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1J79
Asym. Unit
Info
Asym.Unit (134 KB)
Biol.Unit 1 (128 KB)
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(1)
Title
:
MOLECULAR STRUCTURE OF DIHYDROOROTASE: A PARADIGM FOR CATALYSIS THROUGH THE USE OF A BINUCLEAR METAL CENTER
Authors
:
J. B. Thoden, G. N. Phillips Jr. , T. M. Neal, F. M. Raushel, H. M. Holden
Date
:
16 May 01 (Deposition) - 20 Jun 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Tim Barrel, Metalloenzyme, Pyrimidine Biosynthesis, Hydrolase
(Keyword Search:
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Reference
:
J. B. Thoden, G. N. Phillips Jr. , T. M. Neal, F. M. Raushel, H. M. Holden
Molecular Structure Of Dihydroorotase: A Paradigm For Catalysis Through The Use Of A Binuclear Metal Center.
Biochemistry V. 40 6989 2001
(for further references see the
PDB file header
)
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Hetero Components
(4, 9)
Info
All Hetero Components
1a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
1b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
2a: N-CARBAMOYL-L-ASPARTATE (NCDa)
2b: N-CARBAMOYL-L-ASPARTATE (NCDb)
3a: OROTIC ACID (OROa)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
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No.
Name
Count
Type
Full Name
1
KCX
2
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
2
NCD
2
Ligand/Ion
N-CARBAMOYL-L-ASPARTATE
3
ORO
1
Ligand/Ion
OROTIC ACID
4
ZN
4
Ligand/Ion
ZINC ION
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:16 , HIS A:18 , KCX A:102 , ASP A:250 , ZN A:401 , HOH A:1407
BINDING SITE FOR RESIDUE ZN A 400
2
AC2
SOFTWARE
KCX A:102 , HIS A:139 , HIS A:177 , ZN A:400 , ORO A:410 , HOH A:1407
BINDING SITE FOR RESIDUE ZN A 401
3
AC3
SOFTWARE
HIS B:16 , HIS B:18 , KCX B:102 , ASP B:250 , NCD B:411
BINDING SITE FOR RESIDUE ZN B 400
4
AC4
SOFTWARE
KCX B:102 , HIS B:139 , HIS B:177 , NCD B:411
BINDING SITE FOR RESIDUE ZN B 401
5
AC5
SOFTWARE
HIS A:18 , ARG A:20 , ASN A:44 , HIS A:139 , CYS A:221 , LEU A:222 , ASP A:250 , ALA A:252 , HIS A:254 , ALA A:266 , GLY A:267 , ZN A:401 , HOH A:1160 , HOH A:1407
BINDING SITE FOR RESIDUE ORO A 410
6
AC6
SOFTWARE
HIS B:18 , ARG B:20 , ASN B:44 , KCX B:102 , HIS B:139 , CYS B:221 , LEU B:222 , ASP B:250 , ALA B:252 , HIS B:254 , ALA B:266 , GLY B:267 , ZN B:400 , ZN B:401 , HOH B:1485
BINDING SITE FOR RESIDUE NCD B 411
7
AC7
SOFTWARE
ASN A:208 , HIS A:209 , VAL A:212 , HOH A:1110 , HOH A:1446 , ALA B:145 , ARG B:152
BINDING SITE FOR RESIDUE NCD A 950
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: DIHYDROOROTASE_1 (A:14-22,B:14-22)
2: DIHYDROOROTASE_2 (A:248-259,B:248-259)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DIHYDROOROTASE_1
PS00482
Dihydroorotase signature 1.
PYRC_ECOLI
15-23
2
A:14-22
B:14-22
2
DIHYDROOROTASE_2
PS00483
Dihydroorotase signature 2.
PYRC_ECOLI
249-260
2
A:248-259
B:248-259
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1j79a_ (A:)
1b: SCOP_d1j79b_ (B:)
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)
Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Dihydroorotase
(16)
Protein domain
:
Dihydroorotase
(14)
Escherichia coli [TaxId: 562]
(14)
1a
d1j79a_
A:
1b
d1j79b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1j79B00 (B:4-346)
1b: CATH_1j79A00 (A:4-346)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Escherichia coli. Organism_taxid: 562.
(27)
1a
1j79B00
B:4-346
1b
1j79A00
A:4-346
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (134 KB)
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