6CTY
Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution
Replaces: 5V0GFunctional 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 | ACT_SITE: ACT_SITE => ECO:0000255|HAMAP-Rule:MF_00219 |
Chain | Residue | Details |
A | ASP251 | |
B | ASP251 | |
C | ASP251 | |
D | ASP251 | |
E | ASP251 | |
F | ASP251 |
site_id | SWS_FT_FI2 |
Number of Residues | 30 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00219, ECO:0000269|Ref.4 |
Chain | Residue | Details |
C | HIS140 | |
C | HIS178 | |
C | ASP251 | |
D | HIS17 | |
D | HIS19 | |
D | HIS140 | |
D | HIS178 | |
D | ASP251 | |
E | HIS17 | |
E | HIS19 | |
E | HIS140 | |
E | HIS178 | |
E | ASP251 | |
F | HIS17 | |
F | HIS19 | |
F | HIS140 | |
F | HIS178 | |
F | ASP251 | |
A | HIS17 | |
A | HIS19 | |
A | HIS140 | |
A | HIS178 | |
A | ASP251 | |
B | HIS17 | |
B | HIS19 | |
B | HIS140 | |
B | HIS178 | |
B | ASP251 | |
C | HIS17 | |
C | HIS19 |
site_id | SWS_FT_FI3 |
Number of Residues | 24 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00219 |
Chain | Residue | Details |
B | HIS255 | |
B | ALA267 | |
C | ASN45 | |
C | LEU223 | |
C | HIS255 | |
C | ALA267 | |
D | ASN45 | |
D | LEU223 | |
D | HIS255 | |
D | ALA267 | |
E | ASN45 | |
E | LEU223 | |
E | HIS255 | |
E | ALA267 | |
F | ASN45 | |
F | LEU223 | |
F | HIS255 | |
F | ALA267 | |
A | ASN45 | |
A | LEU223 | |
A | HIS255 | |
A | ALA267 | |
B | ASN45 | |
B | LEU223 |
site_id | SWS_FT_FI4 |
Number of Residues | 6 |
Details | BINDING: via carbamate group => ECO:0000255|HAMAP-Rule:MF_00219, ECO:0000269|Ref.4 |
Chain | Residue | Details |
C | KCX103 | |
F | KCX103 | |
A | KCX103 | |
B | KCX103 | |
D | KCX103 | |
E | KCX103 |
site_id | SWS_FT_FI5 |
Number of Residues | 6 |
Details | MOD_RES: N6-carboxylysine => ECO:0000255|HAMAP-Rule:MF_00219 |
Chain | Residue | Details |
C | KCX103 | |
F | KCX103 | |
A | KCX103 | |
B | KCX103 | |
D | KCX103 | |
E | KCX103 |