4O8R | pdb_00004o8r

Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate

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)
M	d4o8rm_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
L	d4o8rl_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
K	d4o8rk_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
J	d4o8rj_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
I	d4o8ri_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
H	d4o8rh_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
G	d4o8rg_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
F	d4o8rf_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
E	d4o8re_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
D	d4o8rd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
C	d4o8rc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
B	d4o8rb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
A	d4o8ra_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	automated matches	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
M	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8033549	3000216	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)
M	PepSY_like	e4o8rM1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
L	PepSY_like	e4o8rL1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
K	PepSY_like	e4o8rK1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
J	PepSY_like	e4o8rJ1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
I	PepSY_like	e4o8rI1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
H	PepSY_like	e4o8rH1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
G	PepSY_like	e4o8rG1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
F	PepSY_like	e4o8rF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
E	PepSY_like	e4o8rE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
D	PepSY_like	e4o8rD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
C	NiFe_hyd_SSU_C	e4o8rC1	A: a/b three-layered sandwiches	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (v294.1)
B	PepSY_like	e4o8rB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)
A	PepSY_like	e4o8rA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PepSY_like	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
M	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
L	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
K	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
J	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
I	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
H	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
F	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	PF00215	Orotidine 5'-phosphate decarboxylase / HUMPS family (OMPdecase)	Orotidine 5'-phosphate decarboxylase / HUMPS family	This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly ...	This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly related to Pfam:PF00834.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	Orotidine 5'-phosphate decarboxylase	orotidine-5'-phosphate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase 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 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 cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR047595	Orotidine 5'-phosphate decarboxylase, archaeal	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR018089	Orotidine 5'-phosphate decarboxylase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR001754	Orotidine 5'-phosphate decarboxylase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR014732	Orotidine 5'-phosphate decarboxylase	Family

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.