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1UUV
Asym. Unit
Info
Asym.Unit (121 KB)
Biol.Unit 1 (336 KB)
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(1)
Title
:
NAPHTHALENE 1,2-DIOXYGENASE WITH NITRIC OXIDE AND INDOLE BOUND IN THE ACTIVE SITE.
Authors
:
A. Karlsson, J. V. Parales, R. E. Parales, D. T. Gibson, H. Eklund, S. Ramaswamy
Date
:
11 Jan 04 (Deposition) - 09 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Oxidoreductase, Non-Heme Iron Dioxygenase, Enzyme-Substrate Complex, Aromatic Hydrocarbons Catabolism,
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Karlsson, J. V. Parales, R. E. Parales, D. T. Gibson, H. Eklund, S. Ramaswamy
No Binding To Naphthalene Dioxygenase.
J. Biol. Inorg. Chem. V. 10 483 2005
[
close entry info
]
Hetero Components
(6, 12)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2a: FE (III) ION (FEa)
4a: INDOLE (INDa)
5a: NITRIC OXIDE (NOa)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
2
FE
1
Ligand/Ion
FE (III) ION
3
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
IND
1
Ligand/Ion
INDOLE
5
NO
1
Ligand/Ion
NITRIC OXIDE
6
SO4
3
Ligand/Ion
SULFATE ION
[
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]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:201 , HIS A:208 , HIS A:213 , ASP A:362 , NO A:1453
BINDING SITE FOR RESIDUE FE A1454
02
AC2
SOFTWARE
GLN B:563 , GLN B:565 , HOH B:2045 , HOH B:2065 , HOH B:2148 , HOH B:2149
BINDING SITE FOR RESIDUE SO4 B1697
03
AC3
SOFTWARE
GLY B:559 , SER B:560 , LYS B:664 , LYS B:672 , HOH B:2150
BINDING SITE FOR RESIDUE SO4 B1698
04
AC4
SOFTWARE
ARG B:665 , ARG B:671 , HOH B:2123
BINDING SITE FOR RESIDUE SO4 B1699
05
AC5
SOFTWARE
CYS A:81 , HIS A:83 , ARG A:84 , CYS A:101 , TYR A:103 , HIS A:104 , TRP A:106
BINDING SITE FOR RESIDUE FES A1448
06
AC6
SOFTWARE
LEU A:31 , PHE A:35 , ALA A:36 , MET A:59 , GLY A:60 , ILE A:61 , ASP A:62 , PHE A:152 , TYR A:376 , GLN A:377
BINDING SITE FOR RESIDUE EDO A1449
07
AC7
SOFTWARE
HIS A:18 , VAL A:80 , CYS A:81 , ARG A:82 , SER A:381 , ASP A:382 , HOH A:2311 , HOH A:2312
BINDING SITE FOR RESIDUE EDO A1450
08
AC8
SOFTWARE
THR A:56 , GLU A:92 , PRO A:186 , LYS A:188 , TRP A:327 , GLU B:570 , ARG B:683
BINDING SITE FOR RESIDUE EDO A1451
09
AC9
SOFTWARE
ASN A:201 , ASP A:205 , HIS A:295 , ASN A:297 , NO A:1453
BINDING SITE FOR RESIDUE IND A1452
10
BC1
SOFTWARE
HIS A:208 , HIS A:213 , IND A:1452 , FE A:1454
BINDING SITE FOR RESIDUE NO A1453
11
BC2
SOFTWARE
TYR B:588 , MET B:691 , VAL B:692 , PHE B:693 , HOH B:2145 , HOH B:2146
BINDING SITE FOR RESIDUE EDO B1695
12
BC3
SOFTWARE
ASN B:591 , GLN B:594 , HOH B:2147
BINDING SITE FOR RESIDUE EDO B1696
