Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3ZDS

Structure of homogentisate 1,2-dioxygenase in complex with reaction intermediates of homogentisate with oxygen.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000976	molecular_function	transcription cis-regulatory region binding
A	0001217	molecular_function	DNA-binding transcription repressor activity
A	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
A	0005506	molecular_function	iron ion binding
A	0005737	cellular_component	cytoplasm
A	0006559	biological_process	L-phenylalanine catabolic process
A	0006570	biological_process	tyrosine metabolic process
A	0006572	biological_process	L-tyrosine catabolic process
A	0016491	molecular_function	oxidoreductase activity
A	0032993	cellular_component	protein-DNA complex
A	0045892	biological_process	negative regulation of DNA-templated transcription
A	0046872	molecular_function	metal ion binding
A	0051213	molecular_function	dioxygenase activity
B	0000976	molecular_function	transcription cis-regulatory region binding
B	0001217	molecular_function	DNA-binding transcription repressor activity
B	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
B	0005506	molecular_function	iron ion binding
B	0005737	cellular_component	cytoplasm
B	0006559	biological_process	L-phenylalanine catabolic process
B	0006570	biological_process	tyrosine metabolic process
B	0006572	biological_process	L-tyrosine catabolic process
B	0016491	molecular_function	oxidoreductase activity
B	0032993	cellular_component	protein-DNA complex
B	0045892	biological_process	negative regulation of DNA-templated transcription
B	0046872	molecular_function	metal ion binding
B	0051213	molecular_function	dioxygenase activity
C	0000976	molecular_function	transcription cis-regulatory region binding
C	0001217	molecular_function	DNA-binding transcription repressor activity
C	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
C	0005506	molecular_function	iron ion binding
C	0005737	cellular_component	cytoplasm
C	0006559	biological_process	L-phenylalanine catabolic process
C	0006570	biological_process	tyrosine metabolic process
C	0006572	biological_process	L-tyrosine catabolic process
C	0016491	molecular_function	oxidoreductase activity
C	0032993	cellular_component	protein-DNA complex
C	0045892	biological_process	negative regulation of DNA-templated transcription
C	0046872	molecular_function	metal ion binding
C	0051213	molecular_function	dioxygenase activity
D	0000976	molecular_function	transcription cis-regulatory region binding
D	0001217	molecular_function	DNA-binding transcription repressor activity
D	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
D	0005506	molecular_function	iron ion binding
D	0005737	cellular_component	cytoplasm
D	0006559	biological_process	L-phenylalanine catabolic process
D	0006570	biological_process	tyrosine metabolic process
D	0006572	biological_process	L-tyrosine catabolic process
D	0016491	molecular_function	oxidoreductase activity
D	0032993	cellular_component	protein-DNA complex
D	0045892	biological_process	negative regulation of DNA-templated transcription
D	0046872	molecular_function	metal ion binding
D	0051213	molecular_function	dioxygenase activity
E	0000976	molecular_function	transcription cis-regulatory region binding
E	0001217	molecular_function	DNA-binding transcription repressor activity
E	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
E	0005506	molecular_function	iron ion binding
E	0005737	cellular_component	cytoplasm
E	0006559	biological_process	L-phenylalanine catabolic process
E	0006570	biological_process	tyrosine metabolic process
E	0006572	biological_process	L-tyrosine catabolic process
E	0016491	molecular_function	oxidoreductase activity
E	0032993	cellular_component	protein-DNA complex
E	0045892	biological_process	negative regulation of DNA-templated transcription
E	0046872	molecular_function	metal ion binding
E	0051213	molecular_function	dioxygenase activity
F	0000976	molecular_function	transcription cis-regulatory region binding
F	0001217	molecular_function	DNA-binding transcription repressor activity
F	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
F	0005506	molecular_function	iron ion binding
F	0005737	cellular_component	cytoplasm
F	0006559	biological_process	L-phenylalanine catabolic process
F	0006570	biological_process	tyrosine metabolic process
F	0006572	biological_process	L-tyrosine catabolic process
F	0016491	molecular_function	oxidoreductase activity
F	0032993	cellular_component	protein-DNA complex
F	0045892	biological_process	negative regulation of DNA-templated transcription
F	0046872	molecular_function	metal ion binding
F	0051213	molecular_function	dioxygenase activity
G	0000976	molecular_function	transcription cis-regulatory region binding
G	0001217	molecular_function	DNA-binding transcription repressor activity
G	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
G	0005506	molecular_function	iron ion binding
G	0005737	cellular_component	cytoplasm
G	0006559	biological_process	L-phenylalanine catabolic process
G	0006570	biological_process	tyrosine metabolic process
G	0006572	biological_process	L-tyrosine catabolic process
G	0016491	molecular_function	oxidoreductase activity
G	0032993	cellular_component	protein-DNA complex
G	0045892	biological_process	negative regulation of DNA-templated transcription
G	0046872	molecular_function	metal ion binding
G	0051213	molecular_function	dioxygenase activity
H	0000976	molecular_function	transcription cis-regulatory region binding
H	0001217	molecular_function	DNA-binding transcription repressor activity
H	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
H	0005506	molecular_function	iron ion binding
H	0005737	cellular_component	cytoplasm
H	0006559	biological_process	L-phenylalanine catabolic process
H	0006570	biological_process	tyrosine metabolic process
H	0006572	biological_process	L-tyrosine catabolic process
H	0016491	molecular_function	oxidoreductase activity
H	0032993	cellular_component	protein-DNA complex
H	0045892	biological_process	negative regulation of DNA-templated transcription
H	0046872	molecular_function	metal ion binding
H	0051213	molecular_function	dioxygenase activity
I	0000976	molecular_function	transcription cis-regulatory region binding
I	0001217	molecular_function	DNA-binding transcription repressor activity
I	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
I	0005506	molecular_function	iron ion binding
I	0005737	cellular_component	cytoplasm
I	0006559	biological_process	L-phenylalanine catabolic process
I	0006570	biological_process	tyrosine metabolic process
I	0006572	biological_process	L-tyrosine catabolic process
I	0016491	molecular_function	oxidoreductase activity
I	0032993	cellular_component	protein-DNA complex
I	0045892	biological_process	negative regulation of DNA-templated transcription
I	0046872	molecular_function	metal ion binding
I	0051213	molecular_function	dioxygenase activity
J	0000976	molecular_function	transcription cis-regulatory region binding
J	0001217	molecular_function	DNA-binding transcription repressor activity
J	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
J	0005506	molecular_function	iron ion binding
J	0005737	cellular_component	cytoplasm
J	0006559	biological_process	L-phenylalanine catabolic process
J	0006570	biological_process	tyrosine metabolic process
J	0006572	biological_process	L-tyrosine catabolic process
J	0016491	molecular_function	oxidoreductase activity
J	0032993	cellular_component	protein-DNA complex
J	0045892	biological_process	negative regulation of DNA-templated transcription
J	0046872	molecular_function	metal ion binding
J	0051213	molecular_function	dioxygenase activity
K	0000976	molecular_function	transcription cis-regulatory region binding
K	0001217	molecular_function	DNA-binding transcription repressor activity
K	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
K	0005506	molecular_function	iron ion binding
K	0005737	cellular_component	cytoplasm
K	0006559	biological_process	L-phenylalanine catabolic process
K	0006570	biological_process	tyrosine metabolic process
K	0006572	biological_process	L-tyrosine catabolic process
K	0016491	molecular_function	oxidoreductase activity
K	0032993	cellular_component	protein-DNA complex
K	0045892	biological_process	negative regulation of DNA-templated transcription
K	0046872	molecular_function	metal ion binding
K	0051213	molecular_function	dioxygenase activity
L	0000976	molecular_function	transcription cis-regulatory region binding
L	0001217	molecular_function	DNA-binding transcription repressor activity
L	0004411	molecular_function	homogentisate 1,2-dioxygenase activity
L	0005506	molecular_function	iron ion binding
L	0005737	cellular_component	cytoplasm
L	0006559	biological_process	L-phenylalanine catabolic process
L	0006570	biological_process	tyrosine metabolic process
L	0006572	biological_process	L-tyrosine catabolic process
L	0016491	molecular_function	oxidoreductase activity
L	0032993	cellular_component	protein-DNA complex
L	0045892	biological_process	negative regulation of DNA-templated transcription
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 A 2000

