1EP2

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B COMPLEXED WITH OROTATE

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

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ep2a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Dihydroorotate dehydrogenase	(Lactococcus lactis ) [TaxId: 1358 ],	SCOPe (2.08)
B	d1ep2b1	All beta proteins	Reductase/isomerase/elongation factor common domain	Riboflavin synthase domain-like	Ferredoxin reductase FAD-binding domain-like	Dihydroorotate dehydrogenase B, PyrK subunit	(Lactococcus lactis ) [TaxId: 1358 ],	SCOPe (2.08)
B	d1ep2b2	Alpha and beta proteins (a/b)	Ferredoxin reductase-like, C-terminal NADP-linked domain	Ferredoxin reductase-like, C-terminal NADP-linked domain	Dihydroorotate dehydrogenase B, PyrK subunit	Dihydroorotate dehydrogenase B, PyrK subunit	(Lactococcus lactis ) [TaxId: 1358 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FMN-linked oxidoreductases	8058086	3000014	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Riboflavin synthase domain-like	8042062	3001812	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ferredoxin reductase-like C-terminal NADP-linked domain	8044196	3001461	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	DHO_dh	e1ep2A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHO_dh	ECOD (1.6)
B	FAD_binding_6	e1ep2B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: FAD_binding_6	ECOD (1.6)
B	NAD_binding_1	e1ep2B2	A: a/b three-layered sandwiches	X: Ferredoxin reductase-like, C-terminal NADP-linked domain (From Topology)	H: Ferredoxin reductase-like, C-terminal NADP-linked domain (From Topology)	T: Ferredoxin reductase-like, C-terminal NADP-linked domain	F: NAD_binding_1	ECOD (1.6)
B	DHODB_Fe-S_bind_like	e1ep2B3	A: few secondary structure elements	X: Dihydroorotate dehydrogenase B PyrK subunit 2Fe-2S cluster-binding domain (From Topology)	H: Dihydroorotate dehydrogenase B PyrK subunit 2Fe-2S cluster-binding domain (From Topology)	T: Dihydroorotate dehydrogenase B PyrK subunit 2Fe-2S cluster-binding domain	F: DHODB_Fe-S_bind_like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	3.40.50.80	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module	CATH (4.3.0)
B	2.10.240.10	Mainly Beta	Ribbon	Dihydroorotate dehydrogenase B (pyrk subunit)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01180	Dihydroorotate dehydrogenase (DHO_dh)	Dihydroorotate dehydrogenase	-	Domain
B	PF10418	Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B (DHODB_Fe-S_bind)	Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B	Lactococcus lactis is one of the few organisms with two dihydroorotate dehydrogenases, DHODs, A and B [1]. The B enzyme is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a hetero-tetramer composed of a ...	Lactococcus lactis is one of the few organisms with two dihydroorotate dehydrogenases, DHODs, A and B [1]. The B enzyme is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a hetero-tetramer composed of a central homodimer of PyrDB subunits resembling the DHODA structure and two PyrK subunits along with three different cofactors: FMN, FAD, and a [2Fe-2S] cluster. The [2Fe-2S] iron-sulfur cluster binds to this C-terminal domain of the PyrK subunit, which is at the interface between the flavin and NAD binding domains and contains three beta-strands. The four cysteine residues at the N-terminal part of this domain are the ones that bind, in pairs, to the iron-sulfur cluster. The conformation of the whole molecule means that the iron-sulfur cluster is localised in a well-ordered part of this domain close to the FAD binding site [1]. The FAD and and NAD binding domains are FAD_binding_6, Pfam:PF00970 and NAD_binding_1, Pfam:PF00175.	Domain
B	PF00175	Oxidoreductase NAD-binding domain (NAD_binding_1)	Oxidoreductase NAD-binding domain	Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)	dihydroorotate dehydrogenase (NAD+) activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor dihydroorotate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity	organonitrogen compound metabolic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process organonitrogen compound biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process organonitrogen compound metabolic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process organonitrogen compound biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process 'de novo' pyrimidine nucleobase biosynthetic process small molecule metabolic process metabolic process pyrimidine-containing compound biosynthetic process ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process 'de novo' UMP biosynthetic process ribonucleotide biosynthetic process UMP biosynthetic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process phosphate-containing compound metabolic process UMP metabolic process phosphorus metabolic process nucleoside monophosphate metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process cellular metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process cellular process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity
B	DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding electron transfer activity cation binding iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding electron transfer activity cation binding metal ion binding	ribose phosphate metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process 'de novo' UMP biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process UMP biosynthetic process organic substance metabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process ribose phosphate metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process 'de novo' UMP biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process UMP biosynthetic process organic substance metabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process UMP metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process nucleoside monophosphate metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process pyrimidine-containing compound metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process organic cyclic compound metabolic process biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012135	Dihydroorotate dehydrogenase, class 1/ 2	Family
A	IPR049622	Dihydroorotate dehydrogenase class I, catalytic	Domain
A	IPR024920	Dihydroorotate dehydrogenase, class 1	Family
A	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A	IPR005720	Dihydroorotate dehydrogenase, catalytic	Domain
A	IPR001295	Dihydroorotate dehydrogenase, conserved site	Conserved Site
A	IPR033888	Dihydroorotate dehydrogenase, class 1B	Family
B	IPR001433	Oxidoreductase FAD/NAD(P)-binding	Domain
B	IPR023455	Dihydroorotate dehydrogenase electron transfer subunit	Family
B	IPR019480	Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain	Domain
B	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain	Homologous Superfamily
B	IPR017938	Riboflavin synthase-like beta-barrel	Homologous Superfamily
B	IPR017927	FAD-binding domain, ferredoxin reductase-type	Domain
B	IPR012165	Cytochrome-c3 hydrogenase, gamma subunit	Family
B	IPR037117	Dihydroorotate dehydrogenase, electron transfer subunit, Fe-S binding domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.