228725"
FT MUTAGEN 227
FT /note="K->A: Complete loss of RNA ligase activity in vitro.
FT Almost complete loss of adenylyltransferase activity and
FT RNA ligation."
FT /evidence="ECO:0000269|PubMed:12228725,
FT ECO:0000269|PubMed:12611899"
FT MUTAGEN 227
FT /note="K->R,Q: Complete loss of RNA ligase activity in
FT vitro. Almost complete loss of adenylyltransferase
FT activity. Partial loss of RNA ligation."
FT /evidence="ECO:0000269|PubMed:12611899"
FT HELIX 14..23
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 30..34
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 38..48
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 50..54
FT /evidence="ECO:0007829|PDB:1S68"
FT TURN 66..68
FT /evidence="ECO:0007829|PDB:1S68"
FT HELIX 69..74
FT /evidence="ECO:0007829|PDB:1S68"
FT HELIX 76..89
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 91..102
FT /evidence="ECO:0007829|PDB:1S68"
FT TURN 103..105
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 106..108
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 115..125
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:1S68"
FT HELIX 135..145
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 152..156
FT /evidence="ECO:0007829|PDB:1S68"
FT HELIX 158..161
FT /evidence="ECO:0007829|PDB:1S68"
FT HELIX 172..182
FT /evidence="ECO:0007829|PDB:1S68"
FT HELIX 184..189
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 198..200
FT /evidence="ECO:0007829|PDB:2HVQ"
FT STRAND 205..212
FT /evidence="ECO:0007829|PDB:1S68"
FT STRAND 224..227
FT /evidence="ECO:0007829|PDB:1S68"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:1S68"
FT HELIX 249..258
FT /evidence="ECO:0007829|PDB:2HVQ"
FT HELIX 259..261
FT /evidence="ECO:0007829|PDB:2HVQ"
FT HELIX 264..272
FT /evidence="ECO:0007829|PDB:2HVQ"
FT HELIX 282..299
FT /evidence="ECO:0007829|PDB:2HVQ"
FT STRAND 305..308
FT /evidence="ECO:0007829|PDB:2HVQ"
FT HELIX 310..323
FT /evidence="ECO:0007829|PDB:2HVQ"
FT TURN 324..327
FT /evidence="ECO:0007829|PDB:2HVQ"
FT TURN 329..331
FT /evidence="ECO:0007829|PDB:2HVR"
SQ SEQUENCE 334 AA; 37627 MW; 1E272FBFCE02605A CRC64;
MFKKYSSLEN HYNSKFIEKL YSLGLTGGEW VAREKIHGTN FSLIIERDKV TCAKRTGPIL
PAEDFFGYEI ILKNYADSIK AVQDIMETSA VVSYQVFGEF AGPGIQKNVD YCDKDFYVFD
IIVTTESGDV TYVDDYMMES FCNTFKFKMA PLLGRGKFEE LIKLPNDLDS VVQDYNFTVD
HAGLVDANKC VWNAEAKGEV FTAEGYVLKP CYPSWLRNGN RVAIKCKNSK FSEKKKSDKP
IKAKVELSEA DNKLVGILAC YVTLNRVNNV ISKIGEIGPK DFGKVMGLTV QDILEETSRE
GITLTQADNP SLIKKELVKM VQDVLRPAWI ELVS
//
