4gi7: Difference between revisions
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==Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue== | ==Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue== | ||
<StructureSection load='4gi7' size='340' side='right' caption='[[4gi7]], [[Resolution|resolution]] 1.95Å' scene=''> | <StructureSection load='4gi7' size='340' side='right'caption='[[4gi7]], [[Resolution|resolution]] 1.95Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4gi7]] is a 8 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4gi7]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae_342 Klebsiella pneumoniae 342]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GI7 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0JR:(2R)-2,4-DIHYDROXY-3,3-DIMETHYL-N-{3-OXO-3-[(PYRIDIN-3-YLMETHYL)AMINO]PROPYL}BUTANAMIDE'>0JR</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0JR:(2R)-2,4-DIHYDROXY-3,3-DIMETHYL-N-{3-OXO-3-[(PYRIDIN-3-YLMETHYL)AMINO]PROPYL}BUTANAMIDE'>0JR</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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=4gi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gi7 OCA], [https://pdbe.org/4gi7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gi7 RCSB], [https://www.ebi.ac.uk/pdbsum/4gi7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gi7 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/COAA_KLEP3 COAA_KLEP3] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[Pantothenate kinase|Pantothenate kinase]] | *[[Pantothenate kinase 3D structures|Pantothenate kinase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Klebsiella pneumoniae 342]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Bolshan | [[Category: Bolshan Y]] | ||
[[Category: Hong | [[Category: Hong BS]] | ||
[[Category: Li | [[Category: Li B]] | ||
[[Category: Park | [[Category: Park HW]] | ||
[[Category: Smil D]] | |||
[[Category: Smil | [[Category: Tempel W]] | ||
[[Category: Tempel | |||
Revision as of 09:57, 26 October 2022
Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogueCrystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue
Structural highlights
FunctionPublication Abstract from PubMedN-substituted pantothenamides are derivatives of pantothenate, the precursor in the biosynthesis of the essential metabolic cofactor coenzyme A (CoA). These compounds are substrates of pantothenate kinase (PanK) in the first step of CoA biosynthesis and possess antimicrobial activity against various pathogenic bacteria. Here we solved the crystal structure of the Klebsiella pneumoniae PanK (KpPanK) in complex with N-pentylpantothenamide (N5-Pan) to understand the molecular basis of its antimicrobial activity. The structure reveals a polar pocket interacting with the pantothenate moiety of N5-Pan and an aromatic pocket loosely protecting the pentyl tail, suggesting that the introduction of an aromatic ring to a new pantothenamide may enhance its binding affinity to KpPanK. To test this idea, we synthesized N-pyridin-3-ylmethylpantothenamide (Np-Pan) and solved its co-crystal structure with KpPanK. The structure reveals two alternative conformations of the aromatic ring of Np-Pan bound at the aromatic pocket, providing the basis for further improvement of pantothenamide binding to KpPanK. (c) Proteins 2013;. (c) 2013 Wiley Periodicals, Inc. Crystal structures of Klebsiella pneumoniae pantothenate kinase in complex with N-substituted pantothenamides.,Li B, Tempel W, Smil D, Bolshan Y, Schapira M, Park HW Proteins. 2013 Mar 30. doi: 10.1002/prot.24290. PMID:23553820[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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