[
close Site info
]
SAPs(SNPs)/Variants
(23, 23)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_NDOB_PSEPU_001 (N4K, chain A, )
02: VAR_NDOB_PSEPU_002 (S12F, chain A, )
03: VAR_NDOB_PSEPU_003 (S15T, chain A, )
04: VAR_NDOB_PSEPU_004 (K32R, chain A, )
05: VAR_NDOB_PSEPU_005 (A50S, chain A, )
06: VAR_NDOB_PSEPU_006 (N70S, chain A, )
07: VAR_NDOB_PSEPU_007 (D122E, chain A, )
08: VAR_NDOB_PSEPU_008 (M173I, chain A, )
09: VAR_NDOB_PSEPU_009 (S225A, chain A, )
10: VAR_NDOB_PSEPU_010 (S225C, chain A, )
11: VAR_NDOB_PSEPU_011 (A232V, chain A, )
12: VAR_NDOB_PSEPU_012 (A275S, chain A, )
13: VAR_NDOB_PSEPU_013 (E391K, chain A, )
14: VAR_NDOB_PSEPU_014 (Q421R, chain A, )
15: VAR_NDOB_PSEPU_015 (H434D, chain A, )
16: VAR_NDOC_PSEPU_001 (E517Q, chain B, )
17: VAR_NDOC_PSEPU_002 (I519F, chain B, )
18: VAR_NDOC_PSEPU_003 (S528A, chain B, )
19: VAR_NDOC_PSEPU_004 (V599I, chain B, )
20: VAR_NDOC_PSEPU_005 (G609S, chain B, )
21: VAR_NDOC_PSEPU_006 (M627R, chain B, )
22: VAR_NDOC_PSEPU_007 (N630D, chain B, )
23: VAR_NDOC_PSEPU_008 (K632E, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_NDOB_PSEPU_001
*
N
4
K
NDOB_PSEPU
---
---
A
N
4
K
02
UniProt
VAR_NDOB_PSEPU_002
*
S
12
F
NDOB_PSEPU
---
---
A
S
12
F
03
UniProt
VAR_NDOB_PSEPU_003
*
S
15
T
NDOB_PSEPU
---
---
A
S
15
T
04
UniProt
VAR_NDOB_PSEPU_004
*
K
32
R
NDOB_PSEPU
---
---
A
K
32
R
05
UniProt
VAR_NDOB_PSEPU_005
*
A
50
S
NDOB_PSEPU
---
---
A
A
50
S
06
UniProt
VAR_NDOB_PSEPU_006
*
N
70
S
NDOB_PSEPU
---
---
A
N
70
S
07
UniProt
VAR_NDOB_PSEPU_007
*
D
122
E
NDOB_PSEPU
---
---
A
D
122
E
08
UniProt
VAR_NDOB_PSEPU_008
*
M
173
I
NDOB_PSEPU
---
---
A
M
173
I
09
UniProt
VAR_NDOB_PSEPU_009
*
S
225
A
NDOB_PSEPU
---
---
A
S
225
A
10
UniProt
VAR_NDOB_PSEPU_010
*
S
225
C
NDOB_PSEPU
---
---
A
S
225
C
11
UniProt
VAR_NDOB_PSEPU_011
*
A
232
V
NDOB_PSEPU
---
---
A
A
232
V
12
UniProt
VAR_NDOB_PSEPU_012
*
A
275
S
NDOB_PSEPU
---
---
A
A
275
S
13
UniProt
VAR_NDOB_PSEPU_013
*
E
391
K
NDOB_PSEPU
---
---
A
E
391
K
14
UniProt
VAR_NDOB_PSEPU_014
*
Q
421
R
NDOB_PSEPU
---
---
A
Q
421
R
15
UniProt
VAR_NDOB_PSEPU_015
*
H
434
D
NDOB_PSEPU
---
---
A
H
434
D
16
UniProt
VAR_NDOC_PSEPU_001
*
E
17
Q
NDOC_PSEPU
---
---
B
E
517
Q
17
UniProt
VAR_NDOC_PSEPU_002
*
I
19
F
NDOC_PSEPU
---
---
B
I
519
F
18
UniProt
VAR_NDOC_PSEPU_003
*
S
28
A
NDOC_PSEPU
---
---
B
S
528
A
19
UniProt
VAR_NDOC_PSEPU_004
*
V
99
I
NDOC_PSEPU
---
---
B
V
599
I
20
UniProt
VAR_NDOC_PSEPU_005
*
G
109
S
NDOC_PSEPU
---
---
B
G
609
S
21
UniProt
VAR_NDOC_PSEPU_006
*
M
127
R
NDOC_PSEPU
---
---
B
M
627
R
22
UniProt
VAR_NDOC_PSEPU_007
*
N
130
D
NDOC_PSEPU
---
---
B
N
630
D
23
UniProt
VAR_NDOC_PSEPU_008
*
K
132
E
NDOC_PSEPU
