Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4O8R

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
A	0005829	cellular_component	cytosol
A	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
A	0006221	biological_process	pyrimidine nucleotide biosynthetic process
A	0016829	molecular_function	lyase activity
A	0016831	molecular_function	carboxy-lyase activity
A	0044205	biological_process	'de novo' UMP biosynthetic process
B	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
B	0005829	cellular_component	cytosol
B	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
B	0006221	biological_process	pyrimidine nucleotide biosynthetic process
B	0016829	molecular_function	lyase activity
B	0016831	molecular_function	carboxy-lyase activity
B	0044205	biological_process	'de novo' UMP biosynthetic process
C	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
C	0005829	cellular_component	cytosol
C	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
C	0006221	biological_process	pyrimidine nucleotide biosynthetic process
C	0016829	molecular_function	lyase activity
C	0016831	molecular_function	carboxy-lyase activity
C	0044205	biological_process	'de novo' UMP biosynthetic process
D	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
D	0005829	cellular_component	cytosol
D	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
D	0006221	biological_process	pyrimidine nucleotide biosynthetic process
D	0016829	molecular_function	lyase activity
D	0016831	molecular_function	carboxy-lyase activity
D	0044205	biological_process	'de novo' UMP biosynthetic process
E	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
E	0005829	cellular_component	cytosol
E	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
E	0006221	biological_process	pyrimidine nucleotide biosynthetic process
E	0016829	molecular_function	lyase activity
E	0016831	molecular_function	carboxy-lyase activity
E	0044205	biological_process	'de novo' UMP biosynthetic process
F	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
F	0005829	cellular_component	cytosol
F	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
F	0006221	biological_process	pyrimidine nucleotide biosynthetic process
F	0016829	molecular_function	lyase activity
F	0016831	molecular_function	carboxy-lyase activity
F	0044205	biological_process	'de novo' UMP biosynthetic process
G	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
G	0005829	cellular_component	cytosol
G	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
G	0006221	biological_process	pyrimidine nucleotide biosynthetic process
G	0016829	molecular_function	lyase activity
G	0016831	molecular_function	carboxy-lyase activity
G	0044205	biological_process	'de novo' UMP biosynthetic process
H	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
H	0005829	cellular_component	cytosol
H	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
H	0006221	biological_process	pyrimidine nucleotide biosynthetic process
H	0016829	molecular_function	lyase activity
H	0016831	molecular_function	carboxy-lyase activity
H	0044205	biological_process	'de novo' UMP biosynthetic process
I	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
I	0005829	cellular_component	cytosol
I	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
I	0006221	biological_process	pyrimidine nucleotide biosynthetic process
I	0016829	molecular_function	lyase activity
I	0016831	molecular_function	carboxy-lyase activity
I	0044205	biological_process	'de novo' UMP biosynthetic process
J	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
J	0005829	cellular_component	cytosol
J	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
J	0006221	biological_process	pyrimidine nucleotide biosynthetic process
J	0016829	molecular_function	lyase activity
J	0016831	molecular_function	carboxy-lyase activity
J	0044205	biological_process	'de novo' UMP biosynthetic process
K	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
K	0005829	cellular_component	cytosol
K	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
K	0006221	biological_process	pyrimidine nucleotide biosynthetic process
K	0016829	molecular_function	lyase activity
K	0016831	molecular_function	carboxy-lyase activity
K	0044205	biological_process	'de novo' UMP biosynthetic process
L	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
L	0005829	cellular_component	cytosol
L	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
L	0006221	biological_process	pyrimidine nucleotide biosynthetic process
L	0016829	molecular_function	lyase activity
L	0016831	molecular_function	carboxy-lyase activity
L	0044205	biological_process	'de novo' UMP biosynthetic process
M	0004590	molecular_function	orotidine-5'-phosphate decarboxylase activity
M	0005829	cellular_component	cytosol
M	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
M	0006221	biological_process	pyrimidine nucleotide biosynthetic process
M	0016829	molecular_function	lyase activity
M	0016831	molecular_function	carboxy-lyase activity
M	0044205	biological_process	'de novo' UMP biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	17
Details	BINDING SITE FOR RESIDUE H2U A 301

Chain	Residue
A	ASP20
A	ARG203
A	HOH404
A	HOH405
A	HOH408
A	HOH420
B	ASP75
B	ILE76
B	THR79
A	LYS42
A	ASP70
A	MET126
A	SER127
A	PRO180
A	VAL182
A	GLN185
A	GLY202

