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(-) Description

Title :  CRYSTAL STRUCTURE OF THE F74Y/H244Y OPR3 DOUBLE MUTANT FROM TOMATO
 
Authors :  T. Clausen, C. Breithaupt
Date :  14 May 09  (Deposition) - 25 Aug 09  (Release) - 13 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
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)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA 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 , HOH A:410 , HOH A:431 , HOH A:516 , HOH A:602BINDING SITE FOR RESIDUE FMN A 401
2AC2SOFTWAREALA 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 , THR B:280 , SER B:319 , GLY B:320 , GLY B:321 , TYR B:341 , GLY B:342 , ARG B:343 , PHE B:369 , TYR B:370 , HOH B:406 , HOH B:421 , HOH B:455 , HOH B:572BINDING SITE FOR RESIDUE FMN B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HGO)

(-) Sequences/Alignments

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:367
 aligned with OPR3_SOLLC | Q9FEW9 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:378
                                    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       376        
           OPR3_SOLLC     7 DGNNPLFSPYKMGKFNLSHRVVLAPMTRCRALNNIPQAALGEYYEQRATAGGFLITEGTMISPTSAGFPHVPGIFTKEQVREWKKIVDVVHAKGAVIFCQLWHVGRASHEVYQPAGAAPISSTEKPISNRWRILMPDGTHGIYPKPRAIGTYEISQVVEDYRRSALNAIEAGFDGIEIHGAHGYLIDQFLKDGINDRTDEYGGSLANRCKFITQVVQAVVSAIGADRVGVRVSPAIDHLDAMDSNPLSLGLAVVERLNKIQLHSGSKLAYLHVTQPRYVAYGQTEAGRLGSEEEEARLMRTLRNAYQGTFICSGGYTRELGIEAVAQGDADLVSYGRLFISNPDLVMRIKLNAPLNKYNRKTFYTQDPVVGYTDYPFL 384
               SCOP domains d3hgoa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3hgoA00 A:7-384 Aldolase class I                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.eee..eee...eee.......hhhhh.hhhhhhhhhhhh....eeeeeee................hhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhh..ee..........eee.....eee....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee...-----------hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hgo A   7 DGNNPLFSPYKMGKFNLSHRVVLAPMTRCRALNNIPQAALGEYYEQRATAGGFLITEGTMISPTSAGYPHVPGIFTKEQVREWKKIVDVVHAKGAVIFCQLWHVGRASHEVYQPAGAAPISSTEKPISNRWRILMPDGTHGIYPKPRAIGTYEISQVVEDYRRSALNAIEAGFDGIEIHGAHGYLIDQFLKDGINDRTDEYGGSLANRCKFITQVVQAVVSAIGADRVGVRVSPAIDYLDAMDSNPLSLGLAVVERLNKIQLHSGSKLAYLHVTQPR-----------LGSEEEEARLMRTLRNAYQGTFICSGGYTRELGIEAVAQGDADLVSYGRLFISNPDLVMRIKLNAPLNKYNRKTFYTQDPVVGYTDYPFL 384
                                    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      |  -       296       306       316       326       336       346       356       366       376        
                                                                                                                                                                                                                                                                                                              283         295                                                                                         


Chain B from PDB  Type:PROTEIN  Length:363
 aligned with OPR3_SOLLC | Q9FEW9 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:374
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380    
           OPR3_SOLLC    11 PLFSPYKMGKFNLSHRVVLAPMTRCRALNNIPQAALGEYYEQRATAGGFLITEGTMISPTSAGFPHVPGIFTKEQVREWKKIVDVVHAKGAVIFCQLWHVGRASHEVYQPAGAAPISSTEKPISNRWRILMPDGTHGIYPKPRAIGTYEISQVVEDYRRSALNAIEAGFDGIEIHGAHGYLIDQFLKDGINDRTDEYGGSLANRCKFITQVVQAVVSAIGADRVGVRVSPAIDHLDAMDSNPLSLGLAVVERLNKIQLHSGSKLAYLHVTQPRYVAYGQTEAGRLGSEEEEARLMRTLRNAYQGTFICSGGYTRELGIEAVAQGDADLVSYGRLFISNPDLVMRIKLNAPLNKYNRKTFYTQDPVVGYTDYPFL 384
               SCOP domains d3hgob_ B: automated matches                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3hgoB00 B:11-384 Aldolase class I                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee...eee.......hhhhh.hhhhhhhhhhhh....eee...ee...............hhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhh..ee..........eee.....eee....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhh...hhhhhhhhhhhhhhhhhhhh.....eeeee...-----------hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hgo B  11 PLFSPYKMGKFNLSHRVVLAPMTRCRALNNIPQAALGEYYEQRATAGGFLITEGTMISPTSAGYPHVPGIFTKEQVREWKKIVDVVHAKGAVIFCQLWHVGRASHEVYQPAGAAPISSTEKPISNRWRILMPDGTHGIYPKPRAIGTYEISQVVEDYRRSALNAIEAGFDGIEIHGAHGYLIDQFLKDGINDRTDEYGGSLANRCKFITQVVQAVVSAIGADRVGVRVSPAIDYLDAMDSNPLSLGLAVVERLNKIQLHSGSKLAYLHVTQPR-----------LGSEEEEARLMRTLRNAYQGTFICSGGYTRELGIEAVAQGDADLVSYGRLFISNPDLVMRIKLNAPLNKYNRKTFYTQDPVVGYTDYPFL 384
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  |      -    |  300       310       320       330       340       350       360       370       380    
                                                                                                                                                                                                                                                                                                          283         295
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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.

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 Related Entries

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        OPR3_SOLLC | Q9FEW9: 2hs6 2hs8 2hsa 3hgs

(-) Related Entries Specified in the PDB File

3hgr CRYSTAL STRUCTURE OF TOMATO OPR1 IN COMPLEX WITH PHB
3hgs CRYSTAL STRUCTURE OF TOMATO OPR3 IN COMPLEX WITH PHB