2hvr
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 2hvr |SIZE=350|CAPTION= <scene name='initialview01'>2hvr</scene>, resolution 2.450Å | |PDB= 2hvr |SIZE=350|CAPTION= <scene name='initialview01'>2hvr</scene>, resolution 2.450Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=O2C:3'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>O2C</scene>, <scene name='pdbligand=OMC:O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE'>OMC</scene> |
|ACTIVITY= | |ACTIVITY= | ||
| - | |GENE= Y10A, 24.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= Y10A, 24.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2hvq|2HVQ]], [[2hvs|2HVS]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvr OCA], [http://www.ebi.ac.uk/pdbsum/2hvr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2hvr RCSB]</span> | ||
}} | }} | ||
| Line 16: | Line 19: | ||
==About this Structure== | ==About this Structure== | ||
| - | 2HVR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 2HVR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVR OCA]. |
==Reference== | ==Reference== | ||
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:[http://www.ncbi.nlm.nih.gov/pubmed/17018278 17018278] | 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:[http://www.ncbi.nlm.nih.gov/pubmed/17018278 17018278] | ||
| - | [[Category: | + | [[Category: Enterobacteria phage t4]] |
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Lima, C D.]] | [[Category: Lima, C D.]] | ||
[[Category: Nandakumar, J.]] | [[Category: Nandakumar, J.]] | ||
| - | [[Category: BTB]] | ||
[[Category: ligase]] | [[Category: ligase]] | ||
[[Category: lysine adenylate]] | [[Category: lysine adenylate]] | ||
| Line 31: | Line 33: | ||
[[Category: t4]] | [[Category: t4]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:36:05 2008'' |
Revision as of 00:36, 31 March 2008
| |||||||
| , resolution 2.450Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Gene: | Y10A, 24.1 (Enterobacteria phage T4) | ||||||
| Related: | 2HVQ, 2HVS
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 3'-deoxyribonucleotide at the nick
Overview
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
2HVR is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Mon Mar 31 03:36:05 2008