Chain	Residue
A	HIS331
A	GLU337
A	HIS367
A	M8O2001
A	HOH3450

site_id	AC2
Number of Residues	16
Details	BINDING SITE FOR RESIDUE M8O A 2001

Chain	Residue
A	HIS331
A	GLU337
A	MET339
A	TYR346
A	HIS367
A	MET394
A	FE2000
A	HOH3419
A	HOH3450
A	HOH3458
A	HOH3470
A	HOH3481
A	HIS288
A	PRO291
A	PRO328
A	TRP329

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE B 2000

Chain	Residue
B	HIS331
B	GLU337
B	HIS367
B	OMD2001
B	HOH3421

site_id	AC4
Number of Residues	16
Details	BINDING SITE FOR RESIDUE OMD B 2001

Chain	Residue
B	HIS288
B	PRO291
B	PRO328
B	TRP329
B	HIS331
B	GLU337
B	MET339
B	TYR346
B	ALA348
B	HIS367
B	MET394
B	FE2000
B	HOH3419
B	HOH3429
B	HOH3442
B	HOH3455

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE OXY C 1999

Chain	Residue
A	PHE52
C	PRO291
C	HIS331
C	GLU337
C	MET394
C	FE2000
C	HQ92001
C	HOH3414

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE C 2000

Chain	Residue
C	HIS331
C	GLU337
C	HIS367
C	OXY1999
C	HQ92001

site_id	AC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE HQ9 C 2001

Chain	Residue
C	HIS288
C	PHE314
C	PRO328
C	TRP329
C	GLU337
C	MET339
C	TYR346
C	HIS367
C	MET394
C	OXY1999
C	FE2000
C	HOH3412
C	HOH3419
C	HOH3427
C	HOH3481

