Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6CTY

Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution

Replaces: 5V0G

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue ZN A 401

Chain	Residue
A	KCX103
A	HIS140
A	HIS178
A	ZN402
A	MLT403

site_id	AC2
Number of Residues	6
Details	binding site for residue ZN A 402

Chain	Residue
A	ZN401
A	MLT403
A	HIS17
A	HIS19
A	KCX103
A	ASP251

site_id	AC3
Number of Residues	16
Details	binding site for residue MLT A 403

Chain	Residue
A	HIS19
A	ARG21
A	ASN45
A	KCX103
A	THR110
A	THR111
A	HIS140
A	HIS178
A	LEU223
A	ASP251
A	ALA253
A	HIS255
A	ALA267
A	ZN401
A	ZN402
A	HOH504

site_id	AC4
Number of Residues	5
Details	binding site for residue ZN B 401

Chain	Residue
B	KCX103
B	HIS140
B	HIS178
B	ZN402
B	MLT403

site_id	AC5
Number of Residues	6
Details	binding site for residue ZN B 402

Chain	Residue
B	HIS17
B	HIS19
B	KCX103
B	ASP251
B	ZN401
B	MLT403

site_id	AC6
Number of Residues	15
Details	binding site for residue MLT B 403

Chain	Residue
B	HIS19
B	ARG21
B	ASN45
B	KCX103
B	THR110
B	THR111
B	HIS140
B	HIS178
B	ASP251
B	ALA253
B	HIS255
B	ALA267
B	ZN401
B	ZN402
B	HOH551

site_id	AC7
Number of Residues	5
Details	binding site for residue ZN C 401

Chain	Residue
C	KCX103
C	HIS140
C	HIS178
C	ZN402
C	MLT403

site_id	AC8
Number of Residues	6
Details	binding site for residue ZN C 402

Chain	Residue
C	HIS17
C	HIS19
C	KCX103
C	ASP251
C	ZN401
C	MLT403

site_id	AC9
Number of Residues	16
Details	binding site for residue MLT C 403

Chain	Residue
C	HIS19
C	ARG21
C	ASN45
C	KCX103
C	THR110
C	THR111
C	HIS140
C	HIS178
C	LEU223
C	ASP251
C	ALA253
C	HIS255
C	ALA267
C	ZN401
C	ZN402
C	HOH511

site_id	AD1
Number of Residues	6
Details	binding site for residue ZN D 401

Chain	Residue
D	HIS17
D	HIS19
D	KCX103
D	ASP251
D	ZN402
D	MLT403

site_id	AD2
Number of Residues	5
Details	binding site for residue ZN D 402

Chain	Residue
D	KCX103
D	HIS140
D	HIS178
D	ZN401
D	MLT403

site_id	AD3
Number of Residues	16
Details	binding site for residue MLT D 403

Chain	Residue
D	LEU223
D	ASP251
D	ALA253
D	HIS255
D	ALA267
D	ZN401
D	ZN402
D	HOH530
D	HIS19
D	ARG21
D	ASN45
D	KCX103
D	THR110
D	THR111
D	HIS140
D	HIS178

site_id	AD4
Number of Residues	6
Details	binding site for residue ZN E 401

Chain	Residue
E	HIS17
E	HIS19
E	KCX103
E	ASP251
E	ZN402
E	HOH605

site_id	AD5
Number of Residues	5
Details	binding site for residue ZN E 402

Chain	Residue
E	KCX103
E	HIS140
E	HIS178
E	ZN401
E	HOH605

site_id	AD6
Number of Residues	5
Details	binding site for residue ZN F 401

Chain	Residue
F	KCX103
F	HIS140
F	HIS178
F	ZN402
F	MLT403

site_id	AD7
Number of Residues	6
Details	binding site for residue ZN F 402

Chain	Residue
F	HIS17
F	HIS19
F	KCX103
F	ASP251
F	ZN401
F	MLT403

site_id	AD8
Number of Residues	15
Details	binding site for residue MLT F 403

Chain	Residue
F	HIS19
F	ARG21
F	ASN45
F	KCX103
F	THR110
F	THR111
F	HIS140
F	HIS178
F	LEU223
F	ASP251
F	HIS255
F	ALA267
F	ZN401
F	ZN402
F	HOH516

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	GLY249-LYS260

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00219","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	30
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00219","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2017","submissionDatabase":"PDB data bank","title":"Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and unknown ligand at 2.4 A resolution.","authors":["Lipowska J.","Shabalin I.G.","Anderson W.F.","Minor W."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00219","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
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":"FEB-2017","submissionDatabase":"PDB data bank","title":"Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and unknown ligand at 2.4 A resolution.","authors":["Lipowska J.","Shabalin I.G.","Anderson W.F.","Minor W."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Modified residue: {"description":"N6-carboxylysine","evidences":[{"source":"HAMAP-Rule","id":"MF_00219","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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