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T4 RNA ligase 1 (EC 6.5.1.3) (Gene product 63) (gp63) (Rnl1)

 RLIG_BPT4               Reviewed;         374 AA.
P00971;
21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
21-JUL-1986, sequence version 1.
05-JUL-2017, entry version 92.
RecName: Full=T4 RNA ligase 1;
EC=6.5.1.3 {ECO:0000305};
AltName: Full=Gene product 63;
Short=gp63;
AltName: Full=Rnl1;
Name=63;
Enterobacteria phage T4 (Bacteriophage T4).
Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae;
Tevenvirinae; T4virus.
NCBI_TaxID=10665;
NCBI_TaxID=562; Escherichia coli.
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=6370680;
Rand K.N., Gait M.J.;
"Sequence and cloning of bacteriophage T4 gene 63 encoding RNA ligase
and tail fibre attachment activities.";
EMBO J. 3:397-402(1984).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=12626685; DOI=10.1128/MMBR.67.1.86-156.2003;
Miller E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Ruger W.;
"Bacteriophage T4 genome.";
Microbiol. Mol. Biol. Rev. 67:86-156(2003).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-89.
PubMed=3530746;
Sjoeberg B.-M., Hahne S., Mathews C.Z., Mathews C.K., Rand K.N.,
Gait M.J.;
"The bacteriophage T4 gene for the small subunit of ribonucleotide
reductase contains an intron.";
EMBO J. 5:2031-2036(1986).
[4]
ACTIVE SITE.
PubMed=3882425; DOI=10.1111/j.1432-1033.1985.tb08753.x;
Thoegersen H.C., Morris H.R., Rand K.N., Gait M.J.;
"Location of the adenylylation site in T4 RNA ligase.";
Eur. J. Biochem. 147:325-329(1985).
[5]
FUNCTION.
PubMed=2444436;
Amitsur M., Levitz R., Kaufmann G.;
"Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA
ligase reprocess the host lysine tRNA.";
EMBO J. 6:2499-2503(1987).
[6]
X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
PubMed=16263720; DOI=10.1074/jbc.M509658200;
El Omari K., Ren J., Bird L.E., Bona M.K., Klarmann G.,
LeGrice S.F.J., Stammers D.K.;
"Molecular architecture and ligand recognition determinants for T4 RNA
ligase.";
J. Biol. Chem. 281:1573-1579(2006).
-!- FUNCTION: Involved in countering a host defense mechanism which
activates T4-induced anticodon nuclease and shuts off viral
translation. Repairs 5'-PO4 and 3'-OH groups in tRNA(Lys).
{ECO:0000269|PubMed:2444436}.
-!- CATALYTIC ACTIVITY: ATP + (ribonucleotide)(n)-3'-hydroxyl + 5'-
phospho-(ribonucleotide)(m) = (ribonucleotide)(n+m) + AMP +
diphosphate. {ECO:0000305}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Note=Binds 2 magnesium ions per subunit.;
-----------------------------------------------------------------------
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EMBL; X00365; CAA25107.1; -; Genomic_DNA.
EMBL; X04140; CAA27760.1; -; Genomic_DNA.
EMBL; AF158101; AAD42514.1; -; Genomic_DNA.
EMBL; M10160; -; NOT_ANNOTATED_CDS; Genomic_DNA.
PIR; A01202; LQBPR4.
RefSeq; NP_049839.1; NC_000866.4.
PDB; 2C5U; X-ray; 2.21 A; A/B=1-374.
PDB; 5TT6; X-ray; 2.19 A; A=1-374.
PDBsum; 2C5U; -.
PDBsum; 5TT6; -.
ProteinModelPortal; P00971; -.
SMR; P00971; -.
GeneID; 1258717; -.
KEGG; vg:1258717; -.
KO; K18961; -.
OrthoDB; VOG090000AX; -.
EvolutionaryTrace; P00971; -.
Proteomes; UP000009087; Genome.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0003972; F:RNA ligase (ATP) activity; IMP:CACAO.
