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(-) Description

Title :  12-0XO-PHYTODIENOATE REDUCTASE ISOFORM 3
 
Authors :  G. N. Phillips Jr. , K. A. Johnson, C. A. Bingman, D. W. Smith, Center For Eukaryotic Structural Genomics (Cesg)
Date :  01 Aug 03  (Deposition) - 25 Nov 03  (Release) - 24 Feb 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 :  Flavoprotein, Flavoenzyme, Oxidoreductase; Xenobiotic Reductase; Old Yellow Enzyme; Secondary Messenger, Structural Genomics, Psi, Protein Structure Initiative, Center For Eukaryotic Structural Genomics, Cesg (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. E. Malone, S. E. Madson, R. L. Wrobel, W. B. Jeon, N. S. Rosenberg, K. A. Johnson, C. A. Bingman, D. W. Smith, G. N. Phillips Jr. , J. L. Markley, B. G. Fox
X-Ray Structure Of Arabidopsis At2G06050, 12-Oxophytodienoate Reductase Isoform 3
Proteins V. 58 243 2005
PubMed-ID: 15468319  |  Reference-DOI: 10.1002/PROT.20162
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 12-OXOPHYTODIENOATE-10,11-REDUCTASE
    ChainsA, B
    EC Number1.3.1.42
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPVP13
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAT2G06050
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Synonym12-0XO-PHYTODIENOATE REDUCTASE ISOFORM 3

 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:186 , HIS A:189 , ARG A:238 , SER A:320 , GLY A:321 , GLY A:322 , TYR A:342 , GLY A:343 , ARG A:344 , TYR A:371 , HOH A:570 , HOH A:571 , HOH A:607BINDING SITE FOR RESIDUE FMN A 7401
2AC2SOFTWAREALA B:30 , PRO B:31 , MET B:32 , THR B:33 , GLY B:64 , GLN B:106 , HIS B:186 , HIS B:189 , ARG B:238 , SER B:320 , GLY B:321 , GLY B:322 , TYR B:342 , GLY B:343 , ARG B:344 , PHE B:370 , TYR B:371 , HOH B:529 , HOH B:532 , HOH B:702 , HOH B:791BINDING SITE FOR RESIDUE FMN B 9401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q45)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q45)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q45)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q45)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q45)

(-) 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:365
 aligned with OPR3_ARATH | Q9FUP0 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:380
                                    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       367       377       387
           OPR3_ARATH     8 SNETLFSSYKMGRFDLSHRVVLAPMTRCRALNGVPNAALAEYYAQRTTPGGFLISEGTMVSPGSAGFPHVPGIYSDEQVEAWKQVVEAVHAKGGFIFCQLWHVGRASHAVYQPNGGSPISSTNKPISENRWRVLLPDGSHVKYPKPRALEASEIPRVVEDYCLSALNAIRAGFDGIEIHGAHGYLIDQFLKDGINDRTDQYGGSIANRCRFLKQVVEGVVSAIGASKVGVRVSPAIDHLDATDSDPLSLGLAVVGMLNKLQGVNGSKLAYLHVTQPRYHAYGQTESGRQGSDEEEAKLMKSLRMAYNGTFMSSGGFNKELGMQAVQQGDADLVSYGRLFIANPDLVSRFKIDGELNKYNRKTFYTQDPVVGYTDYPFLAP 387
               SCOP domains d1q45a_ A: 12-oxophytodienoate reductase (OPR, OYE homolog)                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1q45A00 A:8-387 Aldolase class I                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eee...eee.......hhhhh.hhhhhhhhhhh.....eeeeeeee...............hhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhh..ee............ee.....ee.....ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhh...hhhhhhhhhhhhhhhhhhh......eeeee...---------------hhhhhhhhhhhhhh...eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhh.......hhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q45 A   8 SNETLFSSYKMGRFDLSHRVVLAPMTRCRALNGVPNAALAEYYAQRTTPGGFLISEGTMVSPGSAGFPHVPGIYSDEQVEAWKQVVEAVHAKGGFIFCQLWHVGRASHAVYQPNGGSPISSTNKPISENRWRVLLPDGSHVKYPKPRALEASEIPRVVEDYCLSALNAIRAGFDGIEIHGAHGYLIDQFLKDGINDRTDQYGGSIANRCRFLKQVVEGVVSAIGASKVGVRