Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3JZE

1.8 Angstrom resolution crystal structure of dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Replaces: 3IHN

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004151	molecular_function	dihydroorotase activity
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
A	0006221	biological_process	pyrimidine nucleotide biosynthetic process
A	0008270	molecular_function	zinc ion binding
A	0016787	molecular_function	hydrolase activity
A	0016812	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
A	0019856	biological_process	pyrimidine nucleobase biosynthetic process
A	0044205	biological_process	'de novo' UMP biosynthetic process
A	0046872	molecular_function	metal ion binding
B	0004151	molecular_function	dihydroorotase activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
B	0006221	biological_process	pyrimidine nucleotide biosynthetic process
B	0008270	molecular_function	zinc ion binding
B	0016787	molecular_function	hydrolase activity
B	0016812	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
B	0019856	biological_process	pyrimidine nucleobase biosynthetic process
B	0044205	biological_process	'de novo' UMP biosynthetic process
B	0046872	molecular_function	metal ion binding
C	0004151	molecular_function	dihydroorotase activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
C	0006221	biological_process	pyrimidine nucleotide biosynthetic process
C	0008270	molecular_function	zinc ion binding
C	0016787	molecular_function	hydrolase activity
C	0016812	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
C	0019856	biological_process	pyrimidine nucleobase biosynthetic process
C	0044205	biological_process	'de novo' UMP biosynthetic process
C	0046872	molecular_function	metal ion binding
D	0004151	molecular_function	dihydroorotase activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
D	0006221	biological_process	pyrimidine nucleotide biosynthetic process
D	0008270	molecular_function	zinc ion binding
D	0016787	molecular_function	hydrolase activity
D	0016812	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
D	0019856	biological_process	pyrimidine nucleobase biosynthetic process
D	0044205	biological_process	'de novo' UMP biosynthetic process
D	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN A 401

Chain	Residue
A	HIS17
A	HIS19
A	KCX103
A	ASP251
A	ZN402
A	HOH419

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 402

Chain	Residue
A	ZN401
A	HOH419
A	KCX103
A	HIS140
A	HIS178

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BME A 411

Chain	Residue
A	CYS264
A	GLY265
A	BME415
B	GLY214
B	GLY215

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BME A 415

Chain	Residue
A	HIS255
A	CYS266
A	BME411
A	HOH570
A	HOH915

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PGE A 420

Chain	Residue
A	LYS173
A	ASP193
A	TYR194
A	GLN302
A	PHE303
A	GLY305
A	HOH764

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACY A 423

Chain	Residue
A	HIS19
A	ARG21
A	ASN45
A	THR110
A	THR111
A	ALA253
A	HIS255
A	ALA267

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 403

Chain	Residue
B	HIS17
B	HIS19
B	KCX103
B	ASP251
B	ZN404
B	HOH1334

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ZN B 404

Chain	Residue
B	KCX103
B	HIS140
B	HIS178
B	ZN403
B	ACY428
B	HOH435
B	HOH1334

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE BME B 413

Chain	Residue
A	GLY214
A	GLY215
B	CYS264
B	GLY265
B	BME417
B	HOH453

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BME B 417

Chain	Residue
B	HIS255
B	CYS266
B	BME413
B	HOH444
B	HOH1152

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PG4 B 419

Chain	Residue
B	LYS173
B	ASP193
B	TYR194
B	GLN302
B	PHE303

site_id	BC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ACY B 425

Chain	Residue
B	HIS19
B	ARG21
B	ASN45
B	HIS255
B	ALA267
B	HOH371
B	ACY428
B	HOH575
B	HOH1023

site_id	BC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ACY B 428

Chain	Residue
B	KCX103
B	TYR105
B	HIS140
B	HOH371
B	ZN404
B	ACY425
B	HOH435
B	HOH575
B	HOH1334

