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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR INHIBITOR SELECTIVITY REVEALED BY CRYSTAL STRUCTURES OF PLANT AND MAMMALIAN 4-HYDROXYPHENYLPYRUVATE DIOXYGENASES

Authors :   C. Yang, J. W. Pflugrath, D. L. Camper, M. L. Foster, D. J. Pernich, T. A. Walsh

Date :   18 Mar 04 (Deposition) - 17 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A,B

Keywords :   Rat 4-Hydroxyphenylpyruvate Dioxygenase, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Yang, J. W. Pflugrath, D. L. Camper, M. L. Foster, D. J. Pernich, T. A. Walsh
Structural Basis For Herbicidal Inhibitor Selectivity Revealed By Comparison Of Crystal Structures Of Plant And Mammalian 4-Hydroxyphenylpyruvate Dioxygenases
Biochemistry V. 43 10414 2004
PubMed-ID: 15301540 | Reference-DOI: 10.1021/BI049323O
(for further references see the PDB file header)

Molecule 1 - 4-HYDROXYPHENYLPYRUVIC ACID DIOXYGENASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLAMID
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	869	2	Ligand/Ion	(1-TERT-BUTYL-5-HYDROXY-1H-PYRAZOL-4-YL)[6-(METHYLSULFONYL)-4'-METHOXY-2-METHYL-1,1'-BIPHENYL-3-YL]METHANONE
2	FE	4	Ligand/Ion	FE (III) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:183 , HIS A:266 , GLU A:349 , 869 A:1501 , HOH A:1552	BINDING SITE FOR RESIDUE FE A 1450
2	AC2	SOFTWARE	HIS A:280 , HOH A:1654 , HOH A:1655 , HOH A:1710 , HOH A:1712 , ASP B:315	BINDING SITE FOR RESIDUE FE A 1451
3	AC3	SOFTWARE	HIS B:183 , HIS B:266 , GLU B:349 , 869 B:1502 , HOH B:1531	BINDING SITE FOR RESIDUE FE B 1452
4	AC4	SOFTWARE	ASP A:315 , ARG B:279 , HIS B:280 , HOH B:1541 , HOH B:1648 , HOH B:1659 , HOH B:1660	BINDING SITE FOR RESIDUE FE B 1453
5	AC5	SOFTWARE	HIS A:183 , SER A:226 , PRO A:239 , ASN A:241 , GLN A:251 , HIS A:266 , PHE A:336 , PHE A:347 , GLU A:349 , PHE A:359 , ASN A:363 , PHE A:364 , FE A:1450 , HOH A:1552	BINDING SITE FOR RESIDUE 869 A 1501
6	AC6	SOFTWARE	HIS B:183 , SER B:226 , PRO B:239 , ASN B:241 , GLN B:251 , HIS B:266 , LEU B:289 , PHE B:336 , GLU B:349 , PHE B:359 , ASN B:363 , PHE B:364 , FE B:1452 , HOH B:1531 , HOH B:1737	BINDING SITE FOR RESIDUE 869 B 1502

(no "SS Bond" information available for 1SQI)

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

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	HPPD_RAT	18-149 180-338	4	A:18-149 B:18-149 A:180-338 B:180-338

Asymmetric/Biological Unit (11, 22)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000001809	1	ENSRNOE00000012523	chr12:34548316-34548427	112	HPPD_RAT	1-36	36	2	A:8-36 B:7-36	29 30
1.2	ENSRNOT00000001809	2	ENSRNOE00000012524	chr12:34548915-34548957	43	HPPD_RAT	37-51	15	2	A:37-51 B:37-51	15 15
1.3	ENSRNOT00000001809	3	ENSRNOE00000012525	chr12:34549104-34549186	83	HPPD_RAT	51-78	28	2	A:51-78 B:51-78	28 28
1.4	ENSRNOT00000001809	4	ENSRNOE00000012526	chr12:34550036-34550125	90	HPPD_RAT	79-108	30	2	A:79-108 B:79-108	30 30
1.5	ENSRNOT00000001809	5	ENSRNOE00000012527	chr12:34552154-34552257	104	HPPD_RAT	109-143	35	2	A:109-143 B:109-143	35 35
1.6	ENSRNOT00000001809	6	ENSRNOE00000012528	chr12:34552832-34552909	78	HPPD_RAT	143-169	27	2	A:143-169 B:143-169	27 27
1.7	ENSRNOT00000001809	7	ENSRNOE00000012529	chr12:34554235-34554397	163	HPPD_RAT	169-223	55	2	A:169-212 B:169-210	44 42
1.8	ENSRNOT00000001809	8	ENSRNOE00000012530	chr12:34554513-34554584	72	HPPD_RAT	224-247	24	2	A:224-244 B:224-244	21 21
1.9	ENSRNOT00000001809	9	ENSRNOE00000012531	chr12:34556118-34556240	123	HPPD_RAT	248-288	41	2	A:250-288 B:250-288	39 39
1.10	ENSRNOT00000001809	10	ENSRNOE00000012532	chr12:34557927-34558043	117	HPPD_RAT	289-327	39	2	A:289-327 B:289-327	39 39
1.11	ENSRNOT00000001809	11	ENSRNOE00000012533	chr12:34558119-34558387	269	HPPD_RAT	328-363	36	2	A:328-363 B:328-363	36 36

