Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5AEW

Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005506	molecular_function	iron ion binding
A	0016491	molecular_function	oxidoreductase activity
A	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
A	0019439	biological_process	aromatic compound catabolic process
A	0044237	biological_process	cellular metabolic process
A	0046872	molecular_function	metal ion binding
A	0051213	molecular_function	dioxygenase activity
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051537	molecular_function	2 iron, 2 sulfur cluster binding
B	0006725	biological_process	cellular aromatic compound metabolic process
B	0016491	molecular_function	oxidoreductase activity
B	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
B	0019380	biological_process	3-phenylpropionate catabolic process
B	0019439	biological_process	aromatic compound catabolic process
B	0051213	molecular_function	dioxygenase activity
C	0005506	molecular_function	iron ion binding
C	0016491	molecular_function	oxidoreductase activity
C	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
C	0019439	biological_process	aromatic compound catabolic process
C	0044237	biological_process	cellular metabolic process
C	0046872	molecular_function	metal ion binding
C	0051213	molecular_function	dioxygenase activity
C	0051536	molecular_function	iron-sulfur cluster binding
C	0051537	molecular_function	2 iron, 2 sulfur cluster binding
D	0006725	biological_process	cellular aromatic compound metabolic process
D	0016491	molecular_function	oxidoreductase activity
D	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
D	0019380	biological_process	3-phenylpropionate catabolic process
D	0019439	biological_process	aromatic compound catabolic process
D	0051213	molecular_function	dioxygenase activity
E	0005506	molecular_function	iron ion binding
E	0016491	molecular_function	oxidoreductase activity
E	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
E	0019439	biological_process	aromatic compound catabolic process
E	0044237	biological_process	cellular metabolic process
E	0046872	molecular_function	metal ion binding
E	0051213	molecular_function	dioxygenase activity
E	0051536	molecular_function	iron-sulfur cluster binding
E	0051537	molecular_function	2 iron, 2 sulfur cluster binding
F	0006725	biological_process	cellular aromatic compound metabolic process
F	0016491	molecular_function	oxidoreductase activity
F	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
F	0019380	biological_process	3-phenylpropionate catabolic process
F	0019439	biological_process	aromatic compound catabolic process
F	0051213	molecular_function	dioxygenase activity
G	0005506	molecular_function	iron ion binding
G	0016491	molecular_function	oxidoreductase activity
G	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
G	0019439	biological_process	aromatic compound catabolic process
G	0044237	biological_process	cellular metabolic process
G	0046872	molecular_function	metal ion binding
G	0051213	molecular_function	dioxygenase activity
G	0051536	molecular_function	iron-sulfur cluster binding
G	0051537	molecular_function	2 iron, 2 sulfur cluster binding
H	0006725	biological_process	cellular aromatic compound metabolic process
H	0016491	molecular_function	oxidoreductase activity
H	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
H	0019380	biological_process	3-phenylpropionate catabolic process
H	0019439	biological_process	aromatic compound catabolic process
H	0051213	molecular_function	dioxygenase activity
I	0005506	molecular_function	iron ion binding
I	0016491	molecular_function	oxidoreductase activity
I	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
I	0019439	biological_process	aromatic compound catabolic process
I	0044237	biological_process	cellular metabolic process
I	0046872	molecular_function	metal ion binding
I	0051213	molecular_function	dioxygenase activity
I	0051536	molecular_function	iron-sulfur cluster binding
I	0051537	molecular_function	2 iron, 2 sulfur cluster binding
J	0006725	biological_process	cellular aromatic compound metabolic process
J	0016491	molecular_function	oxidoreductase activity
J	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
J	0019380	biological_process	3-phenylpropionate catabolic process
J	0019439	biological_process	aromatic compound catabolic process
J	0051213	molecular_function	dioxygenase activity
K	0005506	molecular_function	iron ion binding
K	0016491	molecular_function	oxidoreductase activity
K	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
K	0019439	biological_process	aromatic compound catabolic process
K	0044237	biological_process	cellular metabolic process
K	0046872	molecular_function	metal ion binding
K	0051213	molecular_function	dioxygenase activity
K	0051536	molecular_function	iron-sulfur cluster binding
K	0051537	molecular_function	2 iron, 2 sulfur cluster binding
L	0006725	biological_process	cellular aromatic compound metabolic process
L	0016491	molecular_function	oxidoreductase activity
L	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
L	0019380	biological_process	3-phenylpropionate catabolic process
L	0019439	biological_process	aromatic compound catabolic process
L	0051213	molecular_function	dioxygenase activity
