Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3PCE

STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYPHENYLACETATE

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0005506	molecular_function	iron ion binding
A	0006725	biological_process	obsolete cellular aromatic compound metabolic process
A	0008199	molecular_function	ferric iron binding
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	0019439	biological_process	obsolete aromatic compound catabolic process
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	0006725	biological_process	obsolete cellular aromatic compound metabolic process
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	0019439	biological_process	obsolete aromatic compound catabolic process
B	0042952	biological_process	beta-ketoadipate pathway
B	0051213	molecular_function	dioxygenase activity
C	0003824	molecular_function	catalytic activity
C	0005506	molecular_function	iron ion binding
C	0006725	biological_process	obsolete cellular aromatic compound metabolic process
C	0008199	molecular_function	ferric iron binding
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	0019439	biological_process	obsolete aromatic compound catabolic process
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	0006725	biological_process	obsolete cellular aromatic compound metabolic process
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	0019439	biological_process	obsolete aromatic compound catabolic process
D	0042952	biological_process	beta-ketoadipate pathway
D	0051213	molecular_function	dioxygenase activity
E	0003824	molecular_function	catalytic activity
E	0005506	molecular_function	iron ion binding
E	0006725	biological_process	obsolete cellular aromatic compound metabolic process
E	0008199	molecular_function	ferric iron binding
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	0019439	biological_process	obsolete aromatic compound catabolic process
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	0006725	biological_process	obsolete cellular aromatic compound metabolic process
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	0019439	biological_process	obsolete aromatic compound catabolic process
F	0042952	biological_process	beta-ketoadipate pathway
F	0051213	molecular_function	dioxygenase activity
M	0003824	molecular_function	catalytic activity
M	0005506	molecular_function	iron ion binding
M	0006725	biological_process	obsolete cellular aromatic compound metabolic process
M	0008199	molecular_function	ferric iron binding
M	0016491	molecular_function	oxidoreductase activity
M	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
M	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
M	0019439	biological_process	obsolete aromatic compound catabolic process
M	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
M	0042952	biological_process	beta-ketoadipate pathway
M	0046872	molecular_function	metal ion binding
M	0051213	molecular_function	dioxygenase activity
N	0003824	molecular_function	catalytic activity
N	0005506	molecular_function	iron ion binding
N	0006725	biological_process	obsolete cellular aromatic compound metabolic process
N	0008199	molecular_function	ferric iron binding
N	0016491	molecular_function	oxidoreductase activity
N	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
N	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
N	0019439	biological_process	obsolete aromatic compound catabolic process
N	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
N	0042952	biological_process	beta-ketoadipate pathway
N	0046872	molecular_function	metal ion binding
N	0051213	molecular_function	dioxygenase activity
O	0003824	molecular_function	catalytic activity
O	0005506	molecular_function	iron ion binding
O	0006725	biological_process	obsolete cellular aromatic compound metabolic process
O	0008199	molecular_function	ferric iron binding
O	0016491	molecular_function	oxidoreductase activity
O	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
O	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
O	0019439	biological_process	obsolete aromatic compound catabolic process
O	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
O	0042952	biological_process	beta-ketoadipate pathway
O	0046872	molecular_function	metal ion binding
O	0051213	molecular_function	dioxygenase activity
P	0003824	molecular_function	catalytic activity
P	0005506	molecular_function	iron ion binding
P	0006725	biological_process	obsolete cellular aromatic compound metabolic process
P	0008199	molecular_function	ferric iron binding
P	0016491	molecular_function	oxidoreductase activity
P	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
P	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
P	0019439	biological_process	obsolete aromatic compound catabolic process
P	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
P	0042952	biological_process	beta-ketoadipate pathway
P	0046872	molecular_function	metal ion binding
P	0051213	molecular_function	dioxygenase activity
Q	0003824	molecular_function	catalytic activity
Q	0005506	molecular_function	iron ion binding
Q	0006725	biological_process	obsolete cellular aromatic compound metabolic process
Q	0008199	molecular_function	ferric iron binding
Q	0016491	molecular_function	oxidoreductase activity
Q	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
Q	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
Q	0019439	biological_process	obsolete aromatic compound catabolic process
Q	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
Q	0042952	biological_process	beta-ketoadipate pathway
Q	0046872	molecular_function	metal ion binding
Q	0051213	molecular_function	dioxygenase activity
R	0003824	molecular_function	catalytic activity
R	0005506	molecular_function	iron ion binding
R	0006725	biological_process	obsolete cellular aromatic compound metabolic process
R	0008199	molecular_function	ferric iron binding
R	0016491	molecular_function	oxidoreductase activity
R	0016702	molecular_function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
R	0018578	molecular_function	protocatechuate 3,4-dioxygenase activity
R	0019439	biological_process	obsolete aromatic compound catabolic process
R	0019619	biological_process	3,4-dihydroxybenzoate catabolic process
R	0042952	biological_process	beta-ketoadipate pathway
R	0046872	molecular_function	metal ion binding
R	0051213	molecular_function	dioxygenase activity