GO; GO:0042245; P:RNA repair; IEA:UniProtKB-KW.
GO; GO:0098004; P:virus tail fiber assembly; IMP:CACAO.
InterPro; IPR012648; Phage_T4_Rnl1.
InterPro; IPR019039; RNA_ligase_T4-Rnl1_N.
Pfam; PF09511; RNA_lig_T4_1; 1.
TIGRFAMs; TIGR02308; RNA_lig_T4_1; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome;
Evasion of bacteria-mediated translation shutoff by virus;
Host-virus interaction; Ligase; Magnesium; Metal-binding;
Nucleotide-binding; Reference proteome; RNA repair.
CHAIN 1 374 T4 RNA ligase 1.
/FTId=PRO_0000164976.
ACT_SITE 99 99 N6-AMP-lysine intermediate.
{ECO:0000269|PubMed:3882425}.
METAL 269 269 Magnesium 2; via carbonyl oxygen.
METAL 272 272 Magnesium 2.
HELIX 1 11 {ECO:0000244|PDB:5TT6}.
STRAND 18 25 {ECO:0000244|PDB:5TT6}.
STRAND 31 38 {ECO:0000244|PDB:5TT6}.
HELIX 44 46 {ECO:0000244|PDB:5TT6}.
HELIX 50 52 {ECO:0000244|PDB:5TT6}.
TURN 53 55 {ECO:0000244|PDB:2C5U}.
STRAND 57 61 {ECO:0000244|PDB:5TT6}.
STRAND 64 70 {ECO:0000244|PDB:5TT6}.
HELIX 83 85 {ECO:0000244|PDB:5TT6}.
HELIX 90 92 {ECO:0000244|PDB:5TT6}.
STRAND 93 98 {ECO:0000244|PDB:5TT6}.
STRAND 102 110 {ECO:0000244|PDB:5TT6}.
STRAND 113 120 {ECO:0000244|PDB:5TT6}.
STRAND 122 124 {ECO:0000244|PDB:5TT6}.
HELIX 125 135 {ECO:0000244|PDB:5TT6}.
HELIX 137 139 {ECO:0000244|PDB:5TT6}.
HELIX 140 151 {ECO:0000244|PDB:5TT6}.
STRAND 154 161 {ECO:0000244|PDB:5TT6}.
HELIX 163 165 {ECO:0000244|PDB:5TT6}.
STRAND 167 169 {ECO:0000244|PDB:5TT6}.
STRAND 175 183 {ECO:0000244|PDB:5TT6}.
TURN 184 186 {ECO:0000244|PDB:5TT6}.
HELIX 192 197 {ECO:0000244|PDB:5TT6}.
TURN 199 201 {ECO:0000244|PDB:5TT6}.
HELIX 202 204 {ECO:0000244|PDB:5TT6}.
STRAND 208 210 {ECO:0000244|PDB:2C5U}.
HELIX 216 222 {ECO:0000244|PDB:5TT6}.
STRAND 228 233 {ECO:0000244|PDB:5TT6}.
STRAND 238 242 {ECO:0000244|PDB:5TT6}.
HELIX 244 250 {ECO:0000244|PDB:5TT6}.
TURN 253 257 {ECO:0000244|PDB:5TT6}.
HELIX 259 267 {ECO:0000244|PDB:5TT6}.
HELIX 271 277 {ECO:0000244|PDB:5TT6}.
TURN 278 280 {ECO:0000244|PDB:5TT6}.
HELIX 282 313 {ECO:0000244|PDB:5TT6}.
STRAND 314 316 {ECO:0000244|PDB:2C5U}.
HELIX 318 331 {ECO:0000244|PDB:5TT6}.
HELIX 337 343 {ECO:0000244|PDB:5TT6}.
TURN 344 346 {ECO:0000244|PDB:5TT6}.
HELIX 351 364 {ECO:0000244|PDB:5TT6}.
HELIX 366 369 {ECO:0000244|PDB:5TT6}.
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


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