2b0t: Difference between revisions

Revision as of 19:42, 3 May 2008

Structure of Monomeric NADP Isocitrate dehydrogenase

OverviewOverview

Both monomeric and dimeric NADP+-dependent isocitrate dehydrogenase (IDH) belong to the metal-dependent beta-decarboxylating dehydrogenase family and catalyze the oxidative decarboxylation from 2R,3S-isocitrate to yield 2-oxoglutarate, CO2, and NADPH. It is important to solve the structures of IDHs from various species to correlate with its function and evolutionary significance. So far, only two crystal structures of substrate/cofactor-bound (isocitrate/NADP) NADP+-dependent monomeric IDH from Azotobacter vinelandii (AvIDH) have been solved. Herein, we report for the first time the substrate/cofactor-free structure of a monomeric NADP+-dependent IDH from Corynebacterium glutamicum (CgIDH) in the presence of Mg2+. The 1.75 A structure of CgIDH-Mg2+ showed a distinct open conformation in contrast to the closed conformation of AvIDH-isocitrate/NADP+ complexes. Fluorescence studies on CgIDH in the presence of isocitrate/or NADP+ suggest the presence of low energy barrier conformers. In CgIDH, the amino acid residues corresponding to the Escherichia coli IDH phosphorylation-loop are alpha-helical compared with the more flexible random-coil region in the E. coli protein where IDH activation is controlled by phosphorylation. This more structured region supports the idea that activation of CgIDH is not controlled by phosphorylation. Monomeric NADP+-specific IDHs have been identified from about 50 different bacterial species, such as proteobacteria, actinobacteria, and planctomycetes, whereas, dimeric NADP+-dependent IDHs are diversified in both prokaryotes and eukaryotes. We have constructed a phylogenetic tree based on amino acid sequences of all bacterial monomeric NADP+-dependent IDHs and also another one with specifically chosen species which either contains both monomeric and dimeric NADP+-dependent IDHs or have monomeric NADP+-dependent, as well as NAD+-dependent IDHs. This is done to examine evolutionary relationships.

About this StructureAbout this Structure

2B0T is a Single protein structure of sequence from Corynebacterium glutamicum. Full crystallographic information is available from OCA.

ReferenceReference

Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenase., Imabayashi F, Aich S, Prasad L, Delbaere LT, Proteins. 2006 Apr 1;63(1):100-12. PMID:16416443 Page seeded by OCA on Sat May 3 19:42:50 2008

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OCA

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- {{Structure
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-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase_(NADP(+)) Isocitrate dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.42 1.1.1.42] </span>
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-}}
 '''Structure of Monomeric NADP Isocitrate dehydrogenase'''
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 Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenase., Imabayashi F, Aich S, Prasad L, Delbaere LT, Proteins. 2006 Apr 1;63(1):100-12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16416443 16416443]
 [[Category: Corynebacterium glutamicum]]
-[[Category: Isocitrate dehydrogenase (NADP(+))]]
 [[Category: Single protein]]
 [[Category: Aich, S.]]
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 [[Category: Imabayashi, F.]]
 [[Category: Prasad, L.]]
-[[Category: idh]]
+[[Category: Idh]]
-[[Category: monomeric]]
+[[Category: Monomeric]]
-[[Category: nadp]]
+[[Category: Nadp]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 19:42:50 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:59:57 2008''