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1ULJ
Asym. Unit
Info
Asym.Unit (307 KB)
Biol.Unit 1 (300 KB)
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(1)
Title
:
BIPHENYL DIOXYGENASE (BPHA1A2) IN COMPLEX WITH THE SUBSTRATE
Authors
:
Y. Furusawa, V. Nagarajan, E. Masai, M. Tanokura, M. Fukuda, T. Senda
Date
:
12 Sep 03 (Deposition) - 28 Sep 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Alpha3 Beta3 Hetero Hexamer, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Furusawa, V. Nagarajan, M. Tanokura, E. Masai, M. Fukuda, T. Senda
Crystal Structure Of The Terminal Oxygenase Component Of Biphenyl Dioxygenase Derived From Rhodococcus Sp. Strain Rha1
J. Mol. Biol. V. 342 1041 2004
(for further references see the
PDB file header
)
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: BIPHENYL (BNLa)
1b: BIPHENYL (BNLb)
1c: BIPHENYL (BNLc)
2a: FE (II) ION (FE2a)
2b: FE (II) ION (FE2b)
2c: FE (II) ION (FE2c)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
BNL
3
Ligand/Ion
BIPHENYL
2
FE2
3
Ligand/Ion
FE (II) ION
3
FES
3
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:217 , HIS A:224 , HIS A:230 , ASP A:378 , HOH A:671
BINDING SITE FOR RESIDUE FE2 A 600
2
AC2
SOFTWARE
GLN C:217 , HIS C:224 , HIS C:230 , ASP C:378
BINDING SITE FOR RESIDUE FE2 C 600
3
AC3
SOFTWARE
GLN E:217 , HIS E:224 , HIS E:230 , ASP E:378
BINDING SITE FOR RESIDUE FE2 E 600
4
AC4
SOFTWARE
CYS A:98 , HIS A:100 , ARG A:101 , CYS A:118 , HIS A:121 , TRP A:123
BINDING SITE FOR RESIDUE FES A 500
5
AC5
SOFTWARE
CYS C:98 , HIS C:100 , ARG C:101 , CYS C:118 , HIS C:121 , TRP C:123
BINDING SITE FOR RESIDUE FES C 500
6
AC6
SOFTWARE
CYS E:98 , HIS E:100 , ARG E:101 , CYS E:118 , HIS E:121 , TRP E:123
BINDING SITE FOR RESIDUE FES E 500
7
AC7
SOFTWARE
GLN A:217 , ASP A:221 , MET A:222 , HIS A:224 , ALA A:225 , ILE A:278 , HIS A:313
BINDING SITE FOR RESIDUE BNL A 601
8
AC8
SOFTWARE
GLN C:217 , ASP C:221 , MET C:222 , HIS C:224 , ALA C:225 , HIS C:230 , ILE C:278 , HIS C:313
BINDING SITE FOR RESIDUE BNL C 1001
9
AC9
SOFTWARE
GLN E:217 , PHE E:218 , ASP E:221 , MET E:222 , ALA E:225 , HIS E:230 , ILE E:278 , HIS E:313 , LEU E:323
BINDING SITE FOR RESIDUE BNL E 2001
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: RIESKE (A:56-165,C:56-165,E:56-165)
2: RING_HYDROXYL_ALPHA (A:98-121,C:98-121,E:98-121)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
BPHA1_RHOJR
56-165
3
A:56-165
C:56-165
E:56-165
2
RING_HYDROXYL_ALPHA
PS00570
Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
BPHA1_RHOJR
98-121
3
A:98-121
C:98-121
E:98-121
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Exons
(0, 0)
Info
All Exons
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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
(3, 9)
Info
All SCOP Domains
1a: SCOP_d1ulja1 (A:17-170)
1b: SCOP_d1uljc1 (C:17-170)
1c: SCOP_d1ulje1 (E:17-170)
2a: SCOP_d1uljb_ (B:)
2b: SCOP_d1uljd_ (D:)
2c: SCOP_d1uljf_ (F:)
3a: SCOP_d1ulja2 (A:171-451)
3b: SCOP_d1uljc2 (C:171-451)
3c: SCOP_d1ulje2 (E:171-451)
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)
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)
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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
:
Biphenyl dioxygenase large subunit BphA1, N-terminal domain
(2)
Rhodococcus sp. RHA1 [TaxId: 101510]
(2)
1a
d1ulja1
A:17-170
1b
d1uljc1
C:17-170
1c
d1ulje1
E:17-170
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
NTF2-like
(231)
Family
:
Ring hydroxylating beta subunit
(46)
Protein domain
:
Biphenyl dioxygenase small subunit BphA2
(2)
Rhodococcus sp. RHA1 [TaxId: 101510]
(2)
2a
d1uljb_
B:
2b
d1uljd_
D:
2c
d1uljf_
F:
Fold
:
TBP-like
(289)
Superfamily
:
Bet v1-like
(158)
Family
:
Ring hydroxylating alpha subunit catalytic domain
(42)
Protein domain
:
Biphenyl dioxygenase large subunit BphA1, C-terminal domain
(2)
Rhodococcus sp. RHA1 [TaxId: 101510]
(2)
3a
d1ulja2
A:171-451
3b
d1uljc2
C:171-451
3c
d1ulje2
E:171-451
[
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1uljA01 (A:17-52,A:180-451)
1b: CATH_1uljC01 (C:17-52,C:180-453)
1c: CATH_1uljE01 (E:17-52,E:180-452)
2a: CATH_1uljA02 (A:53-179)
2b: CATH_1uljC02 (C:53-179)
2c: CATH_1uljE02 (E:53-179)
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)
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)
Rha1 (Rhodococcus sp)
(2)
1a
1uljA01
A:17-52,A:180-451
1b
1uljC01
C:17-52,C:180-453
1c
1uljE01
E:17-52,E:180-452
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Rha1 (Rhodococcus sp)
(2)
2a
1uljA02
A:53-179
2b
1uljC02
C:53-179
2c
1uljE02
E:53-179
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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