3E04 | pdb_00003e04

Crystal structure of human fumarate hydratase

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3e04a_	All alpha proteins	L-aspartase-like	L-aspartase-like	L-aspartase/fumarase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3e04b_	All alpha proteins	L-aspartase-like	L-aspartase-like	L-aspartase/fumarase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3e04c_	All alpha proteins	L-aspartase-like	L-aspartase-like	L-aspartase/fumarase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3e04d_	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	SCOP2 Family	L-aspartase/fumarase	8072358	4001433	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	L-aspartase-like	8072359	3001572	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	L-aspartase-like	8072359	3001572	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L-aspartase-like	8072359	3001572	SCOP2B (2022-06-29)
D	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	Peptidase_M16_C	e3e04A1	A: alpha bundles	X: Profilin-like	H: sensor domains	T: sensor domains	F: Peptidase_M16_C	ECOD (develop294)
B	Ras	e3e04B1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Ras	ECOD (develop294)
C	Ras	e3e04C2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Ras	ECOD (develop294)
C	Rhodanese	e3e04C3	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rhodanese	ECOD (develop294)
D	Ras	e3e04D1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Ras	ECOD (develop294)

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 (4.3.0)
A	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
A	1.10.40.30	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase Protein R1	domain 1	CATH (4.3.0)
B	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
B	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
B	1.10.40.30	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase Protein R1	domain 1	CATH (4.3.0)
C	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
C	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
D	1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C	Chain B, domain 1	CATH (4.3.0)
D	1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C	Chain A, domain 2	CATH (4.3.0)
D	1.10.40.30	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase Protein R1	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00206	Lyase (Lyase_1)	Lyase		Domain
A, B, C, D	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, C, D	Fumarate hydratase	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 oxoacid 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 cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process oxoacid 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 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 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 nitrogen cycle metabolic process biosynthetic process urea cycle urea metabolic process arginine metabolic process amino acid metabolic process alpha-amino acid metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol membraneless organelle intracellular membraneless organelle chromosome 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, C, D	IPR000362	Fumarate lyase family	Family
A, B, C, D	IPR022761	Fumarate lyase, N-terminal	Domain
A, B, C, D	IPR024083	Fumarase/histidase, N-terminal	Homologous Superfamily
A, B, C, D	IPR005677	Fumarate hydratase, class II	Family
A, B, C, D	IPR008948	L-Aspartase-like	Homologous Superfamily
A, B, C, D	IPR018951	Fumarase C, C-terminal	Domain
A, B, C, D	IPR020557	Fumarate lyase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.