3HGS - JenaLib

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Title :   CRYSTAL STRUCTURE OF TOMATO OPR3 IN COMPLEX WITH PHB

Authors :   T. Clausen, C. Breithaupt

Date :   14 May 09 (Deposition) - 25 Aug 09 (Release) - 13 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Alpha Beta Barrel, Reductase, Complex, Flavoprotein, Enantioselectivity, Fatty Acid Biosynthesis, Fmn, Lipid Synthesis, Nadp, Oxidoreductase, Oxylipin Biosynthesis, Peroxisome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Breithaupt, R. Kurzbauer, F. Schaller, A. Stintzi, A. Schaller, R. Huber, P. Macheroux, T. Clausen
Structural Basis Of Substrate Specificity Of Plant 12-Oxophytodienoate Reductases.
J. Mol. Biol. V. 392 1266 2009
PubMed-ID: 19660473 | Reference-DOI: 10.1016/J.JMB.2009.07.087
(for further references see the PDB file header)

Molecule 1 - 12-OXOPHYTODIENOATE REDUCTASE 3
	Chains	:	A, B
	EC Number	:	1.3.1.42
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	OPR3
	Organism Common	:	TOMATO
	Organism Scientific	:	SOLANUM LYCOPERSICUM
	Organism Taxid	:	4081
	Synonym	:	12-OXOPHYTODIENOATE-10,11-REDUCTASE 3, OPDA- REDUCTASE 3, LEOPR3

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PHB	2	Ligand/Ion	P-HYDROXYBENZOIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PHB	1	Ligand/Ion	P-HYDROXYBENZOIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PHB	1	Ligand/Ion	P-HYDROXYBENZOIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:30 , PRO A:31 , MET A:32 , THR A:33 , GLY A:64 , GLN A:106 , HIS A:185 , HIS A:188 , ARG A:237 , THR A:280 , SER A:319 , GLY A:320 , GLY A:321 , GLY A:342 , ARG A:343 , PHE A:369 , TYR A:370 , PHB A:402 , HOH A:436 , HOH A:447 , HOH A:450	BINDING SITE FOR RESIDUE FMN A 401
2	AC2	SOFTWARE	THR A:33 , PHE A:74 , TRP A:108 , HIS A:185 , HIS A:188 , TYR A:190 , TYR A:370 , FMN A:401	BINDING SITE FOR RESIDUE PHB A 402
3	AC3	SOFTWARE	ALA B:30 , PRO B:31 , MET B:32 , THR B:33 , GLY B:64 , GLN B:106 , HIS B:185 , HIS B:188 , ARG B:237 , SER B:319 , GLY B:320 , GLY B:321 , GLY B:342 , ARG B:343 , PHE B:369 , TYR B:370 , PHB B:402 , HOH B:455 , HOH B:477 , HOH B:485	BINDING SITE FOR RESIDUE FMN B 401
4	AC4	SOFTWARE	PHE B:74 , TRP B:108 , HIS B:185 , HIS B:188 , TYR B:190 , TYR B:370 , FMN B:401	BINDING SITE FOR RESIDUE PHB B 402

(no "SS Bond" information available for 3HGS)

(no "Cis Peptide Bond" information available for 3HGS)

(no "SAP(SNP)/Variant" information available for 3HGS)

(no "PROSITE Motif" information available for 3HGS)

(no "Exon" information available for 3HGS)

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:368
 aligned with OPR3_SOLLC | Q9FEW9 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:376
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379      
           OPR3_SOLLC    10 NPLFSPYKMGKFNLSHRVVLAPMTRCRALNNIPQAALGEYYEQRATAGGFLITEGTMISPTSAGFPHVPGIFTKEQVREWKKIVDVVHAKGAVIFCQLWHVGRASHEVYQPAGAAPISSTEKPISNRWRILMPDGTHGIYPKPRAIGTYEISQVVEDYRRSALNAIEAGFDGIEIHGAHGYLIDQFLKDGINDRTDEYGGSLANRCKFITQVVQAVVSAIGADRVGVRVSPAIDHLDAMDSNPLSLGLAVVERLNKIQLHSGSKLAYLHVTQPRYVAYGQTEAGRLGSEEEEARLMRTLRNAYQGTFICSGGYTRELGIEAVAQGDADLVSYGRLFISNPDLVMRIKLNAPLNKYNRKTFYTQDPVVGYTDYPFLQ 385
               SCOP domains d3hgsa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3hgsA00 A:10-385 Aldolase class I                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee..eee...eee.......hhhhh.hhhhhhhhhhhh....eee...ee...............hhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhh..ee...........ee.....ee.....ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhhh....eeeee.........--------.hhhhhhhhhhhhhh...eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hgs A  10 NPLFSPYKMGKFNLSHRVVLAPMTRCRALNNIPQAALGEYYEQRATAGGFLITEGTMISPTSAGFPHVPGIFTKEQVREWKKIVDVVHAKGAVIFCQLWHVGRASHEVYQPAGAAPISSTEKPISNRWRILMPDGTHGIYPKPRAIGTYEISQVVEDYRRSALNAIEAGFDGIEIHGAHGYLIDQFLKDGINDRTDEYGGSLANRCKFITQVVQAVVSAIGADRVGVRVSPAIDHLDAMDSNPLSLGLAVVERLNKIQLHSGSKLAYLHVTQPRYVAYGQ--------EEEEARLMRTLRNAYQGTFICSGGYTRELGIEAVAQGDADLVSYGRLFISNPDLVMRIKLNAPLNKYNRKTFYTQDPVVGYTDYPFLQ 385
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379      
                                                                                                                                                                                                                                                                                                                 289      298

