1SP9 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   4-HYDROXYPHENYLPYRUVATE DIOXYGENASE

Authors :   I. M. Fritze, L. Linden, J. Freigang, G. Auerbach, R. Huber, S. Steinbacher

Date :   16 Mar 04 (Deposition) - 21 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. M. Fritze, L. Linden, J. Freigang, G. Auerbach, R. Huber, S. Steinbacher
The Crystal Structures Of Zea Mays And Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase
Plant Physiol. V. 134 1388 2004
PubMed-ID: 15084729 | Reference-DOI: 10.1104/PP.103.034082
(for further references see the PDB file header)

Molecule 1 - 4-HYDROXYPHENYLPYRUVATE DIOXYGENASE
	Chains	:	A, B
	EC Number	:	1.13.11.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B
	Expression System Taxid	:	562
	Expression System Vector	:	PLASMID
	Gene	:	HPD, AT1G06570, F12K11.9
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	4HPPD, HPD, HPPDASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FE2	2	Ligand/Ion	FE (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FE2	1	Ligand/Ion	FE (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FE2	1	Ligand/Ion	FE (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:226 , HIS A:308 , GLU A:394	BINDING SITE FOR RESIDUE FE2 A 446
2	AC2	SOFTWARE	HIS B:226 , HIS B:308 , GLU B:394	BINDING SITE FOR RESIDUE FE2 B 446

Asymmetric Unit

No.	Residues
1	A:401	-	A:416
2	B:401	-	B:416

(no "Cis Peptide Bond" information available for 1SP9)

(no "SAP(SNP)/Variant" information available for 1SP9)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	HPPD_ARATH	46-192 223-383	4	A:46-192 B:46-192 A:223-383 B:223-383

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	HPPD_ARATH	46-192 223-383	2	A:46-192 - A:223-383 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	HPPD_ARATH	46-192 223-383	2	- B:46-192 - B:223-383

(no "Exon" information available for 1SP9)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:362
 aligned with HPPD_ARATH | P93836 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:396
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422      
           HPPD_ARATH    33 VRKNPKSDKFKVKRFHHIEFWCGDATNVARRFSWGLGMRFSAKSDLSTGNMVHASYLLTSGDLRFLFTAPYSPSLSAGEIKPTTTASIPSFDHGSCRSFFSSHGLGVRAVAIEVEDAESAFSISVANGAIPSSPPIVLNEAVTIAEVKLYGDVVLRYVSYKAEDTEKSEFLPGFERVEDASSFPLDYGIRRLDHAVGNVPELGPALTYVAGFTGFHQFAEFTADDVGTAESGLNSAVLASNDEMVLLPINEPVHGTKRKSQIQTYLEHNEGAGLQHLALMSEDIFRTLREMRKRSSIGGFDFMPSPPPTYYQNLKKRVGDVLSDDQIKECEELGILVDRDDQGTLLQIFTKPLGDRPTIFIEIIQRVGCMMKDEEGKAYQSGGCGGFGKGNFSELF 428
               SCOP domains d1sp9a1 A:33-232 4-hydroxyphenylpyruvate dioxygenase, HppD                                                                                                                                              d1sp9a2 A:233-428 4           -hydroxyphenylpyruvate dioxygenase, HppD                                                                                                                               SCOP domains
               CATH domains 1sp9A01 A:33-218 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                                          1sp9A02 A:219-428 2,3-Dihydroxybi           phenyl 1,2-Dioxygenase, domain 1                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeeee..hhhhhhhhhhhhh..eeeee.........eeeeeeee..eeeeeeee....----------.......hhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh...eeeeeeee...eeeeeeeee..eeeeeee..--------.....ee..-----.....eeeeeeeeee..hhhhhhhhhhhhhh.ee..-----------..eeeeeee......eeeeeee.......hhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhh......hhhhhhhhhhhh.eeee...eeeeeeeeee.......eeeeeeeee.ee.......ee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------VOC  PDB: A:46-192 UniProt: 46-192                                                                                                                 ------------------------------VOC  PDB: A:223-383 UniProt: 223-383                                                                                                                             --------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sp9 A  33 VRKNPKSDKFKVKRFHHIEFWCGDATNVARRFSWGLGMRFSAKSDLSTGNMVHASYLLTSGDLRFLFTAPYSPS----------TASIPSFDHGSCRSFFSSHGLGVRAVAIEVEDAESAFSISVANGAIPSSPPIVLNEAVTIAEVKLYGDVVLRYVSYK--------FLPGFERVE-----PLDYGIRRLDHAVGNVPELGPALTYVAGFTGFHQFA-----------SGLNSAVLASNDEMVLLPINEPVHGTKRKSQIQTYLEHNEGAGLQHLALMSEDIFRTLREMRKRSSIGGFDFMPSPPPTYYQNLKKRVGDVLSDDQIKECEELGILVDRDDQGTLLQIFTKPLGDRPTIFIEIIQRVGCMMKDEEGKAYQSGGCGGFGKGNFSELF 428
                                    42        52        62        72        82        92       102   |     -    |  122       132       142       152       162       172       182       192|      202       | -   |   222       232       242        |-         -|      272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422      
                                                                                                   106        117                                                                         193      202     210   216                                251         263

