Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1YKP

Protocatechuate 3,4-Dioxygenase Y408H mutant bound to DHB

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0005506	molecular_function	iron ion binding
A	0008199	molecular_function	ferric iron binding
A	0009056	biological_process	catabolic process
A	0016491	molecular_function	oxidoreductase activity
A	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
A	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
A	0042952	biological_process	beta-ketoadipate pathway
A	0051213	molecular_function	dioxygenase activity
B	0003824	molecular_function	catalytic activity
B	0005506	molecular_function	iron ion binding
B	0008199	molecular_function	ferric iron binding
B	0016491	molecular_function	oxidoreductase activity
B	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
B	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
B	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
B	0042952	biological_process	beta-ketoadipate pathway
B	0046872	molecular_function	metal ion binding
B	0051213	molecular_function	dioxygenase activity
C	0003824	molecular_function	catalytic activity
C	0005506	molecular_function	iron ion binding
C	0008199	molecular_function	ferric iron binding
C	0009056	biological_process	catabolic process
C	0016491	molecular_function	oxidoreductase activity
C	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
C	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
C	0042952	biological_process	beta-ketoadipate pathway
C	0051213	molecular_function	dioxygenase activity
D	0003824	molecular_function	catalytic activity
D	0005506	molecular_function	iron ion binding
D	0008199	molecular_function	ferric iron binding
D	0016491	molecular_function	oxidoreductase activity
D	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
D	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
D	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
D	0042952	biological_process	beta-ketoadipate pathway
D	0046872	molecular_function	metal ion binding
D	0051213	molecular_function	dioxygenase activity
E	0003824	molecular_function	catalytic activity
E	0005506	molecular_function	iron ion binding
E	0008199	molecular_function	ferric iron binding
E	0009056	biological_process	catabolic process
E	0016491	molecular_function	oxidoreductase activity
E	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
E	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
E	0042952	biological_process	beta-ketoadipate pathway
E	0051213	molecular_function	dioxygenase activity
F	0003824	molecular_function	catalytic activity
F	0005506	molecular_function	iron ion binding
F	0008199	molecular_function	ferric iron binding
F	0016491	molecular_function	oxidoreductase activity
F	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
F	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
F	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
F	0042952	biological_process	beta-ketoadipate pathway
F	0046872	molecular_function	metal ion binding
F	0051213	molecular_function	dioxygenase activity
G	0003824	molecular_function	catalytic activity
G	0005506	molecular_function	iron ion binding
G	0008199	molecular_function	ferric iron binding
G	0009056	biological_process	catabolic process
G	0016491	molecular_function	oxidoreductase activity
G	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
G	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
G	0042952	biological_process	beta-ketoadipate pathway
G	0051213	molecular_function	dioxygenase activity
H	0003824	molecular_function	catalytic activity
H	0005506	molecular_function	iron ion binding
H	0008199	molecular_function	ferric iron binding
H	0016491	molecular_function	oxidoreductase activity
H	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
H	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
H	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
H	0042952	biological_process	beta-ketoadipate pathway
H	0046872	molecular_function	metal ion binding
H	0051213	molecular_function	dioxygenase activity
I	0003824	molecular_function	catalytic activity
I	0005506	molecular_function	iron ion binding
I	0008199	molecular_function	ferric iron binding
I	0009056	biological_process	catabolic process
I	0016491	molecular_function	oxidoreductase activity
I	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
I	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
I	0042952	biological_process	beta-ketoadipate pathway
I	0051213	molecular_function	dioxygenase activity
J	0003824	molecular_function	catalytic activity
J	0005506	molecular_function	iron ion binding
J	0008199	molecular_function	ferric iron binding
J	0016491	molecular_function	oxidoreductase activity
J	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
J	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
J	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
J	0042952	biological_process	beta-ketoadipate pathway
J	0046872	molecular_function	metal ion binding
J	0051213	molecular_function	dioxygenase activity
K	0003824	molecular_function	catalytic activity
K	0005506	molecular_function	iron ion binding
K	0008199	molecular_function	ferric iron binding
K	0009056	biological_process	catabolic process
K	0016491	molecular_function	oxidoreductase activity
K	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
K	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
K	0042952	biological_process	beta-ketoadipate pathway
K	0051213	molecular_function	dioxygenase activity
L	0003824	molecular_function	catalytic activity
L	0005506	molecular_function	iron ion binding
L	0008199	molecular_function	ferric iron binding
L	0016491	molecular_function	oxidoreductase activity
L	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
L	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
L	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
L	0042952	biological_process	beta-ketoadipate pathway
L	0046872	molecular_function	metal ion binding
L	0051213	molecular_function	dioxygenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE B 600