---
---
B
K
632
E
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: RIESKE (A:39-123,A:39-123)
2: RING_HYDROXYL_ALPHA (A:81-104,A:81-104)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
NDOB_PSEPU
39-123
1
A:39-123
NDOB_PSEU8
39-123
1
A:39-123
2
RING_HYDROXYL_ALPHA
PS00570
Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
NDOB_PSEPU
81-104
1
A:81-104
NDOB_PSEU8
81-104
1
A:81-104
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1uuva1 (A:1-154)
2a: SCOP_d1uuvb_ (B:)
3a: SCOP_d1uuva2 (A:155-447)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
Ring hydroxylating alpha subunit ISP domain
(40)
Protein domain
:
Naphthalene 1,2-dioxygenase alpha subunit, N-domain
(27)
Pseudomonas putida [TaxId: 303]
(10)
1a
d1uuva1
A:1-154
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
NTF2-like
(231)
Family
:
Ring hydroxylating beta subunit
(46)
Protein domain
:
Naphthalene 1,2-dioxygenase beta subunit
(28)
Pseudomonas putida [TaxId: 303]
(10)
2a
d1uuvb_
B:
Fold
:
TBP-like
(289)
Superfamily
:
Bet v1-like
(158)
Family
:
Ring hydroxylating alpha subunit catalytic domain
(42)
Protein domain
:
Naphthalene 1,2-dioxygenase alpha subunit, C-domain
(29)
Pseudomonas putida [TaxId: 303]
(10)
3a
d1uuva2
A:155-447
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1uuvA01 (A:1-35,A:165-447)
2a: CATH_1uuvB00 (B:502-694)
3a: CATH_1uuvA02 (A:36-164)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
(24)
Homologous Superfamily
:
Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
(24)
Pseudomonas putida. Organism_taxid: 303. Strain: ncib9816-4.
(2)
1a
1uuvA01
A:1-35,A:165-447
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
[code=3.10.450.50, no name defined]
(113)
Pseudomonas putida. Organism_taxid: 303. Strain: ncib9816-4.
(2)
2a
1uuvB00
B:502-694
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Pseudomonas putida. Organism_taxid: 303. Strain: ncib9816-4.
(2)
3a
1uuvA02
A:36-164
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Ring_hydroxyl_A_1uuvA01 (A:159-426)
2a: PFAM_Rieske_1uuvA02 (A:38-139)
3a: PFAM_Ring_hydroxyl_B_1uuvB01 (B:540-688)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Bet_V_1_like
(93)
Family
:
Ring_hydroxyl_A
(10)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(9)
1a
Ring_hydroxyl_A-1uuvA01
A:159-426
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(13)
2a
Rieske-1uuvA02
A:38-139
Clan
:
NTF2
(66)
Family
:
Ring_hydroxyl_B
(10)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(9)
3a
Ring_hydroxyl_B-1uuvB01
B:540-688
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Asym.Unit (121 KB)
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