1YCF | pdb_00001ycf

Oxidized (di-ferric) FprA from Moorella thermoacetica

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ycfa1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Flavodoxin-related	Nitric oxide reductase C-terminal domain	(Neomoorella thermoacetica ) [TaxId: 1525 ],	SCOPe (2.08)
A	d1ycfa2	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	ROO N-terminal domain-like	Nitric oxide reductase N-terminal domain	(Neomoorella thermoacetica ) [TaxId: 1525 ],	SCOPe (2.08)
B	d1ycfb1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	automated matches	automated matches	(Neomoorella thermoacetica ) [TaxId: 1525 ],	SCOPe (2.08)
B	d1ycfb2	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	ROO N-terminal domain-like	automated matches	(Neomoorella thermoacetica ) [TaxId: 1525 ],	SCOPe (2.08)
D	d1ycfd1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	automated matches	automated matches	(Neomoorella thermoacetica ) [TaxId: 1525 ],	SCOPe (2.08)
D	d1ycfd2	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	ROO N-terminal domain-like	automated matches	(Neomoorella thermoacetica ) [TaxId: 1525 ],	SCOPe (2.08)
C	d1ycfc1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	automated matches	automated matches	(Neomoorella thermoacetica ) [TaxId: 1525 ],	SCOPe (2.08)
C	d1ycfc2	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	ROO N-terminal domain-like	automated matches	(Neomoorella thermoacetica ) [TaxId: 1525 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8034345	3001057	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Flavoproteins	8034346	3001217	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flavoproteins	8034346	3001217	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8034345	3001057	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8034345	3001057	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Flavoproteins	8034346	3001217	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8034345	3001057	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Flavoproteins	8034346	3001217	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	Lactamase_B_1	e1ycfA1	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B_1	ECOD (1.6)
A	Flavodoxin_1	e1ycfA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: Flavodoxin_1	ECOD (1.6)
B	Lactamase_B_1	e1ycfB1	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B_1	ECOD (1.6)
B	Flavodoxin_1	e1ycfB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: Flavodoxin_1	ECOD (1.6)
D	Lactamase_B_1	e1ycfD1	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B_1	ECOD (1.6)
D	Flavodoxin_1	e1ycfD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: Flavodoxin_1	ECOD (1.6)
C	Lactamase_B_1	e1ycfC1	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B_1	ECOD (1.6)
C	Flavodoxin_1	e1ycfC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: Flavodoxin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
A	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
B	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
B	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
D	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
D	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
C	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
C	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF19583	ODP family beta lactamase (ODP)	ODP family beta lactamase	The ODP (Oxygen-binding Di-iron Protein) domain is a distinct member of the metallo-beta-lactamase superfamily recruited to various bacterial and archaeal signal transduction pathways, including chemotaxis, to function as oxygen and iron sensors (1). ...	The ODP (Oxygen-binding Di-iron Protein) domain is a distinct member of the metallo-beta-lactamase superfamily recruited to various bacterial and archaeal signal transduction pathways, including chemotaxis, to function as oxygen and iron sensors (1). ODP was shown to act as a sensor for chemotactic responses to both iron and oxygen in the human pathogen Treponema denticola (Td). The ODP di-iron site binds oxygen at high affinity to reversibly form an unusually stable peroxo adduct.	Domain
A, B, C, D	PF00258	Flavodoxin (Flavodoxin_1)	Flavodoxin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Nitric oxide reductase	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity electron transfer activity FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity electron transfer activity cation binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR045761	ODP domain	Domain
A, B, C, D	IPR016440	Rubredoxin-oxygen oxidoreductase	Family
A, B, C, D	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
A, B, C, D	IPR029039	Flavoprotein-like superfamily	Homologous Superfamily
A, B, C, D	IPR001279	Metallo-beta-lactamase	Domain
A, B, C, D	IPR008254	Flavodoxin/nitric oxide synthase	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	nitric-oxide reductase (FMN) M-CSA #497	Moorella thermoacetica is a strictly anaerobic bacterium that utilises dissimilatory nitrate reduction for growth. It contains an A-type flavoprotein (FprA) that catalyses the reduction of nitric oxide to nitrogen dioxide, using FMN and a non-heme, non-sulphur diiron site.	Defined by 8 residues: HIS:A-24 [auth A-25]HIS:A-80 [auth A-81]GLU:A-82 [auth A-83]ASP:A-84 [auth A-85]HIS:A-147 [auth A-148]ASP:A-166 [auth A-167]TYR:A-194 [auth A-195]HIS:A-227 [auth A-228] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1 (PDB Primary Data) Search M-CSA Motif + EC 1

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.