Asymmetric/Biological 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:343
 aligned with HPPD_RAT | P32755 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:359
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357         
             HPPD_RAT     8 GPKPERGRFLHFHSVTFWVGNAKQAASFYCNKMGFEPLAYKGLETGSREVVSHVIKQGKIVFVLCSALNPWNKEMGDHLVKHGDGVKDIAFEVEDCEHIVQKARERGAKIVREPWVEEDKFGKVKFAVLQTYGDTTHTLVEKINYTGRFLPGFEAPTYKDTLLPKLPSCNLEIIDHIVGNQPDQEMESASEWYLKNLQFHRFWSVDDTQVHTEYSSLRSIVVANYEESIKMPINEPAPGRKKSQIQEYVDYNGGAGVQHIALRTEDIITTIRHLRERGMEFLAVPSSYYRLLRENLKTSKIQVKENMDVLEELKILVDYDEKGYLLQIFTKPMQDRPTLFLEVIQRHNHQGFGAGNFNS 366
               SCOP domains d1sqia1 A:8-174 4-hydroxyphenylpyruvate dioxygenase, HppD                                                                                                              d1sqia2 A:175-366 4-hydroxyphenylpyruv           ate dioxygenase, HppD                                                                                                                           SCOP domains
               CATH domains 1sqiA01 A:8-174 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                        1sqiA02 A:175-366 2,3-Dihydroxybipheny           l 1,2-Dioxygenase, do     main 1                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..hhhhhhhhhhhhhh.eeeeeehhhhh...eeeeeeee..eeeeeeee....hhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhh..eeeeeeeeee..eeeeeeeee.....eeeeeeee..................hhhhh....eeeeeeeeee....hhhhhhhhhhhhhh.eee...-----------.eeeeee......eeeeee..-----hhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhh.eee.....eeeeee..........eeeeeeee.....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------VOC  PDB: A:18-149 UniProt: 18-149                                                                                                  ------------------------------VOC  PDB: A:180-338 UniProt: 180-338                                                                                                                           ---------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:8-36        Exon 1.2       ---------------------------Exon 1.4  PDB: A:79-108       Exon 1.5  PDB: A:109-143           -------------------------Exon 1.7  PDB: A:169-212 UniProt: 169-223 [INCOMPLETE] Exon 1.8  PDB: A:224-244Exon 1.9  PDB: A:250-288 UniProt: 248-288Exon 1.10  PDB: A:289-327              Exon 1.11  PDB: A:328-363           --- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: A:51-78      ----------------------------------------------------------------Exon 1.6  PDB: A:143-169   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1sqi A   8 GPKPERGRFLHFHSVTFWVGNAKQAASFYCNKMGFEPLAYKGLETGSREVVSHVIKQGKIVFVLCSALNPWNKEMGDHLVKHGDGVKDIAFEVEDCEHIVQKARERGAKIVREPWVEEDKFGKVKFAVLQTYGDTTHTLVEKINYTGRFLPGFEAPTYKDTLLPKLPSCNLEIIDHIVGNQPDQEMESASEWYLKNLQFHRFWSV-----------LRSIVVANYEESIKMPINEPA-----SQIQEYVDYNGGAGVQHIALRTEDIITTIRHLRERGMEFLAVPSSYYRLLRENLKTSKIQVKENMDVLEELKILVDYDEKGYLLQIFTKPMQDRPTLFLEVIQRHNHQGFGAGNFNS 366
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207    |    -      |227       237      |  -  |    257       267       277       287       297       307       317       327       337       347       357         
                                                                                                                                                                                                                                      212         224                 244   250

