KEGG   ENZYME: 6.5.1.3
Entry
EC 6.5.1.3                  Enzyme                                 
Name
RNA ligase (ATP);
polyribonucleotide synthase (ATP);
RNA ligase;
polyribonucleotide ligase;
ribonucleic ligase;
poly(ribonucleotide):poly(ribonucleotide) ligase (AMP-forming)
Class
Ligases;
Forming phosphoric-ester bonds;
Ligases that form phosphoric-ester bonds (only sub-subclass identified to date)
Sysname
poly(ribonucleotide)-3'-hydroxyl:5'-phospho-poly(ribonucleotide) ligase (ATP)
Reaction(IUBMB)
ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate (overall reaction) [RN:R07640];
(1a) ATP + [RNA ligase]-L-lysine = [RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate;
(1b) [RNA ligase]-N6-(5'-adenylyl)-L-lysine + 5'-phospho-(ribonucleotide)m = 5'-(5'-diphosphoadenosine)-(ribonucleotide)m + [RNA ligase]-L-lysine;
(1c) (ribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(ribonucleotide)m = (ribonucleotide)n+m + AMP
Reaction(KEGG)
R07640;
(other) R00436
Substrate
ATP [CPD:C00002];
(ribonucleotide)n-3'-hydroxyl;
5'-phospho-(ribonucleotide)m;
[RNA ligase]-L-lysine;
[RNA ligase]-N6-(5'-adenylyl)-L-lysine;
5'-(5'-diphosphoadenosine)-(ribonucleotide)m
Product
(ribonucleotide)n+m [CPD:C00046];
AMP [CPD:C00020];
diphosphate [CPD:C00013];
[RNA ligase]-N6-(5'-adenylyl)-L-lysine;
5'-(5'-diphosphoadenosine)-(ribonucleotide)m;
[RNA ligase]-L-lysine
Comment
The enzyme catalyses the ligation of RNA strands with 3'-hydroxyl and 5'-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in RNA. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a lysine residue. The adenylate group is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine)-[RNA]. Finally, the enzyme catalyses a nucleophilic attack of the 3'-OH terminus on the capped terminus, which results in formation of the phosphodiester bond and release of the adenylate.
History
EC 6.5.1.3 created 1976, modified 2016
Orthology
K01973  RNA-editing ligase
K14679  tRNA ligase
K14680  RNA ligase
K18961  T4 RNA ligase 1
K18962  T4 RNA ligase 2
Genes
QSU112013573 112025981
SCEYJL087C(TRL1)
AGOAGOS_AFR099C
ERCEcym_6337
KLAKLLA0_F14399g
KMXKLMA_30170(TRL1)
LTHKLTH0H09548g
VPOKpol_463p3
ZROZYRO0G15070g
CGRCAGL0M03091g
NCSNCAS_0A09580(NCAS0A09580)
NDINDAI_0G05550(NDAI0G05550)
TPFTPHA_0I00970(TPHA0I00970)
TBLTBLA_0C02880(TBLA0C02880)
TDLTDEL_0D01480(TDEL0D01480)
TGBHG536_0F01620
KAFKAFR_0A01500(KAFR0A01500)
ZMKHG535_0H01140
PPAPAS_chr3_0622
DHADEHA2D03498g
PICPICST_89535
PGUPGUG_01548
SPAASPAPADRAFT_57607
LELLELG_05515
CALCAALFM_C702060WA(LIG1)
CTPCTRG_05056
COTCORT_0H01290
CDUCD36_71880
CTENCANTEDRAFT_130409
YLIYALI0D14916g YALI0E06171g
CLUCLUG_02324 CLUG_02325
CLUSA9F13_22g00726
CAURCJI97_004584
SLBAWJ20_2430(TRL1)
PKZC5L36_0B06330
BNNFOA43_003331
BBRXBRETT_004177
NCRNCU04410
NTENEUTE1DRAFT121207(NEUTE1DRAFT_121207)
SMPSMAC_07337
PANPODANSg7455
TTTTHITE_2114865
MTMMYCTH_2298479
CTHRCTHT_0034810
MGRMGG_05169
TMNUCRPA7_7096
SSCKSPSK_07061
FGRFGSG_11594
FPUFPSE_10772
FVRFVEG_08903
FOXFOXG_10255
NHENECHADRAFT_61721
TRETRIREDRAFT_68582
TRRM419DRAFT_133866
MAWMAC_09086
MAJMAA_00264
CMTCCM_00753
PLJVFPFJ_03187
VALVDBG_01414
VDAVDAG_07834
CFJCFIO01_00274
SAPOSAPIO_CDS0021
ELAUCREL1_5593
PFYPFICI_00676
SSLSS1G_06743
BFUBCIN_11g04740(Bctrl1)
MBEMBM_05930
PSCOLY89DRAFT_691256
GLZGLAREA_11832
ANIAN1296.2
AFMAFUA_1G09690
ACTACLA_025810
NFINFIA_015920
AORAO090012000873
ANGANI_1_218074(An08g01480)
AFVAFLA_002592
ALUCAKAW2_30833S
ACHEACHE_30913S
APUUAPUU_50429A
PCSPc16g06530
PDPPDIP_40420
TMFPMAA_025090
