RLIG_BPT4
ID RLIG_BPT4 Reviewed; 374 AA.
AC P00971;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 21-JUL-1986, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=RNA ligase 1 {ECO:0000255|HAMAP-Rule:MF_04149};
DE EC=6.5.1.3 {ECO:0000255|HAMAP-Rule:MF_04149, ECO:0000269|PubMed:12766156, ECO:0000269|PubMed:17068206, ECO:0000269|PubMed:3036206};
DE AltName: Full=Gene product 63;
DE Short=gp63;
DE AltName: Full=Rnl1 {ECO:0000255|HAMAP-Rule:MF_04149};
GN Name=63;
OS Enterobacteria phage T4 (Bacteriophage T4).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Myoviridae; Tevenvirinae; Tequatrovirus.
OX NCBI_TaxID=10665;
OH NCBI_TaxID=562; Escherichia coli.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6370680; DOI=10.1002/j.1460-2075.1984.tb01819.x;
RA Rand K.N., Gait M.J.;
RT "Sequence and cloning of bacteriophage T4 gene 63 encoding RNA ligase and
RT tail fibre attachment activities.";
RL EMBO J. 3:397-402(1984).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-89.
RX PubMed=3530746; DOI=10.1002/j.1460-2075.1986.tb04460.x;
RA Sjoeberg B.-M., Hahne S., Mathews C.Z., Mathews C.K., Rand K.N., Gait M.J.;
RT "The bacteriophage T4 gene for the small subunit of ribonucleotide
RT reductase contains an intron.";
RL EMBO J. 5:2031-2036(1986).
RN [4]
RP ACTIVE SITE.
RX PubMed=3882425; DOI=10.1111/j.1432-1033.1985.tb08753.x;
RA Thoegersen H.C., Morris H.R., Rand K.N., Gait M.J.;
RT "Location of the adenylylation site in T4 RNA ligase.";
RL Eur. J. Biochem. 147:325-329(1985).
RN [5]
RP MUTAGENESIS OF LYS-99; GLU-100 AND ASP-101, AND CATALYTIC ACTIVITY.
RX PubMed=3036206; DOI=10.1021/bi00380a030;
RA Heaphy S., Singh M., Gait M.J.;
RT "Effect of single amino acid changes in the region of the adenylylation
RT site of T4 RNA ligase.";
RL Biochemistry 26:1688-1696(1987).
RN [6]
RP FUNCTION.
RX PubMed=2444436; DOI=10.1002/j.1460-2075.1987.tb02532.x;
RA Amitsur M., Levitz R., Kaufmann G.;
RT "Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase
RT reprocess the host lysine tRNA.";
RL EMBO J. 6:2499-2503(1987).
RN [7]
RP MUTAGENESIS OF ARG-54; LYS-75; PHE-77; LYS-99; GLY-102; LYS-119; GLU-227;
RP GLY-228; LYS-240 AND LYS-242, AND CATALYTIC ACTIVITY.
RX PubMed=12766156; DOI=10.1074/jbc.m304320200;
RA Wang L.K., Ho C.K., Pei Y., Shuman S.;
RT "Mutational analysis of bacteriophage T4 RNA ligase 1. Different functional
RT groups are required for the nucleotidyl transfer and phosphodiester bond
RT formation steps of the ligation reaction.";
RL J. Biol. Chem. 278:29454-29462(2003).
RN [8]
RP FUNCTION, MUTAGENESIS OF TYR-37; TRP-45; GLU-159; ASN-165; LEU-179;
RP VAL-230; TYR-246; ASP-272 AND ASP-273, AND CATALYTIC ACTIVITY.
RX PubMed=17068206; DOI=10.1261/rna.271706;
RA Wang L.K., Schwer B., Shuman S.;
RT "Structure-guided mutational analysis of T4 RNA ligase 1.";
RL RNA 12:2126-2134(2006).
RN [9]
RP BIOPHYSICOCHEMICAL PROPERTIES, AND FUNCTION.
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 [10]
RP DOMAIN.
RX PubMed=17585047; DOI=10.1261/rna.591807;
RA Wang L.K., Nandakumar J., Schwer B., Shuman S.;
RT "The C-terminal domain of T4 RNA ligase 1 confers specificity for tRNA
RT repair.";
RL RNA 13:1235-1244(2007).