Chain B from PDB  Type:PROTEIN  Length:342
 aligned with HPPD_RAT | P32755 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:360
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366
             HPPD_RAT     7 KGPKPERGRFLHFHSVTFWVGNAKQAASFYCNKMGFEPLAYKGLETGSREVVSHVIKQGKIVFVLCSALNPWNKEMGDHLVKHGDGVKDIAFEVEDCEHIVQKARERGAKIVREPWVEEDKFGKVKFAVLQTYGDTTHTLVEKINYTGRFLPGFEAPTYKDTLLPKLPSCNLEIIDHIVGNQPDQEMESASEWYLKNLQFHRFWSVDDTQVHTEYSSLRSIVVANYEESIKMPINEPAPGRKKSQIQEYVDYNGGAGVQHIALRTEDIITTIRHLRERGMEFLAVPSSYYRLLRENLKTSKIQVKENMDVLEELKILVDYDEKGYLLQIFTKPMQDRPTLFLEVIQRHNHQGFGAGNFNS 366
               SCOP domains -d1sqib1 B:8-174 4-hydroxyphenylpyruvate dioxygenase, HppD                                                                                                              d1sqib2 B:175-366 4-hydroxyphenylpyr             uvate dioxygenase, Hp     pD                                                                                                                    SCOP domains
               CATH domains 1sqiB01 B:7-174 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                         1sqiB02 B:175-366 2,3-Dihydroxybiphe             nyl 1,2-Dioxygenase,      domain 1                                                                                                              CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-1sqiB01 B:180-335                                                                                                                                ------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-1sqiB02 B:180-335                                                                                                                                ------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-1sqiB03 B:180-335                                                                                                                                ------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-1sqiB04 B:180-335                                                                                                                                ------------------------------- Pfam domains (4)
         Sec.struct. author ........eeeeeeeeeee..hhhhhhhhhhhhhh.eeeeeehhhhh...eeeeeeee..eeeeeeee....hhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhh..eeeeeeeeee..eeeeeeeee.....eeeeeee...................hhhhh....eeeeeeeeee....hhhhhhhhhhhhhh.ee..-------------.eeeeee......eeeeee..-----hhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhh.eeee....eeeeee..........eeeeeeee.....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------VOC  PDB: B:18-149 UniProt: 18-149                                                                                                  ------------------------------VOC  PDB: B:180-338 UniProt: 180-338                                                                                                                           ---------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:7-36         Exon 1.2       ---------------------------Exon 1.4  PDB: B:79-108       Exon 1.5  PDB: B:109-143           -------------------------Exon 1.7  PDB: B:169-210 UniProt: 169-223 [INCOMPLETE] Exon 1.8  PDB: B:224-244Exon 1.9  PDB: B:250-288 UniProt: 248-288Exon 1.10  PDB: B:289-327              Exon 1.11  PDB: B:328-363           --- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3  PDB: B:51-78      ----------------------------------------------------------------Exon 1.6  PDB: B:143-169   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1sqi B   7 KGPKPERGRFLHFHSVTFWVGNAKQAASFYCNKMGFEPLAYKGLETGSREVVSHVIKQGKIVFVLCSALNPWNKEMGDHLVKHGDGVKDIAFEVEDCEHIVQKARERGAKIVREPWVEEDKFGKVKFAVLQTYGDTTHTLVEKINYTGRFLPGFEAPTYKDTLLPKLPSCNLEIIDHIVGNQPDQEMESASEWYLKNLQFHRFW-------------LRSIVVANYEESIKMPINEPA-----SQIQEYVDYNGGAGVQHIALRTEDIITTIRHLRERGMEFLAVPSSYYRLLRENLKTSKIQVKENMDVLEELKILVDYDEKGYLLQIFTKPMQDRPTLFLEVIQRHNHQGFGAGNFNS 366
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   |     -       226       236       | -   |   256       266       276       286       296       306       316       326       336       346       356       366
                                                                                                                                                                                                                                     210           224                 244   250

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (136)

Superfamily: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (136)

Family: Extradiol dioxygenases (43)

Protein domain: 4-hydroxyphenylpyruvate dioxygenase, HppD (9)

Norway rat (Rattus norvegicus) [TaxId: 10116] (1)

1a	d1sqia1	A:8-174
1b	d1sqia2	A:175-366
1c	d1sqib1	B:8-174
1d	d1sqib2	B:175-366

Asymmetric/Biological 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)

Norway rat (Rattus norvegicus) (1)

1a	1sqiA01	A:8-174
1b	1sqiB01	B:7-174
1c	1sqiB02	B:175-366
1d	1sqiA02	A:175-366

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyoxalase (58)

Family: Glyoxalase (34)

Rattus norvegicus (Rat) (1)

1a	Glyoxalase-1sqiB01	B:180-335
1b	Glyoxalase-1sqiB02	B:180-335
1c	Glyoxalase-1sqiB03	B:180-335
1d	Glyoxalase-1sqiB04	B:180-335

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HPPD_RAT | P32755)

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: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:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sqi)

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	1sqi
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	HPPD_RAT \| P32755
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1sqd	THE SAME PROTEIN FROM PLANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (11, 22)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (15, 15)

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