Isopropylmalate dehydrogenase - Revision history

Michal Harel at 06:10, 30 August 2020

Michal Harel — Sun, 30 Aug 2020 06:10:50 GMT

←Older revision		Revision as of 06:10, 30 August 2020
Line 64:		Line 64:
	**[[4y1p]] - IMDH + 3IPM + Mg – ''Sulfolobus acidarius''<br />		**[[4y1p]] - IMDH + 3IPM + Mg – ''Sulfolobus acidarius''<br />
	**[[5j32]] - AtIMDH + 3IPM + Mg<br />		**[[5j32]] - AtIMDH + 3IPM + Mg<br />
		+	**[[6xxy]] - IMDH (mutant) + NAD + isobutenyl oxalylhydroxamate – ''Haemophilus influenzae''<BR />

	}}		}}

Alexander Berchansky at 10:03, 30 June 2019

Alexander Berchansky — Sun, 30 Jun 2019 10:03:23 GMT

←Older revision		Revision as of 10:03, 30 June 2019
Line 4:		Line 4:

	== Structural highlights ==		== Structural highlights ==
-	<scene name='49/490899/Cv/2'>3-isopropylmalate dehydrogenase complex with 3-isopropylmalate, glycerol, NAD, PMSF, Mn+2 and K- ions</scene>.	+	<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/4'>MN coordination site</scene>.	+	<scene name='49/490899/Cv/12'>MN coordination site</scene>.

-	<scene name='49/490899/Cv/6'>K coordination site</scene>.	+	<scene name='49/490899/Cv/13'>K coordination site</scene>.

-	<scene name='49/490899/Cv/5'>3-isopropylmalate binding site</scene>.	+	<scene name='49/490899/Cv/14'>3-isopropylmalate binding site</scene>.

-	<scene name='49/490899/Cv/10'>Whole IMDH active site</scene>.	+	<scene name='49/490899/Cv/15'>Whole IMDH active site</scene>.
	</StructureSection>		</StructureSection>
	==3D structures of isopropylmalate dehydrogenase==		==3D structures of isopropylmalate dehydrogenase==

Michal Harel at 10:14, 23 July 2018

Michal Harel — Mon, 23 Jul 2018 10:14:26 GMT

←Older revision		Revision as of 10:14, 23 July 2018
Line 33:		Line 33:
	**[[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]], [[~~3udo~~]] - IMDH small subunit – ''Campylobacter jejuni''<br />	+	**[[3q3w]], [[3udu]] - IMDH small subunit – ''Campylobacter jejuni''<br />
	**[[3r8w]] - AtIMDH – ''Arabidopsis thaliana''<br />		**[[3r8w]] - AtIMDH – ''Arabidopsis thaliana''<br />
	**[[3u1h]] - IMDH – ''Bacillus''<br />		**[[3u1h]] - IMDH – ''Bacillus''<br />
Line 59:		Line 59:
	**[[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]], [[3wzw]] - SoIMDH + 3IPM + Mg<br />	+	**[[3vmj]], [[3wzw]], [[3wzv]] - SoIMDH + 3IPM + Mg<br />
	**[[3wzy]], [[3wzx]] - SoIMDH (mutant) + 3IPM + Mg<br />		**[[3wzy]], [[3wzx]] - SoIMDH (mutant) + 3IPM + Mg<br />
	**[[3vmk]] - SoIMDH + 3IPM + Mg <br />		**[[3vmk]] - SoIMDH + 3IPM + Mg <br />

Joel L. Sussman at 06:00, 20 October 2017

Joel L. Sussman — Fri, 20 Oct 2017 06:00:33 GMT

←Older revision		Revision as of 06:00, 20 October 2017
Line 1:		Line 1:
-	<StructureSection load='~~4f7i~~' 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'>	+	<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>.

Michal Harel at 22:25, 19 October 2017

Michal Harel — Thu, 19 Oct 2017 22:25:31 GMT

←Older revision		Revision as of 22:25, 19 October 2017
Line 1:		Line 1:
-	<StructureSection load='4f7i' size='~~450~~' 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'>	+	<StructureSection load='4f7i' 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>.

Michal Harel at 09:22, 25 June 2017

Michal Harel — Sun, 25 Jun 2017 09:22:48 GMT

←Older revision		Revision as of 09:22, 25 June 2017
Line 1:		Line 1:
-	<StructureSection load='4f7i' size='450' side='right' caption='3-isopropylmalate dehydrogenase complex with 3-isopropylmalate, glycerol, NAD, PMSF, Mn+2 and K- ions (PDB entry [[4f7i]])' scene='49/490899/Cv/1'>	+	<StructureSection load='4f7i' size='450' 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>.

