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1O7W
Biol. Unit 1
Info
Asym.Unit (118 KB)
Biol.Unit 1 (330 KB)
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(1)
Title
:
NAPHTHALENE 1,2-DIOXYGENASE, FULLY REDUCED FORM
Authors
:
A. Karlsson, J. V. Parales, R. E. Parales, D. T. Gibson, H. Eklund, S. Ramaswamy
Date
:
14 Nov 02 (Deposition) - 20 Feb 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Oxidoreductase, Non-Heme Iron Dioxygenase, Enzyme-Substrate Complex, Iron-Sulfur, Aromatic Hydrocarbon Catabolism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Karlsson, J. V. Parales, R. E. Parales, D. T. Gibson, H. Eklund, S. Ramaswamy
Crystal Structure Of Naphthalene Dioxygenase: Side-On Binding Of Dioxygen To Iron
Science V. 299 1039 2003
[
close entry info
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Hetero Components
(3, 30)
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)
1f: 1,2-ETHANEDIOL (EDOf)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2a: FE (III) ION (FEa)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
18
Ligand/Ion
1,2-ETHANEDIOL
2
FE
-1
Ligand/Ion
FE (III) ION
3
FES
3
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
SO4
9
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:128 , ASN A:129 , LYS A:130 , LYS A:131
BINDING SITE FOR RESIDUE SO4 A1451
02
AC2
SOFTWARE
HIS A:208 , HIS A:213 , ASP A:362 , HOH A:2144
BINDING SITE FOR RESIDUE FE A1453
03
AC3
SOFTWARE
GLN B:563 , GLN B:565 , HOH B:2054 , HOH B:2125
BINDING SITE FOR RESIDUE SO4 B1697
04
AC4
SOFTWARE
GLY B:559 , SER B:560 , GLU B:561 , GLU B:667 , LYS B:672
BINDING SITE FOR RESIDUE SO4 B1698
05
AC5
SOFTWARE
LEU A:31 , PHE A:35 , 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 A1448
06
AC6
SOFTWARE
HIS A:18 , VAL A:80 , CYS A:81 , ARG A:82 , SER A:381 , ASP A:382 , HOH A:2251 , HOH A:2252
BINDING SITE FOR RESIDUE EDO A1449
07
AC7
SOFTWARE
ARG A:342 , ASP A:346 , HOH A:2138 , ASN B:582
BINDING SITE FOR RESIDUE EDO A1450
08
AC8
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 A1452
09
AC9
SOFTWARE
TYR B:588 , GLN B:602 , MET B:691 , VAL B:692 , PHE B:693 , HOH B:2123 , HOH B:2124
BINDING SITE FOR RESIDUE EDO B1695
10
BC1
SOFTWARE
ALA A:50 , ASP A:53 , HOH A:2044 , ARG B:578 , TYR B:579 , LYS B:580 , LEU B:581
BINDING SITE FOR RESIDUE EDO B1696
11
BC2
SOFTWARE
ARG B:638 , ALA B:658 , GLU B:660 , PHE B:677 , VAL B:678 , ASP B:679 , HOH B:2107 , HOH B:2126
BINDING SITE FOR RESIDUE EDO B1699
[
close Site info
]
SAPs(SNPs)/Variants
(23, 69)
Info
(mutated residues are only available for the asymmetric unit)
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, 12)
Info
All PROSITE Patterns/Profiles
1: RIESKE (A:39-123)
2: RING_HYDROXYL_ALPHA (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
3
A:39-123
NDOB_PSEU8
39-123
3
A:39-123
2
RING_HYDROXYL_ALPHA
PS00570
Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
NDOB_PSEPU
81-104
3
A:81-104
NDOB_PSEU8
81-104
3
A:81-104
[
close PROSITE info
]
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1o7wa1 (A:1-154)
2a: SCOP_d1o7wb_ (B:)
3a: SCOP_d1o7wa2 (A:155-447)
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)
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)
(
)
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
d1o7wa1
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
d1o7wb_
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
d1o7wa2
A:155-447
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1o7wA01 (A:1-35,A:165-447)
2a: CATH_1o7wB00 (B:502-694)
3a: CATH_1o7wA02 (A:36-164)
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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: ncib 9816-4.
(6)
1a
1o7wA01
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: ncib 9816-4.
(6)
2a
1o7wB00
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: ncib 9816-4.
(6)
3a
1o7wA02
A:36-164
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Ring_hydroxyl_A_1o7wA01 (A:159-426)
2a: PFAM_Rieske_1o7wA02 (A:38-139)
3a: PFAM_Ring_hydroxyl_B_1o7wB01 (B:540-688)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
Bet_V_1_like
(93)
Family
:
Ring_hydroxyl_A
(10)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(9)
1a
Ring_hydroxyl_A-1o7wA01
A:159-426
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(13)
2a
Rieske-1o7wA02
A:38-139
Clan
:
NTF2
(66)
Family
:
Ring_hydroxyl_B
(10)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(9)
3a
Ring_hydroxyl_B-1o7wB01
B:540-688
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