Sandbox 201
From Proteopedia
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* <scene name='Sandbox_201/Atp_binding_site_grey/1'>ATP binding site</scene> | * <scene name='Sandbox_201/Atp_binding_site_grey/1'>ATP binding site</scene> | ||
| - | :The N- and C-terminal domains are both able to form interactions with ATP and ATP analogues. But the ß-strands of the core region in the N-terminal domain contain most of the residues involved in binding ATP. <scene name='Sandbox_201/ | + | :The N- and C-terminal domains are both able to form interactions with ATP and ATP analogues. But the ß-strands of the core region in the N-terminal domain contain most of the residues involved in binding ATP. <scene name='Sandbox_201/Atp_binding_site_lys75/2'>Lys75</scene>, <scene name='Sandbox_201/Atp_binding_site_lys99/1'>Lys99</scene> (motif I), <scene name='Sandbox_201/Atp_binding_site_lys119/1'>Lys119</scene> (motif Ia), <scene name='Sandbox_201/Atp_binding_site_lys240/1'>Lys240</scene> (motif V), and <scene name='Sandbox_201/Atp_binding_site_lys242/1'>Lys242</scene> (motif V) interact with the phosphate groups of ATP and ATP analogues. |
:Lys99 is the site of adenylation in Rnl1, <ref>Thogersen, H. C., Morris, H. R., Rand, K. N., and Gait, M. J. (1985) Eur. J. Biochem. | :Lys99 is the site of adenylation in Rnl1, <ref>Thogersen, H. C., Morris, H. R., Rand, K. N., and Gait, M. J. (1985) Eur. J. Biochem. | ||
147, 325–329</ref> but in this structure this residue seems to be situated at a distance incompatible with covalent interaction with the phosphate of ATP (more than 3 Å).<ref name="main_article">K.El Omari, J.Ren, L.E.Bird, M.K.Bona, G.Klarmann, S.F.LeGrice, D.K.Stammers (2006) J. Biol. Chem. 281,1573-1579</ref> That could suggest that the formation of a covalent bond needs some conformational changes. But we do not know if a conformational change has to occur to allow the covalent bond formation, or if the formation of this bond leads to a conformational change. | 147, 325–329</ref> but in this structure this residue seems to be situated at a distance incompatible with covalent interaction with the phosphate of ATP (more than 3 Å).<ref name="main_article">K.El Omari, J.Ren, L.E.Bird, M.K.Bona, G.Klarmann, S.F.LeGrice, D.K.Stammers (2006) J. Biol. Chem. 281,1573-1579</ref> That could suggest that the formation of a covalent bond needs some conformational changes. But we do not know if a conformational change has to occur to allow the covalent bond formation, or if the formation of this bond leads to a conformational change. | ||
Revision as of 22:40, 2 January 2012
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| 2c5u, resolution 2.21Å () | |||||||||
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| Ligands: | , , , | ||||||||
| Non-Standard Residues: | |||||||||
| Activity: | RNA ligase (ATP), with EC number 6.5.1.3 | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
T4 RNA ligase (Rnl1) catalyzes the formation of phosphodiester bonds between the 5'-phosphate and the 3'-hydroxyl termini of single-stranded nucleic acids. T4 RNA ligase is a member of a distinct subgroup of RNA ligases along with a fungal tRNA ligase (Trl1), a putative baculovirus RNA ligase and RNA ligase from the bacteriophages RM378 and TS2126. Rnl1 is also the first RNA ligase whose complete crystal structure was determined. Rnl1 is in fact a tRNA repair enzyme used by the T4 bacteriophage to escape hosts antiviral response. Enzyme functioning requires ATP and divalent metal ions. The T4 ligase repairs the tRNALys by joining its 5'-PO4 and 3'-OH groups via series of three nucleotidyl transfer steps in a ping-pong enzymatic mechanism. First, the Lys99 of the enzyme reacts with the a phosphorus of ATP and forms a covalent intermediate: ligase-(lysyl-N)-AMP. Pyrophosphate is also produced during this step. Secondly, AMP is transferred from the intermediate to the 5'- PO4 terminus of a tRNA to form an tRNA-adenylate intermediate (AppRNA). Finally, the ligase catalyzes the attack of the 3'-OH terminus of the tRNA on the tRNA-adenylate and the two termini are joined via a phosphodiester bond, the AMP is released.
Contents |
Biological role
The biological role of Rnl1 is to repair a break in the anticodon loop of E.coli tRNALys and in this way to evade bacteria host antiviral defense mechanism invoked following phage infection. Bacteria have a tRNALys-specific anticodon nuclease (ACNase) which is normally kept latent by association of its core protein, PrrC, with the endonuclease EcoprrI. Upon infection, the bacteriophage expresses a T4 Stp peptide, which inhibits EcoprrI. EcoprrI dissociates from PrrC and the ACNase becomes active. The anticodon nuclease then cleaves the anticodon loop of the tRNALys which blocks phage protein synthesis and, as a consequence, stops the infection. Bacteriophage T4 has developed way to overcome this defense mechanism using the tRNA ligase and a polynucleotide kinase (PnK) to repair the in the tRNA anticodon loop. T4 Rnl1 and T4 polynucleotide kinase–phosphatase (PnK) together form a two-component repair system that repairs the tRNA break made by the host anticodon nuclease. First, PnK remodels the ends of the broken tRNA by converting the 2',3' cyclic phosphate to a 3'-OH, 2'-OH and by phosphorylating the 5'-OH end to form a 5'-PO4. Rnl1 then joins the 3'-OH and 5'- PO4 RNA ends to form a standard 3'–5' phosphodiester bond.
Structure
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Chemical reaction
The T4 RNA ligase (Enzyme class : E.C.6.5.1.3) catalyzes the formation of phosphodiester bonds between the 5'-phosphate terminus of single-stranded nucleic acid (i) and the 3'-hydroxyl terminus of single-stranded nucleic acid (j).
ATP + ribonucleotide(i) + ribonucleotide(j) → AMP + diphosphate + ribonucleotide(i+j)
