Isopropylmalate dehydrogenase: Difference between revisions

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Michal Harel, Alexander Berchansky, Joel L. Sussman

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-{{STRUCTURE_2y42|  PDB=2y42  | SIZE=400| SCENE= |right|CAPTION=Isopropylmalate dehydrogenase complex with NAD and Mg+2 ion [[2y42]] }}
+<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 ==
+'''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 ==
-Please use the "3D" button above this box to insert a Jmol applet (molecule) on this page.
+<scene name='49/490899/Cv/11'>3-isopropylmalate dehydrogenase complex with 3-isopropylmalate, glycerol, NAD, PMSF, Mn+2 and K- ions</scene>.
-Or use the four-green-boxes-button to insert scrollable text adjacent
-to a Jmol applet. Check out the other buttons as well!
--->
-'''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.
+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/12'>MN coordination site</scene>.
+<scene name='49/490899/Cv/13'>K coordination site</scene>.
+<scene name='49/490899/Cv/14'>3-isopropylmalate binding site</scene>.
+<scene name='49/490899/Cv/15'>Whole IMDH active site</scene>.
+</StructureSection>
 ==3D structures of isopropylmalate dehydrogenase==
-'''3-isopropylmalate dehydrogenase'''
+Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
+{{#tree:id=OrganizedByTopic|openlevels=0|
-[[1ipd]], [[1xaa]], [[1xab]], [[1xac]], [[1xad]], [[1osi]], [[1dpz]], [[1dr0]], [[1dr8]], [[2y3z]] – TtIMDH – ''Thermus thermophilus''<br />
-[[1idm]], [[1osj]], [[1wal]], [[1gc8]], [[1gc9]], [[1g2u]] – TtIMDH (mutant) <br />
-[[2ayq]], [[1v53]] – BcIMDH – ''Bacillus coagulans''<br />
-[[1v5b]] – BcIMDH (mutant) <br />
-[[1cm7]] – IMDH – ''Escherichia coli''<br />
-[[1vlc]] – IMDH – ''Thermotoga maritima''<br />
-[[1v7l]] - IMDH – ''Pyrococcus horikoshii''<br />
-[[1w0d]], [[2g4o]] - MtIMDH - ''Mycobacterium tuberculosis''<br />
-[[3h5e]], [[3h5h]], [[3h5j]] - MtIMDH small subunit<br />
-[[2hcu]] – IMDH small subunit – ''Streptococcus mutans''<br />
-[[3q3w]] - IMDH small subunit – ''Campylobacter jejuni''<br />
-[[3rsw]] - IMDH – ''Arabidopsis thaliana''<br />
-[[3uih]] - IMDH – ''Bacillus''
-'''IMDH binary complexes'''
+*3-isopropylmalate dehydrogenase
-[[1hex]] – TtIMDH + NAD<BR />
+**[[1ipd]], [[1xaa]], [[1xab]], [[1xac]], [[1xad]], [[1osi]], [[1dpz]], [[1dr0]], [[1dr8]], [[2y3z]] – TtIMDH – ''Thermus thermophilus''<br />
-[[2y40]] - TtIMDH + Mn<br />
+**[[1idm]], [[1osj]], [[1wal]], [[1gc8]], [[1gc9]], [[1g2u]] – TtIMDH (mutant) <br />
-[[1cnz]] – IMDH + Mn – ''Salmonella typhimurium''<br />
+**[[2ayq]], [[1v53]] – BcIMDH – ''Bacillus coagulans''<br />
-[[1wpw]] - IMDH + Mg – ''Sulfolobus tokodaii''<br />
+**[[1v5b]] – BcIMDH (mutant) <br />
-[[2pkp]] - IMDH small subunit + Zn – ''Methanocaldococcus jannaschii''
+**[[1cm7]] – IMDH – ''Escherichia coli''<br />
+**[[1vlc]] – IMDH – ''Thermotoga maritima''<br />
+**[[1v7l]] - IMDH – ''Pyrococcus horikoshii''<br />
+**[[1w0d]], [[2g4o]] - MtIMDH - ''Mycobacterium tuberculosis''<br />
+**[[3h5e]], [[3h5h]], [[3h5j]] - MtIMDH small subunit<br />
+**[[2hcu]] – IMDH small subunit – ''Streptococcus mutans''<br />
+**[[3q3w]], [[3udu]] - IMDH small subunit – ''Campylobacter jejuni''<br />
+**[[3r8w]] - AtIMDH – ''Arabidopsis thaliana''<br />
+**[[3u1h]] - IMDH – ''Bacillus''<br />
+**[[3vml]] - SoIMDH – ''Shewanella oneidensis/Shewanella benthica''<br />
-'''IMDH ternary complexes'''
+*IMDH binary complexes
-[[2y42]] - TtIMDH + Mn + NAD<BR />
+**[[1hex]] – TtIMDH + NAD<BR />
-[[2ztw]] - TtIMDH + Mg + inhibitor + NAD<BR />
+**[[2y40]] - TtIMDH + Mn<br />
-[[2y41]] - TtIMDH + 3IPM + Mn<br />
+**[[1cnz]] – IMDH + Mn – ''Salmonella typhimurium''<br />
-[[1a05]] – IMDH + 3IPM + Mg - ''Acidithiobacillus ferrooxidans''<br />
+**[[1wpw]] - IMDH + Mg – ''Sulfolobus tokodaii''<br />
-[[3vkz]], [[3vl2]], [[3vl3]], [[3vl4]], [[3vl6]], [[3vl7]] - SoIMDH + 3IPM + Ca – ''Shewanella oneidensis''<br />
+**[[2pkp]] - IMDH small subunit + Zn – ''Methanocaldococcus jannaschii''<br />
-[[3vmj]] - SoIMDH + 3IPM + Mg<br />
+**[[4iwh]] - BtIMDH + Mg – ''Burkholderia thailandensis''<br />
-[[3vmk]] - IMDH + 3IPM + Mg – ''Shewanella bethica''
+**[[4xxv]] - BtIMDH + NAD<br />
+**[[5j33]] - AtIMDH + NAD<br />
+**[[5j34]] - AtIMDH + Mg<br />
-'''2-isopropylmalate dehydrogenase'''
+*IMDH ternary complexes
-[[3fig]] - MtIMDH (mutant) + Zn
+**[[2y42]] - TtIMDH + Mn + NAD<BR />
+**[[2ztw]] - TtIMDH + Mg + inhibitor + NAD<BR />
+**[[2y41]] - TtIMDH + 3IPM + Mn<br />
+**[[4f7i]] - TtIMDH + Mg + 3IPM + NAD<br />
+**[[4wuo]] - TtIMDH (mutant) + Mn + 3IPM + NAD<br />
+**[[1a05]] – IMDH + 3IPM + Mg - ''Acidithiobacillus ferrooxidans''<br />
+**[[3vkz]], [[3vl2]], [[3vl3]], [[3vl4]], [[3vl6]], [[3vl7]] - SoIMDH + 3IPM + Ca <br />
+**[[3vmj]], [[3wzw]], [[3wzv]] - SoIMDH + 3IPM + Mg<br />
+**[[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 />
+}}
+== References ==
+<references/>
 [[Category:Topic Page]]