M	0005506	molecular_function	iron ion binding
M	0016491	molecular_function	oxidoreductase activity
M	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
M	0019439	biological_process	aromatic compound catabolic process
M	0044237	biological_process	cellular metabolic process
M	0046872	molecular_function	metal ion binding
M	0051213	molecular_function	dioxygenase activity
M	0051536	molecular_function	iron-sulfur cluster binding
M	0051537	molecular_function	2 iron, 2 sulfur cluster binding
N	0006725	biological_process	cellular aromatic compound metabolic process
N	0016491	molecular_function	oxidoreductase activity
N	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
N	0019380	biological_process	3-phenylpropionate catabolic process
N	0019439	biological_process	aromatic compound catabolic process
N	0051213	molecular_function	dioxygenase activity
O	0005506	molecular_function	iron ion binding
O	0016491	molecular_function	oxidoreductase activity
O	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
O	0019439	biological_process	aromatic compound catabolic process
O	0044237	biological_process	cellular metabolic process
O	0046872	molecular_function	metal ion binding
O	0051213	molecular_function	dioxygenase activity
O	0051536	molecular_function	iron-sulfur cluster binding
O	0051537	molecular_function	2 iron, 2 sulfur cluster binding
P	0006725	biological_process	cellular aromatic compound metabolic process
P	0016491	molecular_function	oxidoreductase activity
P	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
P	0019380	biological_process	3-phenylpropionate catabolic process
P	0019439	biological_process	aromatic compound catabolic process
P	0051213	molecular_function	dioxygenase activity
Q	0005506	molecular_function	iron ion binding
Q	0016491	molecular_function	oxidoreductase activity
Q	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
Q	0019439	biological_process	aromatic compound catabolic process
Q	0044237	biological_process	cellular metabolic process
Q	0046872	molecular_function	metal ion binding
Q	0051213	molecular_function	dioxygenase activity
Q	0051536	molecular_function	iron-sulfur cluster binding
Q	0051537	molecular_function	2 iron, 2 sulfur cluster binding
R	0006725	biological_process	cellular aromatic compound metabolic process
R	0016491	molecular_function	oxidoreductase activity
R	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
R	0019380	biological_process	3-phenylpropionate catabolic process
R	0019439	biological_process	aromatic compound catabolic process
R	0051213	molecular_function	dioxygenase activity
S	0005506	molecular_function	iron ion binding
S	0016491	molecular_function	oxidoreductase activity
S	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
S	0019439	biological_process	aromatic compound catabolic process
S	0044237	biological_process	cellular metabolic process
S	0046872	molecular_function	metal ion binding
S	0051213	molecular_function	dioxygenase activity
S	0051536	molecular_function	iron-sulfur cluster binding
S	0051537	molecular_function	2 iron, 2 sulfur cluster binding
T	0006725	biological_process	cellular aromatic compound metabolic process
T	0016491	molecular_function	oxidoreductase activity
T	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
T	0019380	biological_process	3-phenylpropionate catabolic process
T	0019439	biological_process	aromatic compound catabolic process
T	0051213	molecular_function	dioxygenase activity
U	0005506	molecular_function	iron ion binding
U	0016491	molecular_function	oxidoreductase activity
U	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
U	0019439	biological_process	aromatic compound catabolic process
U	0044237	biological_process	cellular metabolic process
U	0046872	molecular_function	metal ion binding
U	0051213	molecular_function	dioxygenase activity
U	0051536	molecular_function	iron-sulfur cluster binding
U	0051537	molecular_function	2 iron, 2 sulfur cluster binding
V	0006725	biological_process	cellular aromatic compound metabolic process
V	0016491	molecular_function	oxidoreductase activity
V	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
V	0019380	biological_process	3-phenylpropionate catabolic process
V	0019439	biological_process	aromatic compound catabolic process
V	0051213	molecular_function	dioxygenase activity
W	0005506	molecular_function	iron ion binding
W	0016491	molecular_function	oxidoreductase activity
W	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
W	0019439	biological_process	aromatic compound catabolic process
W	0044237	biological_process	cellular metabolic process
W	0046872	molecular_function	metal ion binding
W	0051213	molecular_function	dioxygenase activity
W	0051536	molecular_function	iron-sulfur cluster binding
W	0051537	molecular_function	2 iron, 2 sulfur cluster binding
X	0006725	biological_process	cellular aromatic compound metabolic process
X	0016491	molecular_function	oxidoreductase activity
X	0018687	molecular_function	biphenyl 2,3-dioxygenase activity
X	0019380	biological_process	3-phenylpropionate catabolic process
X	0019439	biological_process	aromatic compound catabolic process
X	0051213	molecular_function	dioxygenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FES A 460