RN [11] {ECO:0007744|PDB:2C5U}
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), AND COFACTOR.
RX PubMed=16263720; DOI=10.1074/jbc.m509658200;
RA El Omari K., Ren J., Bird L.E., Bona M.K., Klarmann G., LeGrice S.F.J.,
RA Stammers D.K.;
RT "Molecular architecture and ligand recognition determinants for T4 RNA
RT ligase.";
RL J. Biol. Chem. 281:1573-1579(2006).
RN [12] {ECO:0007744|PDB:5TT6}
RP X-RAY CRYSTALLOGRAPHY (2.19 ANGSTROMS) IN COMPLEX WITH ATP, AND COFACTOR.
RX PubMed=28223499; DOI=10.1073/pnas.1619220114;
RA Unciuleac M.C., Goldgur Y., Shuman S.;
RT "Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-
RT dependent and NAD+-dependent polynucleotide ligases.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:2592-2597(2017).
CC -!- FUNCTION: Involved in countering a host defense mechanism which,
CC following viral infection, activates the host anticodon nuclease and
CC shuts off viral translation. Repairs 5'-PO4 and 3'-OH groups in the
CC cleaved host tRNA (PubMed:16671895, PubMed:17068206, PubMed:2444436).
CC The nick ligation reaction entails three nucleotidyl transfer steps
CC (PubMed:12766156). In the first step, the RNA ligase reacts with ATP in
CC the absence of nucleic acid to form a covalent ligase-AMP intermediate
CC and release pyrophosphate (PubMed:12766156). In step 2, the ligase-AMP
CC binds to the nicked duplex nucleic acid and transfers the adenylate to
CC the 5'-PO4 terminus to form an adenylylated nicked intermediate
CC (PubMed:12766156). In step 3, the RNA ligase directs the attack of the
CC nick 3'-OH on the 5'-phosphoanhydride linkage, resulting in a repaired
CC 3'-5' phosphodiester and release of AMP (By similarity)
CC (PubMed:12766156). {ECO:0000255|HAMAP-Rule:MF_04149,
CC ECO:0000269|PubMed:12766156, ECO:0000269|PubMed:16671895,
CC ECO:0000269|PubMed:17068206, ECO:0000269|PubMed:2444436}.
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_04149,
CC ECO:0000269|PubMed:12766156, ECO:0000269|PubMed:17068206,
CC ECO:0000269|PubMed:3036206};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_04149,
CC ECO:0000269|PubMed:16263720, ECO:0000269|PubMed:28223499};
CC Note=Binds 2 magnesium ions that perform the catalytic activity via a
CC two-metal mechanism (PubMed:28223499, PubMed:16263720). One of the
CC catalytic Mg(2+), which is coordinated by 5 water molecules, engages
CC the lysine nucleophile and the ATP alpha phosphate while the Mg(2+)
CC orients the PPi leaving group (PubMed:28223499). {ECO:0000255|HAMAP-
CC Rule:MF_04149, ECO:0000269|PubMed:16263720,
CC ECO:0000269|PubMed:28223499};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8.0. {ECO:0000269|PubMed:16671895};
CC -!- DOMAIN: The N-terminus contains the nucleotidyltransferase domain
CC (PubMed:17585047). The C-terminus probably confers tRNA specificity
CC (PubMed:17585047). {ECO:0000269|PubMed:17585047}.
CC -!- SIMILARITY: Belongs to the Tequatrovirus RNA ligase 1 family.
CC {ECO:0000255|HAMAP-Rule:MF_04149}.
CC -!- CAUTION: An interaction between the carbonyl oxygen of Gly-269 and the
CC magnesium ion may occur. {ECO:0000269|PubMed:16263720}.
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DR EMBL; X00365; CAA25107.1; -; Genomic_DNA.
DR EMBL; X04140; CAA27760.1; -; Genomic_DNA.
DR EMBL; AF158101; AAD42514.1; -; Genomic_DNA.
DR EMBL; M10160; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; A01202; LQBPR4.
DR RefSeq; NP_049839.1; NC_000866.4.
DR PDB; 2C5U; X-ray; 2.21 A; A/B=1-374.
DR PDB; 5TT6; X-ray; 2.19 A; A=1-374.
DR PDBsum; 2C5U; -.
