3OCE | pdb_00003oce

Crystal structure of fumarate lyase:delta crystallin from Brucella melitensis bound to cobalt

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3oced1	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
D	d3oced2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
C	d3ocec1	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
C	d3ocec2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
B	d3oceb1	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
B	d3oceb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
A	d3ocea1	All alpha proteins	L-aspartase-like	L-aspartase-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
A	d3ocea2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	L-aspartase-like	8072375	3001572	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L-aspartase-like	8072375	3001572	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L-aspartase-like	8072375	3001572	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L-aspartase-like	8072375	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)
D	Sdh_cyt	e3oceD3	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Sdh_cyt	ECOD (develop294)
D	SRP_SPB	e3oceD4	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: SRP_SPB	ECOD (develop294)
C	Sdh_cyt	e3oceC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Sdh_cyt	ECOD (develop294)
B	Sdh_cyt	e3oceB3	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Sdh_cyt	ECOD (develop294)
B	SRP_SPB	e3oceB4	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: SRP_SPB	ECOD (develop294)
A	Sdh_cyt	e3oceA3	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Sdh_cyt	ECOD (develop294)
A	SRP_SPB	e3oceA4	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: SRP_SPB	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
C	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)
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)

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 lyase:Delta crystallin	aspartate ammonia-lyase activity lyase activity ammonia-lyase activity catalytic activity carbon-nitrogen lyase activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process small molecule metabolic process aspartate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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	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
A, B, C, D	IPR051546	Class-II Aspartate Ammonia-Lyase	Family

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.