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1EP2
Biol. Unit 1
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Asym.Unit (98 KB)
Biol.Unit 1 (182 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B COMPLEXED WITH OROTATE
Authors
:
P. Rowland, S. Norager, K. F. Jensen, S. Larsen
Date
:
27 Mar 00 (Deposition) - 17 Jan 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Heterotetramer, Oxidoreductase
(Keyword Search:
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Reference
:
P. Rowland, S. Norager, K. F. Jensen, S. Larsen
Structure Of Dihydroorotate Dehydrogenase B: Electron Transfer Between Two Flavin Groups Bridged By An Iron-Sulphur Cluster.
Structure Fold. Des. V. 8 1227 2000
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3a: FLAVIN MONONUCLEOTIDE (FMNa)
4a: OROTIC ACID (OROa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
3
FMN
2
Ligand/Ion
FLAVIN MONONUCLEOTIDE
4
ORO
2
Ligand/Ion
OROTIC ACID
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:23 , SER A:24 , GLY A:25 , LYS A:48 , ALA A:49 , ASN A:72 , ASN A:104 , ASN A:132 , LYS A:170 , ILE A:196 , ASN A:197 , THR A:198 , SER A:221 , GLY A:222 , MET A:247 , GLY A:248 , GLY A:249 , GLY A:270 , THR A:271 , ORO A:502 , HOH A:1003 , HOH A:1020
BINDING SITE FOR RESIDUE FMN A 501
2
AC2
SOFTWARE
LYS A:48 , ASN A:72 , ILE A:74 , GLY A:75 , LEU A:76 , ASN A:132 , CYS A:135 , PRO A:136 , ASN A:137 , ASN A:197 , THR A:198 , FMN A:501
BINDING SITE FOR RESIDUE ORO A 502
3
AC3
SOFTWARE
GLU A:65 , LEU B:51 , ARG B:53 , PRO B:54 , ILE B:55 , SER B:56 , LEU B:70 , TYR B:71 , ARG B:72 , THR B:78 , GLY B:79 , THR B:80 , ILE B:120 , GLU B:221 , SER B:222 , ARG B:223 , MET B:224 , HOH B:1006 , HOH B:1046 , HOH B:1050
BINDING SITE FOR RESIDUE FAD B 503
4
AC4
SOFTWARE
MET B:224 , ALA B:225 , CYS B:226 , GLY B:227 , GLY B:229 , ALA B:230 , CYS B:231 , TYR B:232 , CYS B:234 , CYS B:249
BINDING SITE FOR RESIDUE FES B 504
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: FAD_FR (B:3-104)
2: DHODEHASE_1 (A:43-62)
3: DHODEHASE_2 (A:244-264)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FAD_FR
PS51384
Ferredoxin reductase-type FAD binding domain profile.
PYRK_LACLM
3-104
2
B:3-104
2
DHODEHASE_1
PS00911
Dihydroorotate dehydrogenase signature 1.
PYRDB_LACLM
43-62
2
A:43-62
3
DHODEHASE_2
PS00912
Dihydroorotate dehydrogenase signature 2.
PYRDB_LACLM
244-264
2
A:244-264
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1ep2b1 (B:2-102)
2a: SCOP_d1ep2b2 (B:103-262)
3a: SCOP_d1ep2a_ (A:)
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Families
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Riboflavin synthase domain-like
(130)
Family
:
Ferredoxin reductase FAD-binding domain-like
(72)
Protein domain
:
Dihydroorotate dehydrogenase B, PyrK subunit
(3)
Lactococcus lactis, isozyme B [TaxId: 1358]
(3)
1a
d1ep2b1
B:2-102
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ferredoxin reductase-like, C-terminal NADP-linked domain
(120)
Superfamily
:
Ferredoxin reductase-like, C-terminal NADP-linked domain
(120)
Family
:
Dihydroorotate dehydrogenase B, PyrK subunit
(3)
Protein domain
:
Dihydroorotate dehydrogenase B, PyrK subunit
(3)
Lactococcus lactis, isozyme B [TaxId: 1358]
(3)
2a
d1ep2b2
B:103-262
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
FMN-linked oxidoreductases
(290)
Family
:
FMN-linked oxidoreductases
(242)
Protein domain
:
Dihydroorotate dehydrogenase
(90)
Lactococcus lactis, isozyme B [TaxId: 1358]
(3)
3a
d1ep2a_
A:
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CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_1ep2B02 (B:104-220)
2a: CATH_1ep2A00 (A:3-311)
3a: CATH_1ep2B01 (B:2-100)
4a: CATH_1ep2B03 (B:221-262)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
(85)
Lactococcus lactis. Organism_taxid: 1358.
(3)
1a
1ep2B02
B:104-220
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Lactococcus lactis. Organism_taxid: 1358.
(10)
2a
1ep2A00
A:3-311
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Elongation Factor Tu (Ef-tu); domain 3
(323)
Homologous Superfamily
:
Translation factors
(223)
Lactococcus lactis. Organism_taxid: 1358.
(3)
3a
1ep2B01
B:2-100
Architecture
:
Ribbon
(789)
Topology
:
Dihydroorotate dehydrogenase B (pyrk subunit); domain 3
(3)
Homologous Superfamily
:
Dihydroorotate dehydrogenase b (pyrk subunit), domain 3
(3)
Lactococcus lactis. Organism_taxid: 1358.
(3)
4a
1ep2B03
B:221-262
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Pfam Domains
(0, 0)
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all PFAM domains
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