DR PDBsum; 5TT6; -.
DR SMR; P00971; -.
DR GeneID; 1258717; -.
DR KEGG; vg:1258717; -.
DR EvolutionaryTrace; P00971; -.
DR Proteomes; UP000009087; 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; IMP:CACAO.
DR GO; GO:0042245; P:RNA repair; IEA:UniProtKB-UniRule.
DR GO; GO:0098004; P:virus tail fiber assembly; IMP:CACAO.
DR HAMAP; MF_04149; RNALIG_T4; 1.
DR InterPro; IPR019039; RNA_ligase_T4-Rnl1_N.
DR InterPro; IPR012648; Rnl1.
DR Pfam; PF09511; RNA_lig_T4_1; 1.
DR TIGRFAMs; TIGR02308; RNA_lig_T4_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding;
KW Evasion of bacteria-mediated translation shutoff by virus;
KW Host-virus interaction; Ligase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; RNA repair.
FT CHAIN 1..374
FT /note="RNA ligase 1"
FT /id="PRO_0000164976"
FT ACT_SITE 99
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04149,
FT ECO:0000269|PubMed:3882425"
FT BINDING 37
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04149,
FT ECO:0000269|PubMed:28223499"
FT BINDING 54
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04149,
FT ECO:0000269|PubMed:28223499"
FT BINDING 75
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04149,
FT ECO:0000269|PubMed:28223499"
FT BINDING 159
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04149,
FT ECO:0000269|PubMed:28223499"
FT BINDING 240
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04149,
FT ECO:0000269|PubMed:28223499"
FT BINDING 242
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04149,
FT ECO:0000269|PubMed:28223499"
FT BINDING 272
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04149,
FT ECO:0000269|PubMed:16263720, ECO:0000269|PubMed:28223499"
FT SITE 159
FT /note="Essential for RNA ligase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04149,
FT ECO:0000269|PubMed:17068206"
FT SITE 246
FT /note="Essential for RNA ligase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04149,
FT ECO:0000269|PubMed:17068206"
FT MUTAGEN 37
FT /note="Y->A: No effect on the ligation of 5'-PO4 and 3'-OH
FT termini of the RNA strand and on tRNA repair."
FT /evidence="ECO:0000269|PubMed:17068206"
FT MUTAGEN 45
FT /note="W->A: Partial loss of the ligation of 5'-PO4 and 3'-
FT OH termini of the RNA strand and on tRNA repair."
FT /evidence="ECO:0000269|PubMed:17068206"
FT MUTAGEN 54
FT /note="R->A: 65% loss of adenylyltransferase activity. 70%
FT loss of ligase activity."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 75
FT /note="K->A: 95% loss of adenylyltransferase activity.
FT Impaired ligase activity."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 77
FT /note="F->A: 90% loss of adenylyltransferase activity.
FT Impaired ligase activity."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 99
FT /note="K->A: Complete loss of adenylyltransferase activity
FT and ligase activity."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 99
FT /note="K->N: Complete loss of ligase activity."
FT /evidence="ECO:0000269|PubMed:3036206"
FT MUTAGEN 99
FT /note="K->R: About 50% loss of ligase activity."
FT /evidence="ECO:0000269|PubMed:3036206"
FT MUTAGEN 100
FT /note="E->Q: No effect on ligase activity."
FT /evidence="ECO:0000269|PubMed:3036206"
FT MUTAGEN 100
FT /note="E->T: About 50% loss of ligase activity."
FT /evidence="ECO:0000269|PubMed:3036206"
FT MUTAGEN 101
FT /note="D->N,S,E: Complete loss of ligase activity."
FT /evidence="ECO:0000269|PubMed:3036206"
FT MUTAGEN 102
FT /note="G->A: Complete loss of adenylyltransferase activity
FT and ligase activity."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 119
FT /note="K->A: Increased adenylyltransferase activity. No
FT effect on ligase activity."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 159
FT /note="E->A: Complete loss of ligation of 5'-PO4 and 3'-OH
FT termini of the RNA strand and complete loss of tRNA
FT repair."
FT /evidence="ECO:0000269|PubMed:17068206"
FT MUTAGEN 165
FT /note="N->A: Partial loss of the ligation of 5'-PO4 and 3'-
FT OH termini of the RNA strand; no effect on tRNA repair."
