1ygk: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ygk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YGK FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ygk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YGK FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RRC:R-ROSCOVITINE'>RRC</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]] 2.6&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ygj|1ygj]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RRC:R-ROSCOVITINE'>RRC</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </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=1ygk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ygk OCA], [https://pdbe.org/1ygk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ygk RCSB], [https://www.ebi.ac.uk/pdbsum/1ygk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ygk 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=1ygk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ygk OCA], [https://pdbe.org/1ygk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ygk RCSB], [https://www.ebi.ac.uk/pdbsum/1ygk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ygk ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PDXK_SHEEP PDXK_SHEEP]] Required for synthesis of pyridoxal-5-phosphate from vitamin B6.  
[https://www.uniprot.org/uniprot/PDXK_SHEEP PDXK_SHEEP] Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ygk ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ygk ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Pyridoxal kinase (PDXK) catalyzes the phosphorylation of pyridoxal, pyridoxamine, and pyridoxine in the presence of ATP and Zn2+. This constitutes an essential step in the synthesis of pyridoxal 5'-phosphate (PLP), the active form of vitamin B6, a cofactor for over 140 enzymes. (R)-Roscovitine (CYC202, Seliciclib) is a relatively selective inhibitor of cyclin-dependent kinases (CDKs), currently evaluated for the treatment of cancers, neurodegenerative disorders, renal diseases, and several viral infections. Affinity chromatography investigations have shown that (R)-roscovitine also interacts with PDXK. To understand this interaction, we determined the crystal structure of PDXK in complex with (R)-roscovitine, N6-methyl-(R)-roscovitine, and O6-(R)-roscovitine, the two latter derivatives being designed to bind to PDXK but not to CDKs. Structural analysis revealed that these three roscovitines bind similarly in the pyridoxal-binding site of PDXK rather than in the anticipated ATP-binding site. The pyridoxal pocket has thus an unexpected ability to accommodate molecules different from and larger than pyridoxal. This work provides detailed structural information on the interactions between PDXK and roscovitine and analogs. It could also aid in the design of roscovitine derivatives displaying strict selectivity for either PDXK or CDKs.
Crystal structure of pyridoxal kinase in complex with roscovitine and derivatives.,Tang L, Li MH, Cao P, Wang F, Chang WR, Bach S, Reinhardt J, Ferandin Y, Galons H, Wan Y, Gray N, Meijer L, Jiang T, Liang DC J Biol Chem. 2005 Sep 2;280(35):31220-9. Epub 2005 Jun 28. PMID:15985434<ref>PMID:15985434</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ygk" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Pyridoxal kinase|Pyridoxal kinase]]
*[[Pyridoxal kinase|Pyridoxal kinase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ovis aries]]
[[Category: Ovis aries]]
[[Category: Pyridoxal kinase]]
[[Category: Bach S]]
[[Category: Bach, S]]
[[Category: Cao P]]
[[Category: Cao, P]]
[[Category: Chang W-R]]
[[Category: Chang, W R]]
[[Category: Ferandin Y]]
[[Category: Ferandin, Y]]
[[Category: Galons H]]
[[Category: Galons, H]]
[[Category: Gray N]]
[[Category: Gray, N]]
[[Category: Jiang T]]
[[Category: Jiang, T]]
[[Category: Koken M]]
[[Category: Koken, M]]
[[Category: Li M-H]]
[[Category: Li, M H]]
[[Category: Liang D-C]]
[[Category: Liang, D C]]
[[Category: Meijer L]]
[[Category: Meijer, L]]
[[Category: Reinhardt J]]
[[Category: Reinhardt, J]]
[[Category: Tang L]]
[[Category: Tang, L]]
[[Category: Wan Y]]
[[Category: Wan, Y]]
[[Category: Wang F]]
[[Category: Wang, F]]
[[Category: Alpha-beta structure]]
[[Category: Transferase]]

Latest revision as of 16:37, 13 March 2024

Crystal Structure of Pyridoxal Kinase in Complex with Roscovitine and DerivativesCrystal Structure of Pyridoxal Kinase in Complex with Roscovitine and Derivatives

Structural highlights

1ygk is a 1 chain structure with sequence from Ovis aries. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDXK_SHEEP Required for synthesis of pyridoxal-5-phosphate from vitamin B6.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1ygk, resolution 2.60Å

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