Chain B from PDB  Type:PROTEIN  Length:374
 aligned with HPPD_ARATH | P93836 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:405
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432     
           HPPD_ARATH    33 VRKNPKSDKFKVKRFHHIEFWCGDATNVARRFSWGLGMRFSAKSDLSTGNMVHASYLLTSGDLRFLFTAPYSPSLSAGEIKPTTTASIPSFDHGSCRSFFSSHGLGVRAVAIEVEDAESAFSISVANGAIPSSPPIVLNEAVTIAEVKLYGDVVLRYVSYKAEDTEKSEFLPGFERVEDASSFPLDYGIRRLDHAVGNVPELGPALTYVAGFTGFHQFAEFTADDVGTAESGLNSAVLASNDEMVLLPINEPVHGTKRKSQIQTYLEHNEGAGLQHLALMSEDIFRTLREMRKRSSIGGFDFMPSPPPTYYQNLKKRVGDVLSDDQIKECEELGILVDRDDQGTLLQIFTKPLGDRPTIFIEIIQRVGCMMKDEEGKAYQSGGCGGFGKGNFSELFKSIEEYEKT 437
               SCOP domains d1sp9b1 B:33-193 4-hydroxyphenylpyruvate dioxygenase, HppD                                                                                                               d1sp9b2 B     :202-437 4-hydroxyphenylpyruvate dioxyg        enase, HppD                                                                                                                                                                     SCOP domains
               CATH domains 1sp9B01 B:33-218 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                                          1sp9B02 B:219-437 2,3-Dihydroxybiphe        nyl 1,2-Dioxygenase, domain 1                                                                                                                                                   CATH domains
           Pfam domains (1) --------------------------------------------------------------------------          -----------------------------------------------------------------------------        ---------     -------Glyoxalase-1sp9B01 B:223-380                                                                                                                                  --------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------          -----------------------------------------------------------------------------        ---------     -------Glyoxalase-1sp9B02 B:223-380                                                                                                                                  --------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...........eeeeeeeeee..hhhhhhhhhhhhhh.eeeeeehhhhh...eeeeeeee..eeeeeeee....----------.......hhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhh...eeeeeeee...eeeeeee.....eeeeee..--------.....ee..-----.....eeeeeeeeee..hhhhhhhhhhhhhh.eee....--------..eeeeeee......eeeeeee.......hhhhhhhhhh...eeeeeeeee.hhhhhhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhh...eeee....eeeeeee.........eeeeeeee..eee.....eee.........hhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------VOC  PDB: B:46-192 UniProt: 46-192                                                                                                                 ------------------------------VOC  PDB: B:223-383 UniProt: 223-383                                                                                                                             ------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sp9 B  33 VRKNPKSDKFKVKRFHHIEFWCGDATNVARRFSWGLGMRFSAKSDLSTGNMVHASYLLTSGDLRFLFTAPYSPS----------TASIPSFDHGSCRSFFSSHGLGVRAVAIEVEDAESAFSISVANGAIPSSPPIVLNEAVTIAEVKLYGDVVLRYVSYK--------FLPGFERVE-----PLDYGIRRLDHAVGNVPELGPALTYVAGFTGFHQFAEFT--------SGLNSAVLASNDEMVLLPINEPVHGTKRKSQIQTYLEHNEGAGLQHLALMSEDIFRTLREMRKRSSIGGFDFMPSPPPTYYQNLKKRVGDVLSDDQIKECEELGILVDRDDQGTLLQIFTKPLGDRPTIFIEIIQRVGCMMKDEEGKAYQSGGCGGFGKGNFSELFKSIEEYEKT 437
                                    42        52        62        72        82        92       102   |     -    |  122       132       142       152       162       172       182       192|      202       | -   |   222       232       242       252 |       -|      272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432     
                                                                                                   106        117                                                                         193      202     210   216                                   254      263

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 (113)

Homologous Superfamily: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 (106)

Thale cress (Arabidopsis thaliana) (4)

1a	1sp9A01	A:33-218
1b	1sp9B01	B:33-218
1c	1sp9A02	A:219-428
1d	1sp9B02	B:219-437

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyoxalase (58)

Family: Glyoxalase (34)

Arabidopsis thaliana (Mouse-ear cress) (3)

1a	Glyoxalase-1sp9B01	B:223-380
1b	Glyoxalase-1sp9B02	B:223-380

Asymmetric Unit(hide GO term definitions)

Chain A,B (HPPD_ARATH | P93836)

molecular function
	GO:0003868	4-hydroxyphenylpyruvate dioxygenase activity	Catalysis of the reaction: 4-hydroxyphenylpyruvate + O2 = homogentisate + CO2.
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016701	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and molecular oxygen is incorporated into a donor.
biological process
	GO:0006559	L-phenylalanine catabolic process	The chemical reactions and pathways resulting in the breakdown of phenylalanine, 2-amino-3-phenylpropanoic acid.
	GO:0009072	aromatic amino acid family metabolic process	The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006572	tyrosine catabolic process	The chemical reactions and pathways resulting in the breakdown of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	1sp9
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	1.13.11.27
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	HPPD_ARATH \| P93836	:	1sqd 1tfz 1tg5 5cto 5dhw

1sp8	4-HYDROXYPHENYLPYRUVATE DIOXYGENASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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