Chain	Residue
A	DHB550
B	TYR447
B	HIS460
B	HIS462
B	HOH901

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE FE D 1600

Chain	Residue
D	DHB1550
D	HOH1901
D	HIS408
D	TYR447
D	HIS460
D	HIS462

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE F 2600

Chain	Residue
F	TYR447
F	HIS460
F	HIS462
F	DHB2550
F	HOH2901

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE H 3600

Chain	Residue
H	TYR447
H	HIS460
H	HIS462
H	DHB3550
H	HOH3901

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE J 4600

Chain	Residue
J	TYR447
J	HIS460
J	HIS462
J	DHB4550
J	HOH4901

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE L 5600

Chain	Residue
L	TYR447
L	HIS460
L	HIS462
L	DHB5550
L	HOH5901

site_id	AC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DHB A 550

Chain	Residue
A	THR12
A	GLY14
A	PRO15
A	ARG133
B	TYR324
B	TYR447
B	ARG457
B	HIS460
B	HIS462
B	GLN477
B	ILE491
B	FE600

site_id	AC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE DHB D 1550

Chain	Residue
C	THR12
C	PRO15
C	ARG133
D	TYR324
D	TYR447
D	TRP449
D	ARG457
D	HIS460
D	GLN477
D	ILE491
D	FE1600

site_id	AC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE DHB F 2550

Chain	Residue
E	GLY14
E	PRO15
E	ARG133
F	TYR324
F	TYR447
F	ARG457
F	HIS460
F	HIS462
F	GLN477
F	FE2600

site_id	BC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE DHB H 3550

Chain	Residue
G	GLY14
G	PRO15
G	ARG133
H	TYR324
H	TYR447
H	ARG457
H	HIS460
H	HIS462
H	GLN477
H	FE3600

site_id	BC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE DHB J 4550

Chain	Residue
I	GLY14
I	PRO15
I	ARG133
J	TYR324
J	TYR447
J	TRP449
J	ARG457
J	HIS460
J	HIS462
J	GLN477
J	FE4600

site_id	BC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE DHB L 5550

Chain	Residue
K	GLY14
K	PRO15
K	ARG133
L	TYR324
L	TYR447
L	ARG457
L	HIS460
L	HIS462
L	GLN477
L	ILE491
L	FE5600

Functional Information from PROSITE/UniProt

site_id	PS00083
Number of Residues	29
Details	INTRADIOL_DIOXYGENAS Intradiol ring-cleavage dioxygenases signature. LlGqVydgnGhlVrdsfLEVwqadanGeY

Chain	Residue	Details
A	LEU51-TYR79

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"7990141","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 3pca

Chain	Residue	Details
B	TYR447
B	ARG457

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 3pca

Chain	Residue	Details
D	TYR447
D	ARG457

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 3pca

Chain	Residue	Details
F	TYR447
F	ARG457

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 3pca

Chain	Residue	Details
H	TYR447
H	ARG457

site_id	CSA5
Number of Residues	2
Details	Annotated By Reference To The Literature 3pca

Chain	Residue	Details
J	TYR447
J	ARG457

site_id	CSA6
Number of Residues	2
Details	Annotated By Reference To The Literature 3pca

Chain	Residue	Details
L	TYR447
L	ARG457

site_id	MCSA1
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
B	HIS408	metal ligand
B	ASN451	metal ligand, proton shuttle (general acid/base)
B	ILE461	electrostatic stabiliser
B	GLY464	metal ligand
B	SER466	metal ligand

site_id	MCSA2
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
D	HIS408	metal ligand
D	ASN451	metal ligand, proton shuttle (general acid/base)
D	ILE461	electrostatic stabiliser
D	GLY464	metal ligand
D	SER466	metal ligand

site_id	MCSA3
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
F	HIS408	metal ligand
F	ASN451	metal ligand, proton shuttle (general acid/base)
F	ILE461	electrostatic stabiliser
F	GLY464	metal ligand
F	SER466	metal ligand

site_id	MCSA4
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
H	HIS408	metal ligand
H	ASN451	metal ligand, proton shuttle (general acid/base)
H	ILE461	electrostatic stabiliser
H	GLY464	metal ligand
H	SER466	metal ligand

site_id	MCSA5
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
J	HIS408	metal ligand
J	ASN451	metal ligand, proton shuttle (general acid/base)
J	ILE461	electrostatic stabiliser
J	GLY464	metal ligand
J	SER466	metal ligand

site_id	MCSA6
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
L	HIS408	metal ligand
L	ASN451	metal ligand, proton shuttle (general acid/base)
L	ILE461	electrostatic stabiliser
L	GLY464	metal ligand
L	SER466	metal ligand

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