2BII | pdb_00002bii

crystal structure of nitrate-reducing fragment of assimilatory nitrate reductase from Pichia angusta

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Mo-co_dimer	e2biiB4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Mo-co_dimer	ECOD (1.6)
B	Oxidored_molyb	e2biiB3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)
A	Mo-co_dimer	e2biiA4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Mo-co_dimer	ECOD (1.6)
A	Oxidored_molyb	e2biiA3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
B	2.60.40.650	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
A	2.60.40.650	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00174	Oxidoreductase molybdopterin binding domain (Oxidored_molyb)	Oxidoreductase molybdopterin binding domain	This domain is found in a variety of oxidoreductases. This domain binds to a molybdopterin cofactor. Xanthine dehydrogenases, that also bind molybdopterin, have essentially no similarity.	Domain
A, B	PF03404	Mo-co oxidoreductase dimerisation domain (Mo-co_dimer)	Mo-co oxidoreductase dimerisation domain	This domain is found in molybdopterin cofactor (Mo-co) oxidoreductases. It is involved in dimer formation, and has an Ig-fold structure [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	NITRATE REDUCTASE [NADPH]	FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor nitrate reductase (NADPH) activity nitrate reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor nitrate reductase (NADPH) activity nitrate reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors nitrate reductase [NAD(P)H] activity catalytic activity oxidoreductase activity, acting on a sulfur group of donors sulfite oxidase activity oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor tetrapyrrole binding heme binding cation binding transition metal ion binding molybdenum ion binding metal ion binding molybdopterin cofactor binding	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 nitric oxide metabolic process nitric oxide biosynthetic process biosynthetic process sulfur compound metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase	Domain
A, B	IPR001433	Oxidoreductase FAD/NAD(P)-binding	Domain
A, B	IPR005066	Moybdenum cofactor oxidoreductase, dimerisation	Domain
A, B	IPR008335	Eukaryotic molybdopterin oxidoreductase	Family
A, B	IPR012137	Nitrate reductase NADH dependent	Family
A, B	IPR017938	Riboflavin synthase-like beta-barrel	Homologous Superfamily
A, B	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B	IPR036400	Cytochrome b5-like heme/steroid binding domain superfamily	Homologous Superfamily
A, B	IPR018506	Cytochrome b5, heme-binding site	Binding Site
A, B	IPR022407	Oxidoreductase, molybdopterin binding site	Binding Site
A, B	IPR036374	Oxidoreductase, molybdopterin-binding domain superfamily	Homologous Superfamily
A, B	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain	Homologous Superfamily
A, B	IPR008333	Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain	Domain
A, B	IPR000572	Oxidoreductase, molybdopterin-binding domain	Domain
A, B	IPR017927	FAD-binding domain, ferredoxin reductase-type	Domain
A, B	IPR001199	Cytochrome b5-like heme/steroid binding domain	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
B	Nitrate reductase [NADH] M-CSA #925	This entry represents the NADH dependent nitrate reductase (NR) from plants and fungi, including NIA1 and NIA2 from Arabidopsis. They contain an N-terminal oxidoreductase molybdopterin binding domain and a C-terminal FAD-binding domain. The N-terminal domain is responsible for the reduction of nitrate; the C-terminal domain is responsible for the regeneration of the FAD cofactor. Only the N-terminal domain function is shown here; the C-terminal function can be found in MACiE:862.	Defined by 3 residues: CYS:B-79 [auth B-139]ASP:B-211 [auth B-271]ASN:B-212 [auth B-272] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.7.1.2 (PDB Primary Data) Search M-CSA Motif + EC 1.7.1.2 EC: 1.7.1.3 (UniProt) Search M-CSA Motif + EC 1.7.1.3

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.