Michal Harel at 09:21, 25 June 2017

Michal Harel — Sun, 25 Jun 2017 09:21:43 GMT

←Older revision		Revision as of 09:21, 25 June 2017
Line 34:		Line 34:
	**[[2hcu]] – IMDH small subunit – ''Streptococcus mutans''<br />		**[[2hcu]] – IMDH small subunit – ''Streptococcus mutans''<br />
	**[[3q3w]], [[3udo]] - IMDH small subunit – ''Campylobacter jejuni''<br />		**[[3q3w]], [[3udo]] - IMDH small subunit – ''Campylobacter jejuni''<br />
-	**[[3r8w]] - ~~IMDH~~ – ''Arabidopsis thaliana''<br />	+	**[[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 />
Line 47:		Line 47:
	**[[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
Line 57:		Line 59:
	**[[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]] - SoIMDH + 3IPM + Mg<br />
-	**[[3vmk]] - IMDH + 3IPM + Mg – ''~~Shewanella bethica~~''	+	**[[3wzy]], [[3wzx]] - SoIMDH (mutant) + 3IPM + Mg<br />
		+	**[[3vmk]] - SoIMDH + 3IPM + Mg <br />
		+	**[[4y1p]] - IMDH + 3IPM + Mg – ''Sulfolobus acidarius''<br />
		+	**[[5j32]] - AtIMDH + 3IPM + Mg<br />

	}}		}}

Alexander Berchansky at 11:32, 11 April 2016

Alexander Berchansky — Mon, 11 Apr 2016 11:32:50 GMT

←Older revision		Revision as of 11:32, 11 April 2016
Line 6:		Line 6:
	<scene name='49/490899/Cv/2'>3-isopropylmalate dehydrogenase complex with 3-isopropylmalate, glycerol, NAD, PMSF, Mn+2 and K- ions</scene>.		<scene name='49/490899/Cv/2'>3-isopropylmalate dehydrogenase complex with 3-isopropylmalate, glycerol, NAD, PMSF, Mn+2 and K- ions</scene>.

-	IMDH active site containing the NAD cofactor is located between 2 subunits and contains the substrate and Mn+2 and K- ions<ref>PMID:25211160</ref>.	+	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/4'>MN coordination site</scene>.
		+
		+	<scene name='49/490899/Cv/6'>K coordination site</scene>.
		+
		+	<scene name='49/490899/Cv/5'>3-isopropylmalate binding site</scene>.
		+
		+	<scene name='49/490899/Cv/10'>Whole IMDH active site</scene>.
	</StructureSection>		</StructureSection>
	==3D structures of isopropylmalate dehydrogenase==		==3D structures of isopropylmalate dehydrogenase==

Alexander Berchansky at 10:08, 11 April 2016

Alexander Berchansky — Mon, 11 Apr 2016 10:08:51 GMT

←Older revision		Revision as of 10:08, 11 April 2016
Line 4:		Line 4:

	== Structural highlights ==		== Structural highlights ==
		+	<scene name='49/490899/Cv/2'>3-isopropylmalate dehydrogenase complex with 3-isopropylmalate, glycerol, NAD, PMSF, Mn+2 and K- ions</scene>.
		+
	IMDH active site containing the NAD cofactor is located between 2 subunits and contains the substrate and Mn+2 and K- ions<ref>PMID:25211160</ref>.		IMDH active site containing the NAD cofactor is located between 2 subunits and contains the substrate and Mn+2 and K- ions<ref>PMID:25211160</ref>.
	</StructureSection>		</StructureSection>

Alexander Berchansky at 10:01, 11 April 2016

Alexander Berchansky — Mon, 11 Apr 2016 10:01:40 GMT

←Older revision		Revision as of 10:01, 11 April 2016
Line 1:		Line 1:
-	<StructureSection load='4f7i' size='450' side='right' caption='3-isopropylmalate dehydrogenase complex with 3-isopropylmalate, glycerol, NAD, PMSF, Mn+2 and K- ions (PDB entry [[4f7i]])' scene=''>	+	<StructureSection load='4f7i' size='450' side='right' caption='3-isopropylmalate dehydrogenase complex with 3-isopropylmalate, glycerol, NAD, PMSF, Mn+2 and K- ions (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>.