Chain	Residue
A	CYS100
A	HIS102
A	ARG103
A	CYS120
A	HIS123
A	TRP125

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE FE2 A 461

Chain	Residue
A	ASP388
A	HOH2228
A	HOH2232
A	HOH2236
A	GLN226
A	HIS233
A	HIS239

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FES C 460

Chain	Residue
C	CYS100
C	HIS102
C	ARG103
C	CYS120
C	HIS123
C	TRP125

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE2 C 461

Chain	Residue
C	GLN226
C	HIS233
C	HIS239
C	ASP388
C	HOH2244

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE BNL C 462

Chain	Residue
C	GLN226
C	ASP230
C	MET231
C	HIS233
C	HIS323
C	LEU333
C	HOH2244

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FES E 460

Chain	Residue
E	CYS100
E	HIS102
E	ARG103
E	CYS120
E	HIS123
E	TRP125

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE2 E 461

Chain	Residue
E	GLN226
E	HIS233
E	HIS239
E	ASP388
E	HOH2167

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE BNL E 462

Chain	Residue
E	GLN226
E	ASP230
E	MET231
E	HIS233
E	HIS323
E	LEU333
E	HOH2167

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FES G 460

Chain	Residue
G	CYS100
G	HIS102
G	ARG103
G	CYS120
G	HIS123
G	TRP125

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FE2 G 461

Chain	Residue
G	GLN226
G	HIS233
G	HIS239
G	ASP388
G	HOH2125
G	HOH2131

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE FES I 460

Chain	Residue
I	CYS100
I	HIS102
I	ARG103
I	MET105
I	CYS120
I	HIS123
I	TRP125

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE2 I 461

Chain	Residue
I	GLN226
I	HIS233
I	HIS239
I	ASP388
I	HOH2142

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BNL I 462

Chain	Residue
I	GLN226
I	ASP230
I	HIS233
I	HIS323
I	LEU333

site_id	BC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE FES K 460

Chain	Residue
K	CYS100
K	HIS102
K	ARG103
K	MET105
K	CYS120
K	HIS123
K	TRP125

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FE2 K 461

Chain	Residue
K	GLN226
K	HIS233
K	HIS239
K	ASP388
K	HOH2159
K	HOH2161

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE BNL K 462

Chain	Residue
K	GLN226
K	ASP230
K	HIS233
K	HIS323
K	LEU333
K	PHE384

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FES M 460

Chain	Residue
M	ARG103
M	CYS120
M	HIS123
M	TRP125
M	CYS100
M	HIS102

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FE2 M 461

Chain	Residue
M	GLN226
M	HIS233
M	HIS239
M	ASP388
M	HOH2132
M	HOH2136

site_id	CC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE BNL M 462

Chain	Residue
M	GLN226
M	ASP230
M	HIS233
M	HIS323
M	LEU333
M	PHE378
M	PHE384

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FES O 460

Chain	Residue
O	CYS100
O	HIS102
O	ARG103
O	CYS120
O	HIS123
O	TRP125

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE2 O 461

Chain	Residue
O	GLN226
O	HIS233
O	HIS239
O	ASP388
O	HOH2135

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE BNL O 462

