KEGG   ENZYME: 6.5.1.3Help
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)
BRITE hierarchy
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
Show
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
SCE: YJL087C(TRL1)
AGO: AGOS_AFR099C
ERC: Ecym_6337
KLA: KLLA0F14399g
KMX: KLMA_30170(TRL1)
LTH: KLTH0H09548g
VPO: Kpol_463p3
ZRO: ZYRO0G15070g
CGR: CAGL0M03091g
NCS: NCAS_0A09580(NCAS0A09580)
NDI: NDAI_0G05550(NDAI0G05550)
TPF: TPHA_0I00970(TPHA0I00970)
TBL: TBLA_0C02880(TBLA0C02880)
TDL: TDEL_0D01480(TDEL0D01480)
KAF: KAFR_0A01500(KAFR0A01500)
CAL: CAALFM_C702060WA(LIG1)
SLB: AWJ20_1723(TRL1) AWJ20_2430(TRL1)
NCR: NCU04410
NTE: NEUTE1DRAFT121207(NEUTE1DRAFT_121207)
MGR: MGG_05169
MAW: MAC_09086
MAJ: MAA_00264
CMT: CCM_00753
MBE: MBM_05930
ANI: AN1296.2
ANG: ANI_1_218074(An08g01480)
ABE: ARB_00442
TVE: TRV_07625
PTE: PTT_06606
SPO: SPAC17G8.01c(trl1)
CNE: CND03670
CNB: CNBD2650
ABP: AGABI1DRAFT122028(AGABI1DRAFT_122028) AGABI1DRAFT122582(AGABI1DRAFT_122582)
ABV: AGABI2DRAFT187168(AGABI2DRAFT_187168) AGABI2DRAFT210807(AGABI2DRAFT_210807)
MGL: MGL_3080
NAM: NAMH_1741
BRA: BRADO3560
MET: M446_2212
RER: RER_24960
SCB: SCAB_7471
ASE: ACPL_7466
CAI: Caci_2973
 » show all
Taxonomy
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 (1972) 3009-13.
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 (1974) 7447-56.
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 (1977) 1732-8.
Reference
4  [PMID:6194411]
  Authors
Romaniuk PJ, Uhlenbeck OC
  Title
Joining of RNA molecules with RNA ligase.
  Journal
Methods. Enzymol. 100 (1983) 52-9.
Reference
5  [PMID:14962393]
  Authors
Ho CK, Wang LK, Lima CD, Shuman S
  Title
Structure and mechanism of RNA ligase.
  Journal
Structure. 12 (2004) 327-39.
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 (2006) 71-84.
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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