FT /evidence="ECO:0000269|PubMed:17068206"
FT MUTAGEN 179
FT /note="L->A: Partial loss of the ligation of 5'-PO4 and 3'-
FT OH termini of the RNA strand; no effect on tRNA repair."
FT /evidence="ECO:0000269|PubMed:17068206"
FT MUTAGEN 182
FT /note="R->A: Complete loss of ligation."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 227
FT /note="E->A: Complete loss of adenylyltransferase activity
FT and ligase activity."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 228
FT /note="G->A: Complete loss of adenylyltransferase activity
FT and ligase activity."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 230
FT /note="V->A: Partial loss of the ligation of 5'-PO4 and 3'-
FT OH termini of the RNA strand; no effect on tRNA repair."
FT /evidence="ECO:0000269|PubMed:17068206"
FT MUTAGEN 240
FT /note="K->A: Complete loss of adenylyltransferase activity
FT and ligase activity."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 242
FT /note="K->A: Complete loss of adenylyltransferase activity
FT and ligase activity."
FT /evidence="ECO:0000269|PubMed:12766156"
FT MUTAGEN 246
FT /note="Y->A: Complete loss of ligation of 5'-PO4 and 3'-OH
FT termini of the RNA strand and complete loss of tRNA repair;
FT no effect on adenylyltransferase activity."
FT /evidence="ECO:0000269|PubMed:17068206"
FT MUTAGEN 272
FT /note="D->A: No effect on the ligation of 5'-PO4 and 3'-OH
FT termini of the RNA strand and no effect on tRNA repair."
FT /evidence="ECO:0000269|PubMed:17068206"
FT MUTAGEN 273
FT /note="D->A: No effect on the ligation of 5'-PO4 and 3'-OH
FT termini of the RNA strand and no effect on tRNA repair."
FT /evidence="ECO:0000269|PubMed:17068206"
FT HELIX 1..11
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 18..25
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 31..38
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:5TT6"
FT TURN 53..55
FT /evidence="ECO:0007829|PDB:2C5U"
FT STRAND 57..61
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 64..70
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 90..92
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 93..98
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 102..110
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 113..120
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 122..124
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 125..135
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 137..139
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 140..151
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 154..161
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 163..165
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 167..169
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 175..183
FT /evidence="ECO:0007829|PDB:5TT6"
FT TURN 184..186
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 192..197
FT /evidence="ECO:0007829|PDB:5TT6"
FT TURN 199..201
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 208..210
FT /evidence="ECO:0007829|PDB:2C5U"
FT HELIX 216..222
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 228..233
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 238..242
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 244..250
FT /evidence="ECO:0007829|PDB:5TT6"
FT TURN 253..257
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 259..267
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 271..277
FT /evidence="ECO:0007829|PDB:5TT6"
FT TURN 278..280
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 282..313
FT /evidence="ECO:0007829|PDB:5TT6"
FT STRAND 314..316
FT /evidence="ECO:0007829|PDB:2C5U"
FT HELIX 318..331
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 337..343
FT /evidence="ECO:0007829|PDB:5TT6"
FT TURN 344..346
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 351..364
FT /evidence="ECO:0007829|PDB:5TT6"
FT HELIX 366..369
FT /evidence="ECO:0007829|PDB:5TT6"
SQ SEQUENCE 374 AA; 43509 MW; 04388DBA72A8121C CRC64;
MQELFNNLME LCKDSQRKFF YSDDVSASGR TYRIFSYNYA SYSDWLLPDA LECRGIMFEM
DGEKPVRIAS RPMEKFFNLN ENPFTMNIDL NDVDYILTKE DGSLVSTYLD GDEILFKSKG
SIKSEQALMA NGILMNINHH RLRDRLKELA EDGFTANFEF VAPTNRIVLA YQEMKIILLN
VRENETGEYI SYDDIYKDAT LRPYLVERYE IDSPKWIEEA KNAENIEGYV AVMKDGSHFK
IKSDWYVSLH STKSSLDNPE KLFKTIIDGA SDDLKAMYAD DEYSYRKIEA FETTYLKYLD
RALFLVLDCH NKHCGKDRKT YAMEAQGVAK GAGMDHLFGI IMSLYQGYDS QEKVMCEIEQ
NFLKNYKKFI PEGY
