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3JZE
Asym. Unit
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Asym.Unit (263 KB)
Biol.Unit 1 (251 KB)
Biol.Unit 2 (251 KB)
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(1)
Title
:
1.8 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF DIHYDROOROTASE (PYRC) FROM SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2
Authors
:
G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papa W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date
:
23 Sep 09 (Deposition) - 29 Sep 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (1x)
Keywords
:
Dihydroorotase, Pyrc, Idp00873, Hydrolase, Metal-Binding, Pyrimidine Biosynthesis, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 8 Angstrom Resolution Crystal Structure Of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. Lt2.
To Be Published
[
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Hetero Components
(7, 32)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
1d: ACETIC ACID (ACYd)
1e: ACETIC ACID (ACYe)
1f: ACETIC ACID (ACYf)
2a: BETA-MERCAPTOETHANOL (BMEa)
2b: BETA-MERCAPTOETHANOL (BMEb)
2c: BETA-MERCAPTOETHANOL (BMEc)
2d: BETA-MERCAPTOETHANOL (BMEd)
2e: BETA-MERCAPTOETHANOL (BMEe)
2f: BETA-MERCAPTOETHANOL (BMEf)
2g: BETA-MERCAPTOETHANOL (BMEg)
2h: BETA-MERCAPTOETHANOL (BMEh)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
4a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
4b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
4c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
4d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
5a: TETRAETHYLENE GLYCOL (PG4a)
5b: TETRAETHYLENE GLYCOL (PG4b)
6a: TRIETHYLENE GLYCOL (PGEa)
6b: TRIETHYLENE GLYCOL (PGEb)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
7c: ZINC ION (ZNc)
7d: ZINC ION (ZNd)
7e: ZINC ION (ZNe)
7f: ZINC ION (ZNf)
7g: ZINC ION (ZNg)
7h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
6
Ligand/Ion
ACETIC ACID
2
BME
8
Ligand/Ion
BETA-MERCAPTOETHANOL
3
CL
2
Ligand/Ion
CHLORIDE ION
4
KCX
4
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
5
PG4
2
Ligand/Ion
TETRAETHYLENE GLYCOL
6
PGE
2
Ligand/Ion
TRIETHYLENE GLYCOL
7
ZN
8
Ligand/Ion
ZINC ION
[
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]
Sites
(27, 27)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:17 , HIS A:19 , KCX A:103 , ASP A:251 , ZN A:402 , HOH A:419
BINDING SITE FOR RESIDUE ZN A 401
02
AC2
SOFTWARE
KCX A:103 , HIS A:140 , HIS A:178 , ZN A:401 , HOH A:419
BINDING SITE FOR RESIDUE ZN A 402
03
AC3
SOFTWARE
CYS A:264 , GLY A:265 , BME A:415 , GLY B:214 , GLY B:215
BINDING SITE FOR RESIDUE BME A 411
04
AC4
SOFTWARE
HIS A:255 , CYS A:266 , BME A:411 , HOH A:570 , HOH A:915
BINDING SITE FOR RESIDUE BME A 415
05
AC5
SOFTWARE
LYS A:173 , ASP A:193 , TYR A:194 , GLN A:302 , PHE A:303 , GLY A:305 , HOH A:764
BINDING SITE FOR RESIDUE PGE A 420
06
AC6
SOFTWARE
HIS A:19 , ARG A:21 , ASN A:45 , THR A:110 , THR A:111 , ALA A:253 , HIS A:255 , ALA A:267
BINDING SITE FOR RESIDUE ACY A 423
07
AC7
SOFTWARE
HIS B:17 , HIS B:19 , KCX B:103 , ASP B:251 , ZN B:404 , HOH B:1334
BINDING SITE FOR RESIDUE ZN B 403
08
AC8
SOFTWARE
KCX B:103 , HIS B:140 , HIS B:178 , ZN B:403 , ACY B:428 , HOH B:435 , HOH B:1334
BINDING SITE FOR RESIDUE ZN B 404
09
AC9
SOFTWARE
GLY A:214 , GLY A:215 , CYS B:264 , GLY B:265 , BME B:417 , HOH B:453
BINDING SITE FOR RESIDUE BME B 413
10
BC1
SOFTWARE
HIS B:255 , CYS B:266 , BME B:413 , HOH B:444 , HOH B:1152
BINDING SITE FOR RESIDUE BME B 417
11
BC2
SOFTWARE
LYS B:173 , ASP B:193 , TYR B:194 , GLN B:302 , PHE B:303
BINDING SITE FOR RESIDUE PG4 B 419
12
BC3
SOFTWARE
HIS B:19 , ARG B:21 , ASN B:45 , HIS B:255 , ALA B:267 , HOH B:371 , ACY B:428 , HOH B:575 , HOH B:1023
BINDING SITE FOR RESIDUE ACY B 425
13
BC4
SOFTWARE
