View source for 7ckj


==Crystal structure of CMP kinase in complex with CMP from Thermus thermophilus HB8==
<StructureSection load='7ckj' size='340' side='right'caption='[[7ckj]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7ckj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ake 3ake]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CKJ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</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=7ckj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ckj OCA], [https://pdbe.org/7ckj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ckj RCSB], [https://www.ebi.ac.uk/pdbsum/7ckj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ckj ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KCY_THET8 KCY_THET8] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nucleoside monophosphate kinases play crucial roles in biosynthesis and regeneration of nucleotides. These are bi-substrate enzymes that catalyze reversible transfers of a phosphoryl group between ATP and nucleoside monophosphate. These enzymes are comprised of the CORE domain, the NMP-binding domain, and the LID domain. Large conformational rearrangement of the three domains occurs during the catalytic cycle. Although many structures of CMP kinase have been determined, only limited structural information has been available on the conformational changes along the reaction pathway. We determined five crystal structures of CMP kinase of Thermus thermophilus HB8 in ligand-free form and the CMP "open", CMP "closed", ADP-CDP-Gd3+-, and CDP-bound forms at resolutions of 1.7, 2.2, 1.5, 1.6, and 1.7 A, respectively. The ligand-free form was in an open conformation, whereas the structures of the CMP "closed", ADP-CDP-Gd3+-, and CDP-bound forms were in a closed conformation, in which the shift of the NMP-binding domain and LID domain caused closure of the substrate-binding cleft. Interestingly, the CMP "open" form was in an open conformation even with CMP bound, implying intrinsic conformational fluctuation. The structure of the ADP-CDP complex is the first structure of CMP kinase with a phosphoryl group donor and an acceptor. Upon simultaneous binding of ADP and CDP, the side chains of several residues in the LID domain moved toward the nucleotides without global open-closed conformational changes compared to those in the CMP "closed" and CDP complexes. These global and local conformational changes may be crucial for the substrate recognition and catalysis. The terminal phosphate groups of ADP and CDP had similar geometry to those of two ADP in AMP kinase, suggesting common catalytic mechanisms to other nucleoside monophosphate kinases. Our findings are expected to contribute to detailed understanding of the reaction mechanism of CMP kinase.

The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor.,Mega R, Nakagawa N, Kuramitsu S, Masui R PLoS One. 2020 May 29;15(5):e0233689. doi: 10.1371/journal.pone.0233689., eCollection 2020. PMID:32469932<ref>PMID:32469932</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7ckj" style="background-color:#fffaf0;"></div>

==See Also==
*[[Cytidine monophosphate kinase|Cytidine monophosphate kinase]]
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus HB8]]
[[Category: Kuramitsu S]]
[[Category: Masui R]]
[[Category: Mega R]]
[[Category: Nakagawa N]]