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE D 2000

Chain	Residue
D	HIS331
D	GLU337
D	HIS367
D	OMD2001
D	HOH3440

site_id	AC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE OMD D 2001

Chain	Residue
D	HIS288
D	PRO291
D	PRO328
D	TRP329
D	HIS331
D	GLU337
D	TYR346
D	HIS367
D	MET394
D	FE2000
D	HOH3405
D	HOH3438
D	HOH3448
D	HOH3463
D	HOH3473

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE E 2000

Chain	Residue
E	HIS331
E	GLU337
E	HIS367
E	OMD2001
E	HOH3390

site_id	BC2
Number of Residues	18
Details	BINDING SITE FOR RESIDUE OMD E 2001

Chain	Residue
E	HIS331
E	GLU337
E	TYR346
E	ALA348
E	HIS367
E	MET394
E	FE2000
E	HOH3387
E	HOH3390
E	HOH3399
E	HOH3409
E	HOH3412
E	HOH3497
E	HOH3498
E	HIS288
E	PRO291
E	PRO328
E	TRP329

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 E 2002

Chain	Residue
E	GLU77
E	ARG78
E	LEU79
E	HOH3323
E	HOH3328

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE FE F 2000

Chain	Residue
F	HIS331
F	GLU337
F	HIS367
F	HMQ2001

site_id	BC5
Number of Residues	18
Details	BINDING SITE FOR RESIDUE HMQ F 2001

Chain	Residue
F	HIS288
F	PRO291
F	PRO328
F	TRP329
F	HIS331
F	GLU337
F	TYR346
F	ALA348
F	HIS367
F	MET394
F	FE2000
F	HOH3397
F	HOH3405
F	HOH3406
F	HOH3412
F	HOH3414
F	HOH3415
F	HOH3422

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE G 2000

Chain	Residue
G	HIS331
G	GLU337
G	HIS367
G	OMD2001
G	HOH3362

site_id	BC7
Number of Residues	16
Details	BINDING SITE FOR RESIDUE OMD G 2001

Chain	Residue
G	HIS288
G	PRO291
G	PRO328
G	TRP329
G	HIS331
G	GLU337
G	TYR346
G	HIS367
G	MET394
G	FE2000
G	HOH3339
G	HOH3361
G	HOH3362
G	HOH3368
G	HOH3383
G	HOH3384

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE H 2000

Chain	Residue
H	HIS331
H	GLU337
H	HIS367
H	OMD2001
H	HOH3386

site_id	BC9
Number of Residues	16
Details	BINDING SITE FOR RESIDUE OMD H 2001

Chain	Residue
H	HIS288
H	PRO291
H	PRO328
H	TRP329
H	HIS331
H	GLU337
H	MET339
H	TYR346
H	ALA348
H	HIS367
H	MET394
H	FE2000
H	HOH3384
H	HOH3386
H	HOH3395
H	HOH3416

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE I 2000

Chain	Residue
I	HIS331
I	GLU337
I	HIS367
I	OMD2001
I	HOH3318

site_id	CC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE OMD I 2001

Chain	Residue
I	HIS288
I	PRO291
I	PRO328
I	TRP329
I	HIS331
I	GLU337
I	MET339
I	TYR346
I	ALA348
I	HIS367
I	MET394
I	FE2000
I	HOH3284
I	HOH3316
I	HOH3318
I	HOH3328
I	HOH3343

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE J 2000

Chain	Residue
J	HIS331
J	GLU337
J	HIS367
J	OMD2001
J	HOH3402

site_id	CC4
Number of Residues	18
Details	BINDING SITE FOR RESIDUE OMD J 2001

Chain	Residue
J	HIS288
J	PRO291
J	PRO328
J	TRP329
J	HIS331
J	GLU337
J	MET339
J	TYR346
J	ALA348
J	HIS367
J	MET394
J	FE2000
J	HOH3401
J	HOH3402
J	HOH3410
J	HOH3417
J	HOH3421
J	HOH3426

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FE K 2000

Chain	Residue
K	HIS331
K	GLU337
K	HIS367
K	OMD2001
K	HOH3323

site_id	CC6
Number of Residues	16
Details	BINDING SITE FOR RESIDUE OMD K 2001

Chain	Residue
K	HIS288
K	PRO291
K	PHE314
K	PRO328
K	TRP329
K	HIS331
K	GLU337
K	MET339
K	TYR346
K	HIS367
K	MET394
K	FE2000
K	HOH3322
K	HOH3323
K	HOH3331
K	HOH3400

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE FE L 2000

Chain	Residue
L	HIS331
L	GLU337
L	HIS367
L	HMQ2001

site_id	CC8
Number of Residues	17
Details	BINDING SITE FOR RESIDUE HMQ L 2001

Chain	Residue
L	HIS288
L	PRO291
L	PHE314
L	PRO328
L	TRP329
L	HIS331
L	GLU337
L	MET339
L	TYR346
L	HIS367
L	MET394
L	FE2000
L	HOH3338
L	HOH3346
L	HOH3347
L	HOH3356
L	HOH3405

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_00334","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23858455","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	24
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00334","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23858455","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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