1EP3

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS.

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ep3a_	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	d1ep3b1	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	d1ep3b2	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	SCOP2 Family	FMN-linked oxidoreductases	8058085	4000080	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-linked oxidoreductases	8058086	3000014	SCOP2 (2022-06-29)
B	SCOP2 Family	Ferredoxin reductase FAD-binding domain-like	8029683	4002840	SCOP2 (2022-06-29)
B	SCOP2 Family	Dihydroorotate dehydrogenase B, PyrK subunit	8031818	4003795	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Riboflavin synthase domain-like	8042062	3001812	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ferredoxin reductase-like, C-terminal NADP-linked domain	8044196	3001461	SCOP2 (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	e1ep3A1	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	e1ep3B1	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	e1ep3B3	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	e1ep3B4	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	pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process 'de novo' pyrimidine nucleobase biosynthetic process small molecule metabolic process metabolic process cellular process pyrimidine-containing compound biosynthetic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process 'de novo' pyrimidine nucleobase biosynthetic process small molecule metabolic process metabolic process cellular 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 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 pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm
B	DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)	oxidoreductase activity catalytic activity 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 anion binding nucleotide binding heterocyclic compound binding electron transfer activity oxidoreductase activity catalytic activity 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 anion binding nucleotide binding heterocyclic compound binding electron transfer activity cation binding metal ion binding	ribose phosphate metabolic process nucleotide 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 ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process UMP metabolic process small molecule metabolic process ribose phosphate metabolic process nucleotide 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 ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic 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 primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate 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	cellular anatomical structure intracellular anatomical structure cytoplasm

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	IPR050074	Dihydroorotate dehydrogenase	Family
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	IPR050353	Dihydroorotate dehydrogenase B electron transfer subunit	Family
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 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.