1A05

CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1a05a_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	3-isopropylmalate dehydrogenase, IPMDH	(Acidithiobacillus ferrooxidans ) [TaxId: 920 ],	SCOPe (2.08)
B	d1a05b_	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	3-isopropylmalate dehydrogenase, IPMDH	(Acidithiobacillus ferrooxidans ) [TaxId: 920 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Dimeric isocitrate & isopropylmalate dehydrogenases	8020414	4000791	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8032794	3001375	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Isocitrate/Isopropylmalate dehydrogenase-like	8032794	3001375	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Iso_dh	e1a05A1	A: a/b three-layered sandwiches	X: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	H: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	T: Isocitrate/Isopropylmalate dehydrogenase-like	F: Iso_dh	ECOD (1.6)
B	Iso_dh	e1a05B1	A: a/b three-layered sandwiches	X: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	H: Isocitrate/Isopropylmalate dehydrogenase-like (From Topology)	T: Isocitrate/Isopropylmalate dehydrogenase-like	F: Iso_dh	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)
B	3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00180	Isocitrate/isopropylmalate dehydrogenase (Iso_dh)	Isocitrate/isopropylmalate dehydrogenase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	3-ISOPROPYLMALATE DEHYDROGENASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding NAD binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding oxidoreductase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding NAD binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 3-isopropylmalate dehydrogenase activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity	pyruvate family amino acid metabolic process oxoacid metabolic process pyruvate family amino acid biosynthetic process cellular biosynthetic process organonitrogen compound biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process branched-chain amino acid metabolic process pyruvate family amino acid metabolic process oxoacid metabolic process pyruvate family amino acid biosynthetic process cellular biosynthetic process organonitrogen compound biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process branched-chain amino acid metabolic process L-leucine metabolic process L-leucine biosynthetic process organonitrogen compound metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process branched-chain amino acid biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR019818	Isocitrate/isopropylmalate dehydrogenase, conserved site	Conserved Site
A, B	IPR004429	Isopropylmalate dehydrogenase	Family
A, B	IPR024084	Isopropylmalate dehydrogenase-like domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B	3-isopropylmalate dehydrogenase M-CSA #371	Isocitrate dehydrogenase has long been known to be a key enzyme in the Krebs cycle, and isozymes are found in both the mitochondrial matrix and the cytosol of eukaryotes, and in bacteria. In addition to the usual NADP dependent form (EC 1.1.1.42), eukaryotes have an NAD dependent isozyme (EC 1.1.1.41). More recently, two other NAD dependent enzymes - isopropylmalate dehydrogenase (EC 1.1.1.85) and tartrate dehydrogenase (EC 1.1.1.93) have been recognised to be related by sequence and mechanism to isocitrate dehydrogenase - the unusual feature being that all of them decarboxylate the substrate which they oxidise. These are both found in micro-organisms and are involved in leucine biosynthesis and glyoxylate metabolism respectively. All require an Mg2+ ion for catalysis.	Defined by 5 residues: TYR:A-140ASP:A-246ASP:A-250LYS:B-190ASP:B-222 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.1.85 (PDB Primary Data) Search M-CSA Motif + EC 1.1.1.85

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.