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| | ==Structure of bacterial polynucleotide kinase Michaelis complex bound to GTP and DNA== | | ==Structure of bacterial polynucleotide kinase Michaelis complex bound to GTP and DNA== |
| - | <StructureSection load='4mdf' size='340' side='right' caption='[[4mdf]], [[Resolution|resolution]] 1.73Å' scene=''> | + | <StructureSection load='4mdf' size='340' side='right'caption='[[4mdf]], [[Resolution|resolution]] 1.73Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4mdf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cloth Cloth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MDF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4mdf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MDF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.727Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jsy|4jsy]], [[4jt2|4jt2]], [[4jt4|4jt4]], [[4jst|4jst]], [[4gp6|4gp6]], [[4gp7|4gp7]], [[4mde|4mde]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 CLOTH])</td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4mdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mdf OCA], [https://pdbe.org/4mdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mdf RCSB], [https://www.ebi.ac.uk/pdbsum/4mdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mdf ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mdf OCA], [http://pdbe.org/4mdf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mdf RCSB], [http://www.ebi.ac.uk/pdbsum/4mdf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mdf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/A3DJ38_ACET2 A3DJ38_ACET2] |
| - | Clostridium thermocellum polynucleotide kinase (CthPnk), the 5' end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from an NTP donor to a 5'-OH polynucleotide acceptor. Here we report the crystal structures of CthPnk-D38N in a Michaelis complex with GTP*Mg2+ and a 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and a 5'-PO4 oligonucleotide. The O5' nucleophile is situated 3.0 A from the GTP gamma phosphorus in the Michaelis complex, where it is coordinated by Asn38 and is apical to the bridging beta phosphate oxygen of the GDP leaving group. In the product complex, the transferred phosphate has undergone stereochemical inversion and Asn38 coordinates the 5'-bridging phosphate oxygen of the oligonucleotide. The D38N enzyme is poised for catalysis, but cannot execute because it lacks Asp38-hereby implicated as the essential general base catalyst that abstracts a proton from the 5'-OH during the kinase reaction. Asp38 serves as a general acid catalyst during the 'reverse kinase' reaction by donating a proton to the O5' leaving group of the 5'-PO4 strand. The acceptor strand binding mode of CthPnk is distinct from that of bacteriophage T4 Pnk.
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| - | Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP*Mg2+ and 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition.,Das U, Wang LK, Smith P, Jacewicz A, Shuman S Nucleic Acids Res. 2013 Oct 22. PMID:24150947<ref>PMID:24150947</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4mdf" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cloth]] | + | [[Category: Acetivibrio thermocellus ATCC 27405]] |
| - | [[Category: Das, U]] | + | [[Category: Large Structures]] |
| - | [[Category: Jacewicz, A]] | + | [[Category: Das U]] |
| - | [[Category: Shuman, S]] | + | [[Category: Jacewicz A]] |
| - | [[Category: Smith, P]] | + | [[Category: Shuman S]] |
| - | [[Category: Wang, L K]] | + | [[Category: Smith P]] |
| - | [[Category: Hydrolase-dna complex]]
| + | [[Category: Wang LK]] |
| - | [[Category: P-loop phosphotransferase]]
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| - | [[Category: Rna repair]]
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| - | [[Category: Transferase]]
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| - | [[Category: Transferase-dna complex]]
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