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 405

Chain	Residue
C	HIS17
C	HIS19
C	KCX103
C	ASP251
C	ZN406
C	HOH1333

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 406

Chain	Residue
C	KCX103
C	HIS140
C	HIS178
C	ZN405
C	HOH1333

site_id	BC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL C 409

Chain	Residue
C	ARG228

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE BME C 412

Chain	Residue
C	CYS264
C	BME416
D	GLY214
D	GLY215

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE BME C 416

Chain	Residue
C	CYS266
C	BME412
C	HOH786

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PGE C 421

Chain	Residue
C	LYS173
C	ASP193
C	PHE303
C	HOH688
C	HOH744

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACY C 424

Chain	Residue
C	HIS19
C	ARG21
C	ASN45
C	THR111
C	ALA253
C	HIS255
C	ALA267

site_id	CC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 407

Chain	Residue
D	HIS17
D	HIS19
D	KCX103
D	ASP251
D	ZN408
D	HOH925

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ZN D 408

Chain	Residue
D	KCX103
D	HIS140
D	HIS178
D	ZN407
D	ACY427
D	HOH435
D	HOH925

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE BME D 414

Chain	Residue
C	GLY214
C	GLY215
D	CYS264
D	GLY265
D	BME418
D	HOH452

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE BME D 418

Chain	Residue
D	HIS255
D	CYS266
D	BME414
D	ACY426

site_id	CC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PG4 D 422

Chain	Residue
D	GLY134
D	LYS173
D	ASP193
D	TYR194
D	GLN302
D	PHE303
D	GLY305
D	HOH887

site_id	CC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACY D 426

Chain	Residue
D	HIS19
D	ARG21
D	ASN45
D	HIS255
D	ALA267
D	BME418
D	ACY427

site_id	CC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ACY D 427

Chain	Residue
D	ASN45
D	KCX103
D	TYR105
D	HIS140
D	ZN408
D	ACY426
D	HOH435
D	HOH671
D	HOH925
D	HOH1119

Functional Information from PROSITE/UniProt

site_id	PS00482
Number of Residues	9
Details	DIHYDROOROTASE_1 Dihydroorotase signature 1. DWHVHLRdG

Chain	Residue	Details
A	ASP15-GLY23

site_id	PS00483
Number of Residues	12
Details	DIHYDROOROTASE_2 Dihydroorotase signature 2. GTDsAPHsrhrK

Chain	Residue	Details
A	GLY249-LYS260

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00219","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	20
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00219","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"SEP-2009","submissionDatabase":"PDB data bank","title":"1.8 angstrom resolution crystal structure of dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar typhimurium str. LT2.","authors":["Minasov G.","Halavaty A.","Shuvalova L.","Dubrovska I.","Winsor J.","Papazisi L.","Anderson W.F."]}},{"source":"PDB","id":"3JZE","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00219","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"description":"via carbamate group","evidences":[{"source":"HAMAP-Rule","id":"MF_00219","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"SEP-2009","submissionDatabase":"PDB data bank","title":"1.8 angstrom resolution crystal structure of dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar typhimurium str. LT2.","authors":["Minasov G.","Halavaty A.","Shuvalova L.","Dubrovska I.","Winsor J.","Papazisi L.","Anderson W.F."]}},{"source":"PDB","id":"3JZE","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Modified residue: {"description":"N6-carboxylysine","evidences":[{"source":"HAMAP-Rule","id":"MF_00219","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	1
Details	Annotated By Reference To The Literature 1j79

Chain	Residue	Details
A	ASP251

site_id	CSA2
Number of Residues	1
Details	Annotated By Reference To The Literature 1j79

Chain	Residue	Details
B	ASP251

site_id	CSA3
Number of Residues	1
Details	Annotated By Reference To The Literature 1j79

Chain	Residue	Details
C	ASP251

site_id	CSA4
Number of Residues	1
Details	Annotated By Reference To The Literature 1j79

Chain	Residue	Details
D	ASP251

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