TRGTRUGW13939_03205
CIMCIMG_10259
CPWCPC735_013460
UREUREG_03473
PBLPAAG_02801
PBNPADG_11321
ABEARB_00442
TVETRV_07625
AJEHCAG_01469
BGHBDBG_05908
PNOSNOG_15109
PTEPTT_06606
BZECOCCADRAFT_101661
BSCCOCSADRAFT_185829
BORCOCMIDRAFT_89978
AALTCC77DRAFT_1026326
ZTRMYCGRDRAFT_67486
PFJMYCFIDRAFT_62403
BCOMBAUCODRAFT_60996
NPAUCRNP2_1353
TMLGSTUM_00010625001
SPOSPAC17G8.01c(trl1)
CNECND03670
CNBCNBD2650
CGICGB_D6380C
TMSTREMEDRAFT_20952
TASAA1Q1_01281
PPLPOSPLDRAFT_100403 POSPLDRAFT_101360
TVSTRAVEDRAFT_157117
DSQDICSQDRAFT_139641
PCOPHACADRAFT_253339
SHSSTEHIDRAFT_65753
HIRHETIRDRAFT_390033
PSQPUNSTDRAFT_67333
ADLAURDEDRAFT_117966 AURDEDRAFT_171844 AURDEDRAFT_171860 AURDEDRAFT_71532 AURDEDRAFT_85050
FMEFOMMEDRAFT_78648
GTRGLOTRDRAFT_78807
LBCLACBIDRAFT_232121
MPRMPER_04194
MRRMoror_8390
CCICC1G_08970
SCMSCHCODRAFT_70020
ABPAGABI1DRAFT122028(AGABI1DRAFT_122028) AGABI1DRAFT122582(AGABI1DRAFT_122582)
ABVAGABI2DRAFT187168(AGABI2DRAFT_187168) AGABI2DRAFT210807(AGABI2DRAFT_210807)
CPUTCONPUDRAFT_170168
SLASERLADRAFT_412866
WSEWALSEDRAFT_33865
WICJ056_001013
UMAUMAG_00871
PFPPFL1_02870
MGLMGL_3080
MRTMRET_1402
MSYMMSY001_2898
PGRPGTG_07519 PGTG_12509
MLRMELLADRAFT_117814
DDIDDB_G0289211
TBRTB927.1.3030(KREL2) Tb09.160.2970
TBGTbgDal_I1840 TbgDal_IX2300
TCR506363.110 510155.20 511585.20
LMALMJF_01_0590 LMJF_20_1730(REL2)
LIFLINJ_01_0610 LINJ_20_1700(REL2)
LDOLDBPK_010610 LDBPK_201700
LMILMXM_01_0590 LMXM_20_1730
LBZLBRM_01_0620 LBRM_20_5890
LPANLPMP_010590 LPMP_205830(REL2)
NGRNAEGRDRAFT_73822
NAMNAMH_1741
RECRHECIAT_PA0000344
RLTRleg2_5631
RHIDFFM81_007905
BRABRADO3560
METM446_2212
RERRER_24960
SCBSCAB_7471
SGZC0216_13300
SVNCP980_04315
SFICEIZ62_01975
SGALCP966_05075
SPHVF9278_44150
SCINCP977_02815
SGXH4W23_03000
ASEACPL_7466
AMSAMIS_72120
PRYPrubr_37550
CATICS0771_21500
CAICaci_2973
CYCPCC7424_2432
GMSSOIL9_26690
TSPHKIH39_23305
RHOZGXP67_01440
TAMTheam_0167
 » show all
Reference
1  [PMID:4342972]
  Authors
Silber R, Malathi VG, Hurwitz J.
  Title
Purification and properties of bacteriophage T4-induced RNA ligase.
  Journal
Proc Natl Acad Sci U S A 69:3009-13 (1972)
DOI:10.1073/pnas.69.10.3009
Reference
2  [PMID:4373468]
  Authors
Cranston JW, Silber R, Malathi VG, Hurwitz J
  Title
Studies on ribonucleic acid ligase. Characterization of an adenosine triphosphate-inorganic pyrophosphate exchange reaction and demonstration of an enzyme-adenylate complex with T4 bacteriophage-induced enzyme.
  Journal
J Biol Chem 249:7447-56 (1974)
Reference
3  [PMID:320212]
  Authors
Sugino A, Snoper TJ, Cozzarelli NR
  Title
Bacteriophage T4 RNA ligase. Reaction intermediates and interaction of substrates.
  Journal
J Biol Chem 252:1732-8 (1977)
Reference
4  [PMID:6194411]
  Authors
Romaniuk PJ, Uhlenbeck OC
  Title
Joining of RNA molecules with RNA ligase.
  Journal
Methods Enzymol 100:52-9 (1983)
DOI:10.1016/0076-6879(83)00045-2
Reference
5  [PMID:14962393]
  Authors
Ho CK, Wang LK, Lima CD, Shuman S
  Title
Structure and mechanism of RNA ligase.
  Journal
Structure 12:327-39 (2004)
DOI:10.1016/j.str.2004.01.011
Reference
6  [PMID:17018278]
  Authors
Nandakumar J, Shuman S, Lima CD
  Title
RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.
  Journal
Cell 127:71-84 (2006)
DOI:10.1016/j.cell.2006.08.038
Other DBs
ExplorEnz - The Enzyme Database: 6.5.1.3
IUBMB Enzyme Nomenclature: 6.5.1.3
ExPASy - ENZYME nomenclature database: 6.5.1.3
BRENDA, the Enzyme Database: 6.5.1.3
CAS: 37353-39-2

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