3w34

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Current revision (08:43, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3w34' size='340' side='right'caption='[[3w34]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
<StructureSection load='3w34' size='340' side='right'caption='[[3w34]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3w34]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W34 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3w34]] 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=3W34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W34 FirstGlance]. <br>
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</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=CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE'>CTN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.91&#8491;</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_kinase Uridine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.48 2.7.1.48] </span></td></tr>
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<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=CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE'>CTN</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=3w34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w34 OCA], [https://pdbe.org/3w34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w34 RCSB], [https://www.ebi.ac.uk/pdbsum/3w34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w34 ProSAT]</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=3w34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w34 OCA], [https://pdbe.org/3w34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w34 RCSB], [https://www.ebi.ac.uk/pdbsum/3w34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w34 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/URK_THET8 URK_THET8]
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Uridine-cytidine kinase catalyzes phosphorylation of the pyrimidine nucleosides uridine and cytidine and plays an important role in nucleotide metabolism. However, the detailed molecular mechanism of these reactions remains to be elucidated. Here, we determined the structure of the ternary complex of Uridine-cytidine kinase from Thermus thermophilus HB8 with both cytidine and beta,gamma-methyleneadenosine 5'-triphosphate, a non-hydrolysable ATP analogue. Substrate binding is accompanied by substantial domain movement that allows the substrate-binding cleft to close. The terminal phosphodiester bond of the ATP analogue is in an ideal location for an inline attack of the 5'-hydroxyl group of cytidine. Asp40 is located near the 5'-hydroxyl group of cytidine. Mutation of this conserved residue to Asn or Ala resulted in a complete loss of enzyme activity, which is consistent with the notion that Asp40 acts as a general base that activates the 5'-hydroxyl group of cytidine. The pH profile of the activity showed an apparent pK a value of 7.4. Based on this structure, a likely mechanism of the catalytic step is discussed.
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Structural and Biochemical Studies on the Reaction Mechanism of Uridine-Cytidine Kinase.,Tomoike F, Nakagawa N, Kuramitsu S, Masui R Protein J. 2015 Dec;34(6):411-20. doi: 10.1007/s10930-015-9636-8. PMID:26510656<ref>PMID:26510656</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3w34" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Uridine kinase]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Kuramitsu, S]]
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[[Category: Kuramitsu S]]
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[[Category: Masui, R]]
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[[Category: Masui R]]
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[[Category: Nakagawa, N]]
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[[Category: Nakagawa N]]
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[[Category: Tomoike, F]]
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[[Category: Tomoike F]]
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[[Category: Kinase]]
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[[Category: Nucleoside]]
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[[Category: Transferase]]
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Current revision

Ternary complex of Thermus thermophilus HB8 uridine-cytidine kinase with substrates

PDB ID 3w34

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