2hvs: Difference between revisions
New page: left|200px<br /><applet load="2hvs" size="450" color="white" frame="true" align="right" spinBox="true" caption="2hvs, resolution 2.500Å" /> '''Structure of T4 RNA... |
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[[Image:2hvs.gif|left|200px]]<br /><applet load="2hvs" size=" | [[Image:2hvs.gif|left|200px]]<br /><applet load="2hvs" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="2hvs, resolution 2.500Å" /> | caption="2hvs, resolution 2.500Å" /> | ||
'''Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick'''<br /> | '''Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick'''<br /> | ||
==Overview== | ==Overview== | ||
T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a | T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation (step 1), AMP transfer to the nick 5'PO(4) (step 2), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester (step 3). Crystal structures are reported for Rnl2 at discrete steps along this pathway: the covalent Rnl2-AMP intermediate; Rnl2 bound to an adenylylated nicked duplex, captured immediately following step 2; and Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. Mutational analysis and comparison of nick-bound structures of Rnl2 and human DNA ligase I highlight common and divergent themes of substrate recognition that can explain their specialization for RNA versus DNA repair. | ||
==About this Structure== | ==About this Structure== | ||
2HVS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with BTB as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | 2HVS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with <scene name='pdbligand=BTB:'>BTB</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVS OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Bacteriophage t4]] | [[Category: Bacteriophage t4]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Lima, C | [[Category: Lima, C D.]] | ||
[[Category: Nandakumar, J.]] | [[Category: Nandakumar, J.]] | ||
[[Category: BTB]] | [[Category: BTB]] | ||
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[[Category: t4]] | [[Category: t4]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:46:15 2008'' | ||
Revision as of 18:46, 21 February 2008
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Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick
OverviewOverview
T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation (step 1), AMP transfer to the nick 5'PO(4) (step 2), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester (step 3). Crystal structures are reported for Rnl2 at discrete steps along this pathway: the covalent Rnl2-AMP intermediate; Rnl2 bound to an adenylylated nicked duplex, captured immediately following step 2; and Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. Mutational analysis and comparison of nick-bound structures of Rnl2 and human DNA ligase I highlight common and divergent themes of substrate recognition that can explain their specialization for RNA versus DNA repair.
About this StructureAbout this Structure
2HVS is a Single protein structure of sequence from Bacteriophage t4 with as ligand. Full crystallographic information is available from OCA.
ReferenceReference
RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward., Nandakumar J, Shuman S, Lima CD, Cell. 2006 Oct 6;127(1):71-84. PMID:17018278
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