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Isopropylmalate dehydrogenase
From Proteopedia
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| - | <StructureSection load=' | + | <StructureSection load='' size='350' side='right' caption='3-isopropylmalate dehydrogenase complex with 3-isopropylmalate, glycerol, NAD, PMSF, Mn+2 and K+ ions (purple) (PDB entry [[4f7i]])' scene='49/490899/Cv/1'> |
== Function == | == Function == | ||
'''3-Isopropylmalate dehydrogenase''' (IMDH) catalyzes the oxidative decarboxylation of 3-isopropylmalate (3IPM) to 2-oxo-4-methylvalerate. This reaction is a step in the biosynthesis of leucine in bacteria and fungi. IMDH uses [[NAD]] as a cofactor. IMDH is a bifunctional enzyme that catalyzes dehydrogenation and decarboxylation in the presence of NAD and a divalent cation<ref>PMID:17979826</ref>. | '''3-Isopropylmalate dehydrogenase''' (IMDH) catalyzes the oxidative decarboxylation of 3-isopropylmalate (3IPM) to 2-oxo-4-methylvalerate. This reaction is a step in the biosynthesis of leucine in bacteria and fungi. IMDH uses [[NAD]] as a cofactor. IMDH is a bifunctional enzyme that catalyzes dehydrogenation and decarboxylation in the presence of NAD and a divalent cation<ref>PMID:17979826</ref>. | ||
== Structural highlights == | == Structural highlights == | ||
| - | <scene name='49/490899/Cv/ | + | <scene name='49/490899/Cv/11'>3-isopropylmalate dehydrogenase complex with 3-isopropylmalate, glycerol, NAD, PMSF, Mn+2 and K- ions</scene>. |
IMDH active site containing the <scene name='49/490899/Cv/9'>NAD cofactor is located between 2 subunits</scene> and contains the substrate and Mn+2 and K- ions<ref>PMID:25211160</ref>. Water molecules shown as red spheres. | IMDH active site containing the <scene name='49/490899/Cv/9'>NAD cofactor is located between 2 subunits</scene> and contains the substrate and Mn+2 and K- ions<ref>PMID:25211160</ref>. Water molecules shown as red spheres. | ||
| - | <scene name='49/490899/Cv/ | + | <scene name='49/490899/Cv/12'>MN coordination site</scene>. |
| - | <scene name='49/490899/Cv/ | + | <scene name='49/490899/Cv/13'>K coordination site</scene>. |
| - | <scene name='49/490899/Cv/ | + | <scene name='49/490899/Cv/14'>3-isopropylmalate binding site</scene>. |
| - | <scene name='49/490899/Cv/ | + | <scene name='49/490899/Cv/15'>Whole IMDH active site</scene>. |
</StructureSection> | </StructureSection> | ||
==3D structures of isopropylmalate dehydrogenase== | ==3D structures of isopropylmalate dehydrogenase== | ||
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**[[3h5e]], [[3h5h]], [[3h5j]] - MtIMDH small subunit<br /> | **[[3h5e]], [[3h5h]], [[3h5j]] - MtIMDH small subunit<br /> | ||
**[[2hcu]] – IMDH small subunit – ''Streptococcus mutans''<br /> | **[[2hcu]] – IMDH small subunit – ''Streptococcus mutans''<br /> | ||
| - | **[[3q3w]], [[ | + | **[[3q3w]], [[3udu]] - IMDH small subunit – ''Campylobacter jejuni''<br /> |
| - | **[[3r8w]] - | + | **[[3r8w]] - AtIMDH – ''Arabidopsis thaliana''<br /> |
**[[3u1h]] - IMDH – ''Bacillus''<br /> | **[[3u1h]] - IMDH – ''Bacillus''<br /> | ||
**[[3vml]] - SoIMDH – ''Shewanella oneidensis/Shewanella benthica''<br /> | **[[3vml]] - SoIMDH – ''Shewanella oneidensis/Shewanella benthica''<br /> | ||
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**[[4iwh]] - BtIMDH + Mg – ''Burkholderia thailandensis''<br /> | **[[4iwh]] - BtIMDH + Mg – ''Burkholderia thailandensis''<br /> | ||
**[[4xxv]] - BtIMDH + NAD<br /> | **[[4xxv]] - BtIMDH + NAD<br /> | ||
| + | **[[5j33]] - AtIMDH + NAD<br /> | ||
| + | **[[5j34]] - AtIMDH + Mg<br /> | ||
*IMDH ternary complexes | *IMDH ternary complexes | ||
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**[[1a05]] – IMDH + 3IPM + Mg - ''Acidithiobacillus ferrooxidans''<br /> | **[[1a05]] – IMDH + 3IPM + Mg - ''Acidithiobacillus ferrooxidans''<br /> | ||
**[[3vkz]], [[3vl2]], [[3vl3]], [[3vl4]], [[3vl6]], [[3vl7]] - SoIMDH + 3IPM + Ca <br /> | **[[3vkz]], [[3vl2]], [[3vl3]], [[3vl4]], [[3vl6]], [[3vl7]] - SoIMDH + 3IPM + Ca <br /> | ||
| - | **[[3vmj]] - SoIMDH + 3IPM + Mg<br /> | + | **[[3vmj]], [[3wzw]], [[3wzv]] - SoIMDH + 3IPM + Mg<br /> |
| - | **[[3vmk]] - IMDH + 3IPM + Mg – '' | + | **[[3wzy]], [[3wzx]] - SoIMDH (mutant) + 3IPM + Mg<br /> |
| + | **[[3vmk]] - SoIMDH + 3IPM + Mg <br /> | ||
| + | **[[4y1p]] - IMDH + 3IPM + Mg – ''Sulfolobus acidarius''<br /> | ||
| + | **[[5j32]] - AtIMDH + 3IPM + Mg<br /> | ||
| + | **[[6xxy]] - IMDH (mutant) + NAD + isobutenyl oxalylhydroxamate – ''Haemophilus influenzae''<BR /> | ||
}} | }} | ||
Current revision
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3D structures of isopropylmalate dehydrogenase
Updated on 30-August-2020
References
- ↑ Martignon S, Rossi F, Rizzi M. Expression, purification and characterisation of Haemophilus influenzae 3-isopropylmalate dehydrogenase (LeuB). Protein Pept Lett. 2007;14(8):822-7. PMID:17979826
- ↑ Pallo A, Olah J, Graczer E, Merli A, Zavodszky P, Weiss MS, Vas M. Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis. FEBS J. 2014 Sep 11. doi: 10.1111/febs.13044. PMID:25211160 doi:http://dx.doi.org/10.1111/febs.13044
