ID   RLIG_BPRHR              Reviewed;         438 AA.
AC   P0DTD9;
DT   17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT   17-JUN-2020, sequence version 1.
DT   03-AUG-2022, entry version 5.
DE   RecName: Full=RNA ligase;
DE            EC=6.5.1.- {ECO:0000269|PubMed:14654700};
OS   Rhodothermus phage RM378 (Bacteriophage RM378).
OC   Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC   Caudovirales; Myoviridae.
OX   NCBI_TaxID=148943;
OH   NCBI_TaxID=29549; Rhodothermus marinus (Rhodothermus obamensis).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR,
RP   AND CATALYTIC ACTIVITY.
RX   PubMed=14654700; DOI=10.1093/nar/gkg914;
RA   Blondal T., Hjorleifsdottir S.H., Fridjonsson O.F., Aevarsson A.,
RA   Skirnisdottir S., Hermannsdottir A.G., Hreggvidsson G.O., Smith A.V.,
RA   Kristjansson J.K.;
RT   "Discovery and characterization of a thermostable bacteriophage RNA ligase
RT   homologous to T4 RNA ligase 1.";
RL   Nucleic Acids Res. 31:7247-7254(2003).
CC   -!- FUNCTION: Involved in countering a host defense mechanism which,
CC       following viral infection, activates the host induced anticodon
CC       nuclease and shuts off viral translation. Repairs 5'-PO4 and 3'-OH
CC       groups in the cleaved host tRNA. {ECO:0000250|UniProtKB:P00971}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:14654700};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000269|PubMed:14654700};
CC       Note=Optimum activity is reached at 1 mM and 5 mM for Mn(2+) and Mg(2+)
CC       respectively, with Mn(2+) showing 90% of the Mg(2+) activity.
CC       {ECO:0000269|PubMed:14654700};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       pH dependence:
CC         Optimum pH is 7.;
CC       Temperature dependence:
CC         Optimum temperature is 64 degrees Celsius.;
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DR   EMBL; AX059140; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   RefSeq; NP_835690.1; NC_004735.1.
DR   GeneID; 1260418; -.
DR   KEGG; vg:1260418; -.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0016874; F:ligase activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0042245; P:RNA repair; IEA:UniProtKB-KW.
DR   InterPro; IPR019039; RNA_ligase_T4-Rnl1_N.
DR   Pfam; PF09511; RNA_lig_T4_1; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Evasion of bacteria-mediated translation shutoff by virus;
KW   Host-virus interaction; Ligase; Magnesium; Manganese; Metal-binding;
KW   Nucleotide-binding; RNA repair.
FT   CHAIN           1..438
FT                   /note="RNA ligase"
FT                   /id="PRO_0000450099"
FT   ACT_SITE        127
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000250|UniProtKB:P00971"
FT   BINDING         48
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P00971"
FT   BINDING         63
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P00971"
FT   BINDING         83
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P00971"
FT   BINDING         198
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P00971"
FT   BINDING         311
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P00971"
FT   BINDING         313
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P00971"
FT   BINDING         342
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250|UniProtKB:P00971"
FT   SITE            198
FT                   /note="Essential for RNA ligase activity"
FT                   /evidence="ECO:0000250|UniProtKB:P00971"
FT   SITE            317
FT                   /note="Essential for RNA ligase activity"
FT                   /evidence="ECO:0000250|UniProtKB:P00971"
SQ   SEQUENCE   438 AA;  51700 MW;  6F2EA3AC14034BB3 CRC64;
     MESMNVKYPV EYLIEHLNSF ESPEVAVESL RKEGIMCKNR GDLYMFKYHL GCKFDKIYHL
     ACRGAILRKT DSGWKVLSYP FDKFFNWGEE LQPEIVNYYQ TLRYASPLNE KRKAGFMFKL
     PMKLVEKLDG TCVVLYYDEG WKIHTLGSID ANGSIVKNGM VTTHMDKTYR ELFWETFEKK
     YPPYLLYHLN SSYCYIFEMV HPDARVVVPY EEPNIILIGV RSVDPEKGYF EVGPSEEAVR
     IFNESGGKIN LKLPAVLSQE QNYTLFRANR LQELFEEVTP LFKSLRDGYE VVYEGFVAVQ
     EIAPRVYYRT KIKHPVYLEL HRIKTTITPE KLADLFLENK LDDFVLTPDE QETVMKLKEI
     YTDMRNQLES SFDTIYKEIS EQVSPEENPG EFRKRFALRL MDYHDKSWFF ARLDGDEEKM
     QKSEKKLLTE RIEKGLFK