2JIR | pdb_00002jir

A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	d2jira1	All beta proteins	Double psi beta-barrel	ADC-like	Formate dehydrogenase/DMSO reductase, C-terminal domain	Periplasmic nitrate reductase alpha chain, NapA	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)
A	d2jira2	Alpha and beta proteins (a/b)	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Periplasmic nitrate reductase alpha chain	(Desulfovibrio desulfuricans ) [TaxId: 876 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ADC-like	8034676	3001132	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8034678	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)
A	Peptidase_S46, Trypsin_2	e2jirA1	A: alpha bundles	X: Cloacin translocation domain	H: LigT-related	T: LigT-related	F: Peptidase_S46, Trypsin_2	ECOD (develop294)
A	YkuD	e2jirA2	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.20.25.90	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	ADC-like domains	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PERIPLASMIC NITRATE REDUCTASE	cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding molybdenum ion binding nitrate reductase (cytochrome) activity nitrate reductase activity oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors oxidoreductase activity, acting on a heme group of donors cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding molybdenum ion binding nitrate reductase (cytochrome) activity nitrate reductase activity oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors oxidoreductase activity, acting on a heme group of donors catalytic activity 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 Mo-molybdopterin cofactor biosynthetic process Mo-molybdopterin cofactor metabolic 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A	IPR006656	Molybdopterin oxidoreductase	Domain
A	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A	IPR010051	Periplasmic nitrate reductase, large subunit	Family
A	IPR050123	Prok_molybdopt-oxidoreductase	Unknown
A	IPR041957	Nitrate reductase NapA-like, molybdopterin-binding domain	Domain

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.