2NYA | pdb_00002nya

Crystal structure of the periplasmic nitrate reductase (NAP) from Escherichia coli

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth F]	SCOP2 Family	Formate dehydrogenase/DMSO reductase, domains 1-3	8098633	4000801	SCOP2 (2022-06-29)
B [auth F]	SCOP2 Family	Formate dehydrogenase/DMSO reductase, C-terminal domain	8101083	4002360	SCOP2 (2022-06-29)
B [auth F]	SCOP2 Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8098634	3001453	SCOP2 (2022-06-29)
B [auth F]	SCOP2 Superfamily	ADC-like	8101084	3001132	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	ADC-like	8101084	3001132	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8098634	3001453	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)
B [auth F]	Molydop_binding	e2nyaF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
B [auth F]	Molybdop_Fe4S4	e2nyaF2	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4	ECOD (1.6)
B [auth F]	Molybdopterin_2nd	e2nyaF4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
B [auth F]	Molybdopterin_1st_1	e2nyaF3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
A	Molydop_binding	e2nyaA3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
A	Molybdop_Fe4S4	e2nyaA1	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4	ECOD (1.6)
A	Molybdopterin_1st_1	e2nyaA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
A	Molybdop_Fe4S4,Molybdopterin_2nd	e2nyaA4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdop_Fe4S4,Molybdopterin_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth F]	3.30.200.210	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B [auth F]	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B [auth F]	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
B [auth F]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
A	3.30.200.210	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth F]	PF01568	Molydopterin dinucleotide binding domain (Molydop_binding)	Molydopterin dinucleotide binding domain	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire s ...	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].	Domain
A, B [auth F]	PF04879	Molybdopterin oxidoreductase Fe4S4 domain (Molybdop_Fe4S4)	Molybdopterin oxidoreductase Fe4S4 domain	This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1].	Domain
A, B [auth F]	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth F]	Periplasmic nitrate reductase	cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding nitrate reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity molybdenum ion binding nitrate reductase (cytochrome) activity oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding nitrate reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity molybdenum ion binding nitrate reductase (cytochrome) activity oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor oxidoreductase activity, acting on a heme group of donors molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding electron transfer activity	nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process cellular respiration energy derivation by oxidation of organic compounds generation of precursor metabolites and energy anaerobic respiration Mo-molybdopterin cofactor biosynthetic process nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process cellular respiration energy derivation by oxidation of organic compounds generation of precursor metabolites and energy anaerobic respiration Mo-molybdopterin cofactor biosynthetic process Mo-molybdopterin cofactor metabolic process primary metabolic process prosthetic group metabolic process molybdopterin cofactor biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process molybdopterin cofactor metabolic process phosphate-containing compound metabolic process protein metabolic process macromolecule metabolic process phosphorus metabolic process	cellular anatomical structure membrane protein-containing complex catalytic complex nitrate reductase complex oxidoreductase complex periplasmic space outer membrane-bounded periplasmic space cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth F]	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A, B [auth F]	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A, B [auth F]	IPR006656	Molybdopterin oxidoreductase	Domain
A, B [auth F]	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A, B [auth F]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A, B [auth F]	IPR010051	Periplasmic nitrate reductase, large subunit	Family
A, B [auth F]	IPR041957	Nitrate reductase NapA-like, molybdopterin-binding domain	Domain
A, B [auth F]	IPR050123	Prokaryotic molybdopterin-containing oxidoreductase	Family
A, B [auth F]	IPR027467	Molybdopterin oxidoreductase, molybdopterin cofactor binding site	Binding Site
A, B [auth F]	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site

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.