5x8c: Difference between revisions
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==AMPPCP and TMP bound crystal structure of thymidylate kinase from thermus thermophilus HB8== | ==AMPPCP and TMP bound crystal structure of thymidylate kinase from thermus thermophilus HB8== | ||
<StructureSection load='5x8c' size='340' side='right' caption='[[5x8c]], [[Resolution|resolution]] 2.07Å' scene=''> | <StructureSection load='5x8c' size='340' side='right'caption='[[5x8c]], [[Resolution|resolution]] 2.07Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5x8c]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5x8c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X8C FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.07Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene></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=5x8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x8c OCA], [https://pdbe.org/5x8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x8c RCSB], [https://www.ebi.ac.uk/pdbsum/5x8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x8c ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/KTHY_THET8 KTHY_THET8] Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Thymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg(2+). In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase from Thermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme. High-resolution X-ray crystal structures of thymidylate kinase in apo and ligand-bound states were solved. This is the first report of structures of binary and ternary complexes of thymidylate kinase with its natural substrates ATP and ATP-TMP, respectively. Distinct conformations of the active-site residues, the P-loop and the LID region observed in the apo and ligand-bound structures revealed that their concerted motion is required for the binding and proper positioning of the substrate TMP. Structural analyses provide an insight into the mode of substrate binding at the active site. The residues involved in communication between the substrates were identified through network analysis using molecular-dynamics simulations. The residues identified showed high sequence conservation across species. Biochemical analyses show that mutations of these residues either resulted in a loss of activity or affected the thermal stability of the protein. Further, molecular-dynamics analyses of mutants suggest that the proper positioning of TMP is important for catalysis. These data also provide an insight into the phosphoryl-transfer mechanism. | |||
Structural and functional roles of dynamically correlated residues in thymidylate kinase.,Chaudhary SK, Jeyakanthan J, Sekar K Acta Crystallogr D Struct Biol. 2018 Apr 1;74(Pt 4):341-354. doi:, 10.1107/S2059798318002267. Epub 2018 Apr 6. PMID:29652261<ref>PMID:29652261</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5x8c" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Thymidylate kinase 3D structures|Thymidylate kinase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermus thermophilus HB8]] | ||
[[Category: Chaudhary | [[Category: Chaudhary SK]] | ||
[[Category: Jeyakanthan | [[Category: Jeyakanthan J]] | ||
[[Category: Sekar | [[Category: Sekar K]] | ||
Latest revision as of 10:55, 22 November 2023
AMPPCP and TMP bound crystal structure of thymidylate kinase from thermus thermophilus HB8AMPPCP and TMP bound crystal structure of thymidylate kinase from thermus thermophilus HB8
Structural highlights
FunctionKTHY_THET8 Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. Publication Abstract from PubMedThymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg(2+). In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase from Thermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme. High-resolution X-ray crystal structures of thymidylate kinase in apo and ligand-bound states were solved. This is the first report of structures of binary and ternary complexes of thymidylate kinase with its natural substrates ATP and ATP-TMP, respectively. Distinct conformations of the active-site residues, the P-loop and the LID region observed in the apo and ligand-bound structures revealed that their concerted motion is required for the binding and proper positioning of the substrate TMP. Structural analyses provide an insight into the mode of substrate binding at the active site. The residues involved in communication between the substrates were identified through network analysis using molecular-dynamics simulations. The residues identified showed high sequence conservation across species. Biochemical analyses show that mutations of these residues either resulted in a loss of activity or affected the thermal stability of the protein. Further, molecular-dynamics analyses of mutants suggest that the proper positioning of TMP is important for catalysis. These data also provide an insight into the phosphoryl-transfer mechanism. Structural and functional roles of dynamically correlated residues in thymidylate kinase.,Chaudhary SK, Jeyakanthan J, Sekar K Acta Crystallogr D Struct Biol. 2018 Apr 1;74(Pt 4):341-354. doi:, 10.1107/S2059798318002267. Epub 2018 Apr 6. PMID:29652261[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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