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RNA ligase 2 (Rnl2) (EC 6.5.1.3)

 RLIG2_BPT4              Reviewed;         334 AA.
P32277;
01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
01-OCT-1993, sequence version 1.
15-FEB-2017, entry version 88.
RecName: Full=RNA ligase 2;
Short=Rnl2;
EC=6.5.1.3 {ECO:0000269|PubMed:12228725, ECO:0000269|PubMed:17018278};
Name=Y10A; Synonyms=24.1;
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].
Kaliman A.V., Khasanova M.A., Tanyashin V.I.;
Submitted (NOV-1992) to the EMBL/GenBank/DDBJ databases.
[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]
FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF LYS-35; HIS-37;
GLU-204; LYS-225 AND LYS-227.
PubMed=12228725; DOI=10.1073/pnas.192184699;
Ho C.K., Shuman S.;
"Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA
ligases found in all phylogenetic domains.";
Proc. Natl. Acad. Sci. U.S.A. 99:12709-12714(2002).
[4]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-249 IN COMPLEX WITH AMP.
PubMed=14962393; DOI=10.1016/j.str.2004.01.011;
Ho C.K., Wang L.K., Lima C.D., Shuman S.;
"Structure and mechanism of RNA ligase.";
Structure 12:327-339(2004).
[5]
X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH AMP; ATP AND RNA
SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF THR-39; PHE-65
AND PHE-66, AND ACTIVE SITE.
PubMed=17018278; DOI=10.1016/j.cell.2006.08.038;
Nandakumar J., Shuman S., Lima C.D.;
"RNA ligase structures reveal the basis for RNA specificity and
conformational changes that drive ligation forward.";
Cell 127:71-84(2006).
-!- FUNCTION: Catalyzes intramolecular and intermolecular RNA strand
joining (in vitro). May play a role in the repair of nicked RNA
molecules. {ECO:0000269|PubMed:12228725,
ECO:0000269|PubMed:17018278}.
-!- CATALYTIC ACTIVITY: ATP + (ribonucleotide)(n)-3'-hydroxyl + 5'-
phospho-(ribonucleotide)(m) = (ribonucleotide)(n+m) + AMP +
diphosphate. {ECO:0000269|PubMed:12228725,
ECO:0000269|PubMed:17018278}.
-!- SIMILARITY: Belongs to the RNA ligase 2 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X69459; CAA49218.1; -; Genomic_DNA.
EMBL; AF158101; AAD42430.1; -; Genomic_DNA.
PIR; S28563; S28563.
RefSeq; NP_049790.1; NC_000866.4.
PDB; 1S68; X-ray; 1.90 A; A=1-249.
PDB; 2HVQ; X-ray; 2.40 A; A=1-334.
PDB; 2HVR; X-ray; 2.45 A; A/B=1-334.
PDB; 2HVS; X-ray; 2.50 A; A/B=1-334.
PDBsum; 1S68; -.
PDBsum; 2HVQ; -.
PDBsum; 2HVR; -.
PDBsum; 2HVS; -.
ProteinModelPortal; P32277; -.
SMR; P32277; -.
GeneID; 1258563; -.
KEGG; vg:1258563; -.
KO; K18962; -.
OrthoDB; VOG090000FL; -.
BRENDA; 6.5.1.3; 732.
EvolutionaryTrace; P32277; -.
Proteomes; UP000009087; Genome.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0003972; F:RNA ligase (ATP) activity; IEA:UniProtKB-EC.
GO; GO:0042245; P:RNA repair; IEA:UniProtKB-KW.
InterPro; IPR012647; RNA_lig_RNL2.
InterPro; IPR021122; RNA_ligase_dom_REL/Rnl2.
Pfam; PF09414; RNA_ligase; 1.
TIGRFAMs; TIGR02307; RNA_lig_RNL2; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; Ligase;
Nucleotide-binding; Reference proteome; RNA repair.
CHAIN 1 334 RNA ligase 2.
/FTId=PRO_0000165156.