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL A 302

Chain	Residue
A	TYR37
A	TYR37
A	ALA212
A	ALA212

site_id	AC3
Number of Residues	18
Details	BINDING SITE FOR RESIDUE H2U B 301

Chain	Residue
A	ASP75
A	ILE76
A	THR79
B	ASP20
B	LYS42
B	ASP70
B	LYS72
B	MET126
B	SER127
B	PRO180
B	GLN185
B	GLY202
B	ARG203
B	HOH407
B	HOH411
B	HOH414
B	HOH416
B	HOH421

site_id	AC4
Number of Residues	19
Details	BINDING SITE FOR RESIDUE H2U C 301

Chain	Residue
C	ASP20
C	LYS42
C	ASP70
C	LYS72
C	MET126
C	SER127
C	PRO180
C	GLN185
C	VAL201
C	GLY202
C	ARG203
C	HOH407
C	HOH411
C	HOH423
C	HOH433
C	HOH434
D	ASP75
D	ILE76
D	THR79

site_id	AC5
Number of Residues	17
Details	BINDING SITE FOR RESIDUE H2U D 301

Chain	Residue
C	ASP75
C	ILE76
C	THR79
D	ASP20
D	LYS42
D	ASP70
D	LYS72
D	MET126
D	SER127
D	PRO180
D	GLN185
D	GLY202
D	ARG203
D	HOH409
D	HOH411
D	HOH412
D	HOH418

site_id	AC6
Number of Residues	17
Details	BINDING SITE FOR RESIDUE H2U E 301

Chain	Residue
E	ASP20
E	LYS42
E	ASP70
E	LYS72
E	MET126
E	SER127
E	PRO180
E	GLN185
E	GLY202
E	ARG203
E	HOH404
E	HOH405
E	HOH406
E	HOH407
F	ASP75
F	ILE76
F	THR79

site_id	AC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE H2U F 301

Chain	Residue
F	SER127
F	PRO180
F	GLN185
F	GLY202
F	ARG203
F	HOH409
F	HOH410
E	ASP75
E	ILE76
E	THR79
F	ASP20
F	LYS42
F	ASP70
F	MET126

site_id	AC8
Number of Residues	16
Details	BINDING SITE FOR RESIDUE H2U G 301

Chain	Residue
G	ASP20
G	LYS42
G	ASP70
G	LYS72
G	MET126
G	SER127
G	PRO180
G	GLN185
G	GLY202
G	ARG203
G	HOH403
G	HOH404
G	HOH405
H	ASP75
H	ILE76
H	THR79

site_id	AC9
Number of Residues	17
Details	BINDING SITE FOR RESIDUE H2U H 301

Chain	Residue
G	ASP75
G	ILE76
G	THR79
H	ASP20
H	LYS42
H	ASP70
H	LYS72
H	MET126
H	SER127
H	PRO180
H	VAL182
H	GLN185
H	GLY202
H	ARG203
H	HOH403
H	HOH404
H	HOH405

site_id	BC1
Number of Residues	16
Details	BINDING SITE FOR RESIDUE H2U J 301

Chain	Residue
I	ASP75
I	ILE76
I	THR79
J	ASP20
J	LYS42
J	ASP70
J	LYS72
J	MET126
J	SER127
J	PRO180
J	ALA184
J	GLN185
J	GLY202
J	ARG203
J	HOH419
J	HOH420

site_id	BC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE H2U K 301

Chain	Residue
K	ASP20
K	LYS42
K	ASP70
K	MET126
K	SER127
K	PRO180
K	VAL182
K	GLN185
K	GLY202
K	ARG203
K	HOH402
K	HOH403
L	ASP75
L	ILE76
L	THR79

site_id	BC3
Number of Residues	15
Details	BINDING SITE FOR RESIDUE H2U L 301

Chain	Residue
K	ASP75
K	ILE76
K	THR79
L	ASP20
L	LYS42
L	ASP70
L	LYS72
L	MET126
L	SER127
L	PRO180
L	VAL182
L	GLN185
L	VAL201
L	GLY202
L	ARG203

site_id	BC4
Number of Residues	17
Details	BINDING SITE FOR RESIDUE H2U M 301

Chain	Residue
M	ASP20
M	LYS42
M	ASP70
M	LYS72
M	ASP75
M	ILE76
M	THR79
M	MET126
M	SER127
M	PRO180
M	GLN185
M	GLY202
M	ARG203
M	TYR206
M	HOH418
M	HOH421
M	HOH422

Functional Information from PROSITE/UniProt

site_id	PS00156
Number of Residues	14
Details	OMPDECASE Orotidine 5'-phosphate decarboxylase active site. IIaDfKvaDIPeTN

Chain	Residue	Details
A	ILE67-ASN80

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	13
Details	Active site: {"description":"Proton donor"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	302
Details	Binding site: {}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)