1Y5N

The crystal structure of the NarGHI mutant NarI-K86A in complex with pentachlorophenol

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
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1y5na1	All beta proteins	Double psi beta-barrel	ADC-like	Formate dehydrogenase/DMSO reductase, C-terminal domain	Respiratory nitrate reductase 1 alpha chain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1y5na2	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	Respiratory nitrate reductase 1 alpha chain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1y5nb_	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Respiratory nitrate reductase 1 beta chain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1y5nc_	Membrane and cell surface proteins and peptides	Heme-binding four-helical bundle	Respiratory nitrate reductase 1 gamma chain	Respiratory nitrate reductase 1 gamma chain	Respiratory nitrate reductase 1 gamma chain	(Escherichia coli ) [TaxId: 562 ],	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	8034109	3001132	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8034108	3001453	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	4Fe-4S ferredoxins	8034110	3000020	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Respiratory nitrate reductase 1 gamma chain	8039525	3000332	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	Molydop_binding	e1y5nA4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
A	NarG	e1y5nA1	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: NarG	ECOD (1.6)
A	Molybdopterin_2nd	e1y5nA3	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)
A	Molybdopterin_1st_1	e1y5nA2	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)
B	Fer4_11	e1y5nB2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11	ECOD (1.6)
B	Nitr_red_bet_C_1	e1y5nB1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Nitr_red_bet_C_1	ECOD (1.6)
C	Nitrate_red_gam	e1y5nC1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Respiratory nitrate reductase 1 gamma chain	F: Nitrate_red_gam	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	4.10.1200.10	Few Secondary Structures	Irregular	nitrate reductase tail	nitrate reductase tail	CATH (4.3.0)
A	3.40.50.12440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	1.10.3650.10	Mainly Alpha	Orthogonal Bundle	nitrate reductase domain fold	nitrate reductase domain like	CATH (4.3.0)
C	1.20.950.20	Mainly Alpha	Up-down Bundle	Fumarate Reductase Cytochrome B subunit	Transmembrane di-heme cytochromes, Chain C	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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 entir ...	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	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase	-	Family
A	PF14710	Respiratory nitrate reductase alpha N-terminal (Nitr_red_alph_N)	Respiratory nitrate reductase alpha N-terminal	This is the N-terminal tail of the respiratory nitrate reductase alpha chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. The N-terminal tail of the alpha chain interacts with the beta ...	This is the N-terminal tail of the respiratory nitrate reductase alpha chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. The N-terminal tail of the alpha chain interacts with the beta chain and contributes to the stability of the heterotrimer [1].	Domain
B	PF13247	4Fe-4S dicluster domain (Fer4_11)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain
B	PF14711	Respiratory nitrate reductase beta C-terminal (Nitr_red_bet_C)	Respiratory nitrate reductase beta C-terminal	This domain occurs near the C-terminus of the respiratory nitrate reductase beta chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. This domain plays a role in the interactions between ...	This domain occurs near the C-terminus of the respiratory nitrate reductase beta chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. This domain plays a role in the interactions between subunits and shielding of the Fe-S clusters [1]	Domain
C	PF02665	Nitrate reductase gamma subunit (Nitrate_red_gam)	Nitrate reductase gamma subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Respiratory nitrate reductase 1 alpha chain	nitrate reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity binding organic cyclic compound binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion binding nitrate reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity binding organic cyclic compound binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion binding metal ion binding nitrate reductase (quinone) activity	anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process nitrate assimilation nitrogen cycle metabolic process	cellular anatomical structure membrane respiratory chain complex protein-containing complex NarGHI complex catalytic complex plasma membrane protein complex plasma membrane nitrate reductase complex membrane protein complex cell periphery oxidoreductase complex
B	Respiratory nitrate reductase 1 beta chain	iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding nitrate reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding ion binding metal ion binding iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding nitrate reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding ion binding metal ion binding nitrate reductase (quinone) activity	anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process nitrate assimilation nitrogen cycle metabolic process	cellular anatomical structure membrane respiratory chain complex protein-containing complex NarGHI complex catalytic complex plasma membrane protein complex plasma membrane nitrate reductase complex membrane protein complex cell periphery oxidoreductase complex
C	Respiratory nitrate reductase 1 gamma chain	binding organic cyclic compound binding tetrapyrrole binding heme binding nitrate reductase activity oxidoreductase activity oxidoreductase activity, acting on other nitrogenous compounds as donors catalytic activity electron transfer activity cation binding ion binding metal ion binding small molecule binding nitrate reductase (quinone) activity	anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process nitrate assimilation nitrogen cycle metabolic process	cellular anatomical structure membrane cell periphery plasma membrane protein-containing complex catalytic complex nitrate reductase complex oxidoreductase complex respiratory chain complex NarGHI complex plasma membrane protein complex membrane protein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A	IPR037943	Nitrate reductase alpha subunit-like, MopB domain	Domain
A	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A	IPR006656	Molybdopterin oxidoreductase	Domain
A	IPR006468	Nitrate reductase, alpha subunit	Family
A	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site	Conserved Site
A	IPR050123	Prokaryotic molybdopterin-containing oxidoreductase	Family
A	IPR027467	Molybdopterin oxidoreductase, molybdopterin cofactor binding site	Binding Site
A	IPR028189	Nitrate reductase, alpha subunit, N-terminal	Domain
A	IPR044906	Nitrate reductase, alpha subunit, N-terminal domain superfamily	Homologous Superfamily
B	IPR006547	Nitrate reductase, beta subunit	Family
B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B	IPR038262	Nitrate reductase beta, C-terminal domain superfamily	Homologous Superfamily
B	IPR029263	Respiratory nitrate reductase beta, C-terminal	Domain
C	IPR036197	NarG-like superfamily	Homologous Superfamily
C	IPR003816	Nitrate reductase, gamma subunit	Family
C	IPR051936	Membrane-embedded heme-iron electron transfer protein	Family
C	IPR023234	NarG-like domain	Domain

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Oxidoreductases	NarGHI Nitrate Reductase with pentachlorophenol (PCP)

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	FME	Parent Component: MET RESID: AA0021 , AA0566 PSI-MOD : N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891

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.