Chain B from PDB  Type:PROTEIN  Length:362
 aligned with OPR3_SOLLC | Q9FEW9 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:376
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379      
           OPR3_SOLLC    10 NPLFSPYKMGKFNLSHRVVLAPMTRCRALNNIPQAALGEYYEQRATAGGFLITEGTMISPTSAGFPHVPGIFTKEQVREWKKIVDVVHAKGAVIFCQLWHVGRASHEVYQPAGAAPISSTEKPISNRWRILMPDGTHGIYPKPRAIGTYEISQVVEDYRRSALNAIEAGFDGIEIHGAHGYLIDQFLKDGINDRTDEYGGSLANRCKFITQVVQAVVSAIGADRVGVRVSPAIDHLDAMDSNPLSLGLAVVERLNKIQLHSGSKLAYLHVTQPRYVAYGQTEAGRLGSEEEEARLMRTLRNAYQGTFICSGGYTRELGIEAVAQGDADLVSYGRLFISNPDLVMRIKLNAPLNKYNRKTFYTQDPVVGYTDYPFLQ 385
               SCOP domains d3hgsb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3hgsB00 B:10-385 Aldolase class I                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee..eee...eee.......hhhhh.hhhhhhhhhhhh....eeeeeeee...............hhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhh..ee...........ee.....ee.....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee..--------------..hhhhhhhhhhhhhh...eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hgs B  10 NPLFSPYKMGKFNLSHRVVLAPMTRCRALNNIPQAALGEYYEQRATAGGFLITEGTMISPTSAGFPHVPGIFTKEQVREWKKIVDVVHAKGAVIFCQLWHVGRASHEVYQPAGAAPISSTEKPISNRWRILMPDGTHGIYPKPRAIGTYEISQVVEDYRRSALNAIEAGFDGIEIHGAHGYLIDQFLKDGINDRTDEYGGSLANRCKFITQVVQAVVSAIGADRVGVRVSPAIDHLDAMDSNPLSLGLAVVERLNKIQLHSGSKLAYLHVTQP--------------SEEEEARLMRTLRNAYQGTFICSGGYTRELGIEAVAQGDADLVSYGRLFISNPDLVMRIKLNAPLNKYNRKTFYTQDPVVGYTDYPFLQ 385
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279  |      -       299       309       319       329       339       349       359       369       379      
                                                                                                                                                                                                                                                                                                          282            297

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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: FMN-linked oxidoreductases (290)

Family: FMN-linked oxidoreductases (242)

Protein domain: automated matches (40)

Solanum lycopersicum [TaxId: 4081] (5)

1a	d3hgsa_	A:
1b	d3hgsb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Tomato (Solanum lycopersicum) (3)

1a	3hgsB00	B:10-385
1b	3hgsA00	A:10-385

(no "Pfam Domain" information available for 3HGS)

Asymmetric Unit(hide GO term definitions)

Chain A,B (OPR3_SOLLC | Q9FEW9)

molecular function
	GO:0016629	12-oxophytodienoate reductase activity	Catalysis of the reaction: 8-[(1R,2R)-3-oxo-2-{(Z)-pent-2-en-1-yl}cyclopentyl]octanoate + NADP(+) = (15Z)-12-oxophyto-10,15-dienoate + H(+) + NADPH.
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0003959	NADPH dehydrogenase activity	Catalysis of the reaction: NADPH + H+ + acceptor = NADP+ + reduced acceptor.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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.
biological process
	GO:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0009695	jasmonic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of jasmonic acid, a fatty acid derivative.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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:0031408	oxylipin biosynthetic process	The chemical reactions and pathways resulting in the formation of any oxylipin, any of a group of biologically active compounds formed by oxidative metabolism of polyunsaturated fatty acids.
cellular component
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

Asymmetric Unit
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	3hgs
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	OPR3_SOLLC \| Q9FEW9	:	2hs6 2hs8 2hsa 3hgo

3hgo	CRYSTAL STRUCTURE OF THE F74Y/H244Y OPR3 DOUBLE MUTANT FROM TOMATO
3hgr	CRYSTAL STRUCTURE OF TOMATO OPR1 IN COMPLEX WITH PHB

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Ligands, Modified Residues, Ions (2, 4)

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