Chain	Residue
O	GLN226
O	ASP230
O	HIS233
O	HIS323
O	LEU333
O	PHE384

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FES Q 460

Chain	Residue
Q	CYS100
Q	HIS102
Q	CYS120
Q	HIS123
Q	TRP125

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE2 Q 461

Chain	Residue
Q	GLN226
Q	HIS233
Q	HIS239
Q	ASP388
Q	HOH2106

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE BNL Q 462

Chain	Residue
Q	GLN226
Q	ASP230
Q	HIS233
Q	GLY321
Q	HIS323
Q	LEU333
Q	HOH2106

site_id	CC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FES S 460

Chain	Residue
S	CYS100
S	HIS102
S	ARG103
S	CYS120
S	TYR122
S	HIS123
S	TRP125
S	HOH2021

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE2 S 461

Chain	Residue
S	GLN226
S	HIS233
S	HIS239
S	ASP388
S	HOH2052

site_id	DC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE BNL S 462

Chain	Residue
S	GLN226
S	ASP230
S	MET231
S	HIS233
S	HIS323
S	LEU333
S	PHE384
S	HOH2052

site_id	DC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE FES U 460

Chain	Residue
U	CYS100
U	HIS102
U	ARG103
U	CYS120
U	TYR122
U	HIS123
U	TRP125

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE2 U 461

Chain	Residue
U	GLN226
U	HIS233
U	HIS239
U	ASP388
U	HOH2100

site_id	DC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE FES W 460

Chain	Residue
W	CYS100
W	HIS102
W	ARG103
W	CYS120
W	TYR122
W	HIS123
W	TRP125

site_id	DC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE2 W 461

Chain	Residue
W	GLN226
W	HIS233
W	HIS239
W	ASP388
W	HOH2043

site_id	DC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BNL W 462

Chain	Residue
W	GLN226
W	ASP230
W	HIS233
W	HIS323
W	LEU333

Functional Information from PROSITE/UniProt

site_id	PS00570
Number of Residues	24
Details	RING_HYDROXYL_ALPHA Bacterial ring hydroxylating dioxygenases alpha-subunit signature. CrHRGmricrsdaGNakaftCsYH

Chain	Residue	Details
A	CYS100-HIS123

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	48
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00628

Chain	Residue	Details
A	CYS100
E	HIS102
E	CYS120
E	HIS123
G	CYS100
G	HIS102
G	CYS120
G	HIS123
I	CYS100
I	HIS102
I	CYS120
A	HIS102
I	HIS123
K	CYS100
K	HIS102
K	CYS120
K	HIS123
M	CYS100
M	HIS102
M	CYS120
M	HIS123
O	CYS100
A	CYS120
O	HIS102
O	CYS120
O	HIS123
Q	CYS100
Q	HIS102
Q	CYS120
Q	HIS123
S	CYS100
S	HIS102
S	CYS120
A	HIS123
S	HIS123
U	CYS100
U	HIS102
U	CYS120
U	HIS123
W	CYS100
W	HIS102
W	CYS120
W	HIS123
C	CYS100
C	HIS102
C	CYS120
C	HIS123
E	CYS100

site_id	SWS_FT_FI2
Number of Residues	24
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	HIS233
I	HIS239
K	HIS233
K	HIS239
M	HIS233
M	HIS239
O	HIS233
O	HIS239
Q	HIS233
Q	HIS239
S	HIS233
A	HIS239
S	HIS239
U	HIS233
U	HIS239
W	HIS233
W	HIS239
C	HIS233
C	HIS239
E	HIS233
E	HIS239
G	HIS233
G	HIS239
I	HIS233

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)