NP_BIND 6 8 ATP. {ECO:0000250}.
NP_BIND 34 40 ATP. {ECO:0000269|PubMed:17018278}.
NP_BIND 225 227 ATP. {ECO:0000269|PubMed:17018278}.
REGION 1 234 Adenylyltransferase.
ACT_SITE 35 35 N6-AMP-lysine intermediate.
{ECO:0000269|PubMed:17018278}.
BINDING 55 55 ATP. {ECO:0000269|PubMed:17018278}.
BINDING 99 99 ATP. {ECO:0000269|PubMed:17018278}.
BINDING 119 119 ATP. {ECO:0000250}.
SITE 218 218 Interaction with RNA.
SITE 314 314 Interaction with RNA.
MUTAGEN 35 35 K->A: Complete loss of RNA ligase
activity in vitro.
{ECO:0000269|PubMed:12228725}.
MUTAGEN 37 37 H->D: No effect on RNA ligase activity in
vitro. {ECO:0000269|PubMed:12228725}.
MUTAGEN 39 39 T->A: No effect on RNA ligase activity.
{ECO:0000269|PubMed:17018278}.
MUTAGEN 65 65 F->A: Strongly reduced RNA ligase
activity. {ECO:0000269|PubMed:17018278}.
MUTAGEN 66 66 F->A: Strongly reduced RNA ligase
activity. {ECO:0000269|PubMed:17018278}.
MUTAGEN 204 204 E->A: Complete loss of RNA ligase
activity in vitro.
{ECO:0000269|PubMed:12228725}.
MUTAGEN 225 225 K->A: Complete loss of RNA ligase
activity in vitro.
{ECO:0000269|PubMed:12228725}.
MUTAGEN 227 227 K->A: Complete loss of RNA ligase
activity in vitro.
{ECO:0000269|PubMed:12228725}.
HELIX 14 23 {ECO:0000244|PDB:1S68}.
STRAND 30 34 {ECO:0000244|PDB:1S68}.
STRAND 38 48 {ECO:0000244|PDB:1S68}.
STRAND 50 54 {ECO:0000244|PDB:1S68}.
TURN 66 68 {ECO:0000244|PDB:1S68}.
HELIX 69 74 {ECO:0000244|PDB:1S68}.
HELIX 76 89 {ECO:0000244|PDB:1S68}.
STRAND 91 102 {ECO:0000244|PDB:1S68}.
TURN 103 105 {ECO:0000244|PDB:1S68}.
STRAND 106 108 {ECO:0000244|PDB:1S68}.
STRAND 115 125 {ECO:0000244|PDB:1S68}.
STRAND 130 132 {ECO:0000244|PDB:1S68}.
HELIX 135 145 {ECO:0000244|PDB:1S68}.
STRAND 148 150 {ECO:0000244|PDB:1S68}.
STRAND 152 156 {ECO:0000244|PDB:1S68}.
HELIX 158 161 {ECO:0000244|PDB:1S68}.
HELIX 172 182 {ECO:0000244|PDB:1S68}.
HELIX 184 189 {ECO:0000244|PDB:1S68}.
STRAND 198 200 {ECO:0000244|PDB:2HVQ}.
STRAND 205 212 {ECO:0000244|PDB:1S68}.
STRAND 224 227 {ECO:0000244|PDB:1S68}.
HELIX 229 231 {ECO:0000244|PDB:1S68}.
HELIX 249 258 {ECO:0000244|PDB:2HVQ}.
HELIX 259 261 {ECO:0000244|PDB:2HVQ}.
HELIX 264 272 {ECO:0000244|PDB:2HVQ}.
HELIX 282 299 {ECO:0000244|PDB:2HVQ}.
STRAND 305 308 {ECO:0000244|PDB:2HVQ}.
HELIX 310 323 {ECO:0000244|PDB:2HVQ}.
TURN 324 327 {ECO:0000244|PDB:2HVQ}.
TURN 329 331 {ECO:0000244|PDB:2HVR}.
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


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