KCX B:103 , TYR B:105 , HIS B:140 , HOH B:371 , ZN B:404 , ACY B:425 , HOH B:435 , HOH B:575 , HOH B:1334
BINDING SITE FOR RESIDUE ACY B 428
14
BC5
SOFTWARE
HIS C:17 , HIS C:19 , KCX C:103 , ASP C:251 , ZN C:406 , HOH C:1333
BINDING SITE FOR RESIDUE ZN C 405
15
BC6
SOFTWARE
KCX C:103 , HIS C:140 , HIS C:178 , ZN C:405 , HOH C:1333
BINDING SITE FOR RESIDUE ZN C 406
16
BC7
SOFTWARE
ARG C:228
BINDING SITE FOR RESIDUE CL C 409
17
BC8
SOFTWARE
CYS C:264 , BME C:416 , GLY D:214 , GLY D:215
BINDING SITE FOR RESIDUE BME C 412
18
BC9
SOFTWARE
CYS C:266 , BME C:412 , HOH C:786
BINDING SITE FOR RESIDUE BME C 416
19
CC1
SOFTWARE
LYS C:173 , ASP C:193 , PHE C:303 , HOH C:688 , HOH C:744
BINDING SITE FOR RESIDUE PGE C 421
20
CC2
SOFTWARE
HIS C:19 , ARG C:21 , ASN C:45 , THR C:111 , ALA C:253 , HIS C:255 , ALA C:267
BINDING SITE FOR RESIDUE ACY C 424
21
CC3
SOFTWARE
HIS D:17 , HIS D:19 , KCX D:103 , ASP D:251 , ZN D:408 , HOH D:925
BINDING SITE FOR RESIDUE ZN D 407
22
CC4
SOFTWARE
KCX D:103 , HIS D:140 , HIS D:178 , ZN D:407 , ACY D:427 , HOH D:435 , HOH D:925
BINDING SITE FOR RESIDUE ZN D 408
23
CC5
SOFTWARE
GLY C:214 , GLY C:215 , CYS D:264 , GLY D:265 , BME D:418 , HOH D:452
BINDING SITE FOR RESIDUE BME D 414
24
CC6
SOFTWARE
HIS D:255 , CYS D:266 , BME D:414 , ACY D:426
BINDING SITE FOR RESIDUE BME D 418
25
CC7
SOFTWARE
GLY D:134 , LYS D:173 , ASP D:193 , TYR D:194 , GLN D:302 , PHE D:303 , GLY D:305 , HOH D:887
BINDING SITE FOR RESIDUE PG4 D 422
26
CC8
SOFTWARE
HIS D:19 , ARG D:21 , ASN D:45 , HIS D:255 , ALA D:267 , BME D:418 , ACY D:427
BINDING SITE FOR RESIDUE ACY D 426
27
CC9
SOFTWARE
ASN D:45 , KCX D:103 , TYR D:105 , HIS D:140 , ZN D:408 , ACY D:426 , HOH D:435 , HOH D:671 , HOH D:925 , HOH D:1119
BINDING SITE FOR RESIDUE ACY D 427
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: DIHYDROOROTASE_1 (A:15-23,B:15-23,C:15-23,D:15-23)
2: DIHYDROOROTASE_2 (A:249-260,B:249-260,C:249-260,D:24...)
;
View:
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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_SALTY
15-23
4
A:15-23
B:15-23
C:15-23
D:15-23
2
DIHYDROOROTASE_2
PS00483
Dihydroorotase signature 2.
PYRC_SALTY
249-260
4
A:249-260
B:249-260
C:249-260
D:249-260
[
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Exons
(0, 0)
Info
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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, 4)
Info
All SCOP Domains
1a: SCOP_d3jzea_ (A:)
1b: SCOP_d3jzeb_ (B:)
1c: SCOP_d3jzec_ (C:)
1d: SCOP_d3jzed_ (D:)
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Protein Domains
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Organisms
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(
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Dihydroorotase
(16)
Protein domain
:
automated matches
(2)
Salmonella enterica [TaxId: 99287]
(1)
1a
d3jzea_
A:
1b
d3jzeb_
B:
1c
d3jzec_
C:
1d
d3jzed_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3jzeB00 (B:6-347)
1b: CATH_3jzeD00 (D:6-347)
1c: CATH_3jzeA00 (A:5-348)
1d: CATH_3jzeC00 (C:5-348)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Enterica serovar typhimurium str (Salmonella enterica subsp)
(1)
1a
3jzeB00
B:6-347
1b
3jzeD00
D:6-347
1c
3jzeA00
A:5-348
1d
3jzeC00
C:5-348
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Amidohydro_1_3jzeD01 (D:10-326)
1b: PFAM_Amidohydro_1_3jzeD02 (D:10-326)
1c: PFAM_Amidohydro_1_3jzeD03 (D:10-326)
1d: PFAM_Amidohydro_1_3jzeD04 (D:10-326)
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Clans
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)
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)
Clan
:
Amidohydrolase
(126)
Family
:
Amidohydro_1
(28)
Salmonella typhimurium
(1)
1a
Amidohydro_1-3jzeD01
D:10-326
1b
Amidohydro_1-3jzeD02
D:10-326
1c
Amidohydro_1-3jzeD03
D:10-326
1d
Amidohydro_1-3jzeD04
D:10-326
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