Functional Information from PDB Data

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

Chain	Residue
M	TYR408
M	TYR447
M	HIS460
M	HIS462
M	3HP550

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE N 600

Chain	Residue
N	TYR408
N	TYR447
N	HIS460
N	HIS462
N	3HP550

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE O 600

Chain	Residue
O	TYR408
O	TYR447
O	HIS460
O	HIS462
O	3HP550

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE P 600

Chain	Residue
P	TYR408
P	TYR447
P	HIS460
P	HIS462
P	3HP550

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE Q 600

Chain	Residue
Q	TYR408
Q	TYR447
Q	HIS460
Q	HIS462
Q	3HP550

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE R 600

Chain	Residue
R	TYR408
R	TYR447
R	HIS460
R	HIS462
R	3HP550

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BME M 601

Chain	Residue
M	HIS361
M	CYS429
M	LEU430
M	SER438
M	HOH689

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE 3HP M 550

Chain	Residue
A	PRO15
M	TYR408
M	TYR447
M	TRP449
M	ARG457
M	HIS462
M	ILE491
M	FE600
M	HOH741
M	HOH742

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE BME N 601

Chain	Residue
N	HIS361
N	CYS429
N	SER438
N	HOH693

site_id	ACA
Number of Residues	26
Details	SITE "ACA" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS A AND M.

Chain	Residue
A	THR12
M	TYR408
M	TYR447
M	TRP449
M	ARG450
M	ARG457
M	HIS460
M	HIS462
M	GLN477
M	ILE491
M	FE600
A	ALA13
A	HOH205
M	HOH623
M	HOH630
M	HOH631
M	3HP550
M	HOH741
M	HOH742
A	GLY14
A	PRO15
A	TYR16
A	ARG133
A	GLY134
M	TYR324
M	THR326

site_id	ACB
Number of Residues	26
Details	SITE "ACB" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS B AND N.

Chain	Residue
B	THR12
B	ALA13
B	GLY14
B	PRO15
B	TYR16
B	ARG133
B	GLY134
N	TYR324
N	THR326
N	TYR408
N	TYR447
N	TRP449
N	ARG450
N	ARG457
N	HIS460
N	HIS462
N	GLN477
N	ILE491
N	FE600
B	HOH247
N	HOH627
N	HOH634
N	HOH635
N	3HP550
N	HOH747
N	HOH748

site_id	ACC
Number of Residues	26
Details	SITE "ACC" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS C AND O.

Chain	Residue
C	THR12
C	ALA13
C	GLY14
C	PRO15
C	TYR16
C	ARG133
C	GLY134
O	TYR324
O	THR326
O	TYR408
O	TYR447
O	TRP449
O	ARG450
O	ARG457
O	HIS460
O	HIS462
O	GLN477
O	ILE491
O	FE600
C	HOH206
O	HOH627
O	HOH636
O	HOH637
O	3HP550
O	HOH754
O	HOH755

site_id	ACD
Number of Residues	26
Details	SITE "ACD" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS D AND P.

Chain	Residue
P	HOH640
P	HOH641
P	3HP550
P	HOH749
P	HOH750
D	THR12
D	ALA13
D	GLY14
D	PRO15
D	TYR16
D	ARG133
D	GLY134
P	TYR324
P	THR326
P	TYR408
P	TYR447
P	TRP449
P	ARG450
P	ARG457
P	HIS460
P	HIS462
P	GLN477
P	ILE491
P	FE600
D	HOH729
P	HOH632

site_id	ACE
Number of Residues	26
Details	SITE "ACE" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS E AND Q.

