6EBT

Crystal structure of recombinant mutant N107T of human fumarase

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6ebta_	All alpha proteins	L-aspartase-like	L-aspartase-like	L-aspartase/fumarase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6ebtb_	All alpha proteins	L-aspartase-like	L-aspartase-like	L-aspartase/fumarase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	L-aspartase-like	8072359	3001572	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L-aspartase-like	8072359	3001572	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	Lyase_1_N	e6ebtA2	A: alpha arrays	X: L-aspartase N-terminal domain-like (From Topology)	H: L-aspartase N-terminal domain-like (From Topology)	T: L-aspartase N-terminal domain-like	F: Lyase_1_N	ECOD (1.6)
A	FumaraseC_C	e6ebtA1	A: alpha arrays	X: L-aspartase C-terminal domain-like (From Homology)	H: L-aspartase C-terminal domain-like	T: L-aspartase C-terminal domain-like	F: FumaraseC_C	ECOD (1.6)
A	Lyase_1_C	e6ebtA3	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: Lyase_1_C	ECOD (1.6)
B	Lyase_1_N	e6ebtB1	A: alpha arrays	X: L-aspartase N-terminal domain-like (From Topology)	H: L-aspartase N-terminal domain-like (From Topology)	T: L-aspartase N-terminal domain-like	F: Lyase_1_N	ECOD (1.6)
B	FumaraseC_C	e6ebtB3	A: alpha arrays	X: L-aspartase C-terminal domain-like (From Homology)	H: L-aspartase C-terminal domain-like	T: L-aspartase C-terminal domain-like	F: FumaraseC_C	ECOD (1.6)
B	Lyase_1_C	e6ebtB2	A: alpha arrays	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like (From Topology)	T: L-aspartase middle domain-like	F: Lyase_1_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (utative)
A	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (utative)
A	1.10.40.30	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase Protein R1	domain 1	CATH (utative)
B	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (utative)
B	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (utative)
B	1.10.40.30	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase Protein R1	domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00206	Lyase (Lyase_1)	Lyase	-	Domain
A, B	PF10415	Fumarase C C-terminus (FumaraseC_C)	Fumarase C C-terminus	Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Kreb's cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The ...	Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Kreb's cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit [1]. FumaraseC_C does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Fumarate hydratase, mitochondrial	protein binding binding histone binding hydro-lyase activity lyase activity catalytic activity fumarate hydratase activity carbon-oxygen lyase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process organic substance metabolic process oxoacid metabolic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process fumarate metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process organic substance metabolic process oxoacid metabolic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process fumarate metabolic process organic acid metabolic process multicellular organismal process multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of double-strand break repair via nonhomologous end joining DNA repair double-strand break repair regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of double-strand break repair via nonhomologous end joining double-strand break repair via nonhomologous end joining biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of double-strand break repair regulation of DNA repair organic cyclic compound metabolic process positive regulation of DNA metabolic process regulation of response to stimulus macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process malate metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds generation of precursor metabolites and energy adaptive thermogenesis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process regulation of multicellular organismal process amino acid metabolic process alpha-amino acid metabolic process arginine metabolic process cellular ketone metabolic process regulation of small molecule metabolic process regulation of arginine metabolic process organonitrogen compound metabolic process regulation of cellular ketone metabolic process regulation of cellular amino acid metabolic process regulation of amine metabolic process regulation of cellular metabolic process amine metabolic process organonitrogen compound biosynthetic process amide biosynthetic process urea metabolic process nitrogen cycle metabolic process biosynthetic process urea cycle organic substance biosynthetic process amide metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex catalytic complex tricarboxylic acid cycle heteromeric enzyme complex extracellular exosome extracellular vesicle extracellular organelle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex catalytic complex tricarboxylic acid cycle heteromeric enzyme complex extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol intracellular non-membrane-bounded organelle chromosome non-membrane-bounded organelle site of double-strand break site of DNA damage membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000362	Fumarate lyase family	Family
A, B	IPR022761	Fumarate lyase, N-terminal	Domain
A, B	IPR024083	Fumarase/histidase, N-terminal	Homologous Superfamily
A, B	IPR005677	Fumarate hydratase, class II	Family
A, B	IPR008948	L-Aspartase-like	Homologous Superfamily
A, B	IPR018951	Fumarase C, C-terminal	Domain
A, B	IPR020557	Fumarate lyase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P07954	fumaric aciduria hereditary leiomyomatosis and renal cell cancer lung cancer Malignant neoplasm of kidney ovarian cancer psoriasis adrenal medulla cancer intellectual disability leiomyoma malignant ependymoma malignant pancreatic neoplasm neuroendocrine carcinoma pancreatic ductal adenocarcinoma renal carcinoma acute myeloid leukemia fumaric aciduria hereditary leiomyomatosis and renal cell cancer lung cancer Malignant neoplasm of kidney ovarian cancer psoriasis adrenal medulla cancer intellectual disability leiomyoma malignant ependymoma malignant pancreatic neoplasm neuroendocrine carcinoma pancreatic ductal adenocarcinoma renal carcinoma acute myeloid leukemia astrocytic tumor cancer exocrine pancreatic carcinoma kidney neoplasm leiomyoma cutis medulloblastoma non-small cell lung carcinoma Pick disease ulcerative colitis adenoma benign neoplasm of adrenal gland endometrial carcinoma hydrops fetalis large cell medulloblastoma

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.