5dn9: Difference between revisions
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==Crystal structure of Candida boidinii formate dehydrogenase complexed with NAD+ and azide== | ==Crystal structure of Candida boidinii formate dehydrogenase complexed with NAD+ and azide== | ||
<StructureSection load='5dn9' size='340' side='right' caption='[[5dn9]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='5dn9' size='340' side='right'caption='[[5dn9]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5dn9]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5dn9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candida_boidinii Candida boidinii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DN9 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> | |||
<tr id=' | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5dn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dn9 OCA], [https://pdbe.org/5dn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dn9 RCSB], [https://www.ebi.ac.uk/pdbsum/5dn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dn9 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/A0A0A1EQY0_CANBO A0A0A1EQY0_CANBO] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 5dn9" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5dn9" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Formate dehydrogenase 3D structures|Formate dehydrogenase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Cheatum CM]] | |||
[[Category: Cheatum | [[Category: Francis K]] | ||
[[Category: Francis | [[Category: Gakhar L]] | ||
[[Category: Gakhar | [[Category: Guo Q]] | ||
[[Category: Guo | [[Category: Kohen A]] | ||
[[Category: Kohen | [[Category: Major DT]] | ||
[[Category: Major | [[Category: Vardi-Kilshtain A]] | ||
[[Category: Vardi-Kilshtain | [[Category: Wichersham K]] | ||
[[Category: Wichersham | |||
Latest revision as of 00:51, 29 June 2023
Crystal structure of Candida boidinii formate dehydrogenase complexed with NAD+ and azideCrystal structure of Candida boidinii formate dehydrogenase complexed with NAD+ and azide
Structural highlights
FunctionPublication Abstract from PubMedThe structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD+) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 x 10-7 (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.,Guo Q, Gakhar L, Wickersham K, Francis K, Vardi-Kilshtain A, Major DT, Cheatum CM, Kohen A Biochemistry. 2016 May 3. PMID:27100912[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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