Chain	Residue
E	THR12
E	ALA13
E	GLY14
E	PRO15
E	TYR16
E	ARG133
E	GLY134
Q	TYR324
Q	THR326
Q	TYR408
Q	TYR447
Q	TRP449
Q	ARG450
Q	ARG457
Q	HIS460
Q	HIS462
Q	GLN477
Q	ILE491
Q	FE600
E	HOH206
Q	HOH1007
Q	HOH1022
Q	HOH1023
Q	3HP550
Q	HOH1197
Q	HOH1198

site_id	ACF
Number of Residues	26
Details	SITE "ACF" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS F AND R.

Chain	Residue
F	THR12
F	ALA13
F	GLY14
F	PRO15
F	TYR16
F	ARG133
F	GLY134
R	TYR324
R	THR326
R	TYR408
R	TYR447
R	TRP449
R	ARG450
R	ARG457
R	HIS460
R	HIS462
R	GLN477
R	ILE491
R	FE600
F	HOH1211
R	HOH1248
R	HOH1263
R	HOH1264
R	3HP550
R	HOH1438
R	HOH1439

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 3HP N 550

Chain	Residue
N	TYR408
N	TYR447
N	TRP449
N	ARG457
N	HIS462
N	ILE491
N	FE600
N	HOH747
N	HOH748

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE BME O 601

Chain	Residue
O	HIS361
O	CYS429
O	SER438
O	HOH697

site_id	BC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE 3HP O 550

Chain	Residue
C	GLY14
C	PRO15
C	HOH206
O	TYR408
O	TYR447
O	TRP449
O	ARG457
O	HIS462
O	ILE491
O	FE600
O	HOH754

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BME P 601

Chain	Residue
P	HIS361
P	CYS429
P	LEU430
P	SER438
P	HOH698

site_id	BC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE 3HP P 550

Chain	Residue
D	GLY14
D	PRO15
P	TYR408
P	TYR447
P	TRP449
P	ARG457
P	HIS462
P	ILE491
P	FE600
P	HOH749
P	HOH750

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE BME Q 601

Chain	Residue
Q	HIS361
Q	CYS429
Q	SER438
Q	HOH1111

site_id	BC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE 3HP Q 550

Chain	Residue
E	GLY14
E	PRO15
Q	TYR408
Q	TYR447
Q	TRP449
Q	ARG457
Q	HIS462
Q	ILE491
Q	FE600
Q	HOH1197
Q	HOH1198

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BME R 601

Chain	Residue
R	HIS361
R	CYS429
R	LEU430
R	SER438
R	HOH1352

site_id	BC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE 3HP R 550

Chain	Residue
F	PRO15
F	HOH1211
R	TYR408
R	TYR447
R	TRP449
R	ARG457
R	HIS462
R	ILE491
R	FE600
R	HOH1438

site_id	VEA
Number of Residues	29
Details	SITE "VEA" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS A AND M.

Chain	Residue
A	TYR79
A	VAL114
A	ASN115
A	ASN116
A	ALA117
A	ALA118
A	MET122
A	HIS125
A	ASN127
A	ARG142
A	VAL157
M	ASP304
M	ARG307
M	ILE339
M	PRO340
M	GLN341
M	SER342
M	ILE343
M	SER344
M	GLU345
A	HOH220
A	HOH223
M	HOH635
A	HOH232
M	HOH641
A	HOH235
M	HOH658
A	HOH246
M	HOH716

site_id	VEB
Number of Residues	29
Details	SITE "VEB" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS B AND N.

Chain	Residue
B	TYR79
B	VAL114
B	ASN115
B	ASN116
B	ALA117
B	ALA118
B	MET122
B	HIS125
B	ASN127
B	ARG142
B	VAL157
N	ASP304
N	ARG307
N	ILE339
N	PRO340
N	GLN341
N	SER342
N	ILE343
N	SER344
N	GLU345
B	HOH287
B	HOH295
N	HOH640
B	HOH313
N	HOH647
B	HOH322
N	HOH662
B	HOH364
N	HOH718

site_id	VEC
Number of Residues	29
Details	SITE "VEC" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS C AND O.

Chain	Residue
C	TYR79
C	VAL114
C	ASN115
C	ASN116
C	ALA117
C	ALA118
C	MET122
C	HIS125
C	ASN127
C	ARG142
C	VAL157
O	ASP304
O	ARG307
O	ILE339
O	PRO340
O	GLN341
O	SER342
O	ILE343
O	SER344
O	GLU345
C	HOH223
O	HOH634
C	HOH230
C	HOH235
O	HOH647
O	HOH649
O	HOH663
O	HOH679
O	HOH724

site_id	VED
Number of Residues	29
Details	SITE "VED" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS D AND P.

Chain	Residue
D	TYR79
D	VAL114
D	ASN115
D	ASN116
D	ALA117
D	ALA118
D	MET122
D	HIS125
D	ASN127
D	ARG142
D	VAL157
P	ASP304
P	ARG307
P	ILE339
P	PRO340
P	GLN341
P	SER342
P	ILE343
P	SER344
P	GLU345
D	HOH769
P	HOH638
D	HOH788
D	HOH795
P	HOH651
D	HOH804
P	HOH667
D	HOH846
P	HOH725

site_id	VEE
Number of Residues	29
Details	SITE "VEE" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS E AND Q.

Chain	Residue
E	TYR79
E	VAL114
E	ASN115
E	ASN116
E	ALA117
E	ALA118
E	MET122
E	HIS125
E	ASN127
E	ARG142
E	VAL157
Q	ASP304
Q	ARG307
Q	ILE339
Q	PRO340
Q	GLN341
Q	SER342
Q	ILE343
Q	SER344
Q	GLU345
E	HOH220
E	HOH223
E	HOH228
E	HOH233
Q	HOH1043
E	HOH236
Q	HOH1069
E	HOH246
E	HOH267

site_id	VEF
Number of Residues	29
Details	SITE "VEF" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS F AND R.

Chain	Residue
F	TYR79
F	VAL114
F	ASN115
F	ASN116
F	ALA117
F	ALA118
F	MET122
F	HIS125
F	ASN127
F	ARG142
F	VAL157
R	ASP304
R	ARG307
R	ILE339
R	PRO340
R	GLN341
R	SER342
R	ILE343
R	SER344
R	GLU345
F	HOH1251
F	HOH1259
R	HOH1270
F	HOH1277
R	HOH1284
F	HOH1286
R	HOH1310
F	HOH1328
R	HOH1396

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
M	VAL380-TYR408
A	LEU51-TYR79

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	24
Details	BINDING: BINDING => ECO:0000269\|PubMed:7990141

Chain	Residue	Details
M	ARG409
O	PRO448
O	ILE461
O	PHE463
P	ARG409
P	PRO448
P	ILE461
P	PHE463
Q	ARG409
Q	PRO448
Q	ILE461
M	PRO448
Q	PHE463
R	ARG409
R	PRO448
R	ILE461
R	PHE463
M	ILE461
M	PHE463
N	ARG409
N	PRO448
N	ILE461
N	PHE463
O	ARG409

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
M	ARG409	metal ligand
M	PRO448	metal ligand, proton shuttle (general acid/base)
M	PRO458	electrostatic stabiliser
M	ILE461	metal ligand
M	PHE463	metal ligand

site_id	MCSA2
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
N	ARG409	metal ligand
N	PRO448	metal ligand, proton shuttle (general acid/base)
N	PRO458	electrostatic stabiliser
N	ILE461	metal ligand
N	PHE463	metal ligand

site_id	MCSA3
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
O	ARG409	metal ligand
O	PRO448	metal ligand, proton shuttle (general acid/base)
O	PRO458	electrostatic stabiliser
O	ILE461	metal ligand
O	PHE463	metal ligand

site_id	MCSA4
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
P	ARG409	metal ligand
P	PRO448	metal ligand, proton shuttle (general acid/base)
P	PRO458	electrostatic stabiliser
P	ILE461	metal ligand
P	PHE463	metal ligand

site_id	MCSA5
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
Q	ARG409	metal ligand
Q	PRO448	metal ligand, proton shuttle (general acid/base)
Q	PRO458	electrostatic stabiliser
Q	ILE461	metal ligand
Q	PHE463	metal ligand

site_id	MCSA6
Number of Residues	5
Details	M-CSA 936

Chain	Residue	Details
R	ARG409	metal ligand
R	PRO448	metal ligand, proton shuttle (general acid/base)
R	PRO458	electrostatic stabiliser
R	ILE461	metal ligand
R	PHE463	metal ligand

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)