|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Ensemble structures for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate== | | ==Ensemble structures for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate== |
| - | <StructureSection load='1joq' size='340' side='right' caption='[[1joq]], [[NMR_Ensembles_of_Models | 30 NMR models]]' scene=''> | + | <StructureSection load='1joq' size='340' side='right'caption='[[1joq]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1joq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JOQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1joq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JOQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jok|1jok]], [[1joo|1joo]], [[1jor|1jor]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></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=1joq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1joq OCA], [https://pdbe.org/1joq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1joq RCSB], [https://www.ebi.ac.uk/pdbsum/1joq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1joq 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=1joq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1joq OCA], [http://pdbe.org/1joq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1joq RCSB], [http://www.ebi.ac.uk/pdbsum/1joq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1joq ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU]] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond. | + | [https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 30: |
Line 29: |
| | </div> | | </div> |
| | <div class="pdbe-citations 1joq" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1joq" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Micrococcal nuclease]] | + | [[Category: Large Structures]] |
| - | [[Category: Abildgaard, F]] | + | [[Category: Staphylococcus aureus]] |
| - | [[Category: Dzakula, Z]] | + | [[Category: Abildgaard F]] |
| - | [[Category: Markley, J L]] | + | [[Category: Dzakula Z]] |
| - | [[Category: Truckses, D M]] | + | [[Category: Markley JL]] |
| - | [[Category: Wang, J]] | + | [[Category: Truckses DM]] |
| - | [[Category: Zolnai, Z]] | + | [[Category: Wang J]] |
| - | [[Category: Alpha helix]]
| + | [[Category: Zolnai Z]] |
| - | [[Category: Beta barrel]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Ternary complex]]
| + | |
| Structural highlights
Function
NUC_STAAU Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The solution structures of staphylococcal nuclease (nuclease) H124L and its ternary complex, (nuclease-H124L).pdTp.Ca2+, were determined by ab initio dynamic simulated annealing using 1925 NOE, 119 phi, 20 chi 1 and 112 hydrogen bond constraints for the free protein, and 2003 NOE, 118 phi, 20 chi 1 and 114 hydrogen bond constraints for the ternary complex. In both cases, the final structures display only small deviations from idealized covalent geometry. In structured regions, the overall root-mean-square deviations from mean atomic coordinates are 0.46 (+/- 0.05) A and 0.41 (+/- 0.05) A for the backbone heavy atoms of nuclease and its ternary complex, respectively. The backbone conformations of residues in the loop formed by Arg81-Gly86, which is adjacent to the active site, are more precisely defined in the ternary complex than in unligated nuclease. Also, the protein side chains that show NOEs and evidence for hydrogen bonds to pdTp (Arg35, Lys84, Tyr85, Arg87, Tyr113, and Tyr115) are better defined in the ternary complex. As has been observed previously in the X-ray structures of nuclease-WT, the binding of pdTp causes the backbone of Tyr113 to change from an extended to a left-handed alpha-helical conformation. The NMR structures reported here were compared with available X-ray structures: nuclease-H124L [Truckses et al. (1996) Protein Sci., 5, 1907-1916] and the ternary complex of wild-type staphylococcal nuclease [Loll and Lattman (1989) Proteins Struct. Funct. Genet., 5, 183-201]. Overall, the solution structures of nuclease-H124L are consistent with these crystal structures, but small differences were observed between the structures in the solution and crystal environments. These included differences in the conformations of certain side chains, a reduction in the extent of helix 1 in solution, and many fewer hydrogen bonds involving side chains in solution.
Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate.,Wang J, Truckses DM, Abildgaard F, Dzakula Z, Zolnai Z, Markley JL J Biomol NMR. 1997 Sep;10(2):143-64. PMID:9369015[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wang J, Truckses DM, Abildgaard F, Dzakula Z, Zolnai Z, Markley JL. Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate. J Biomol NMR. 1997 Sep;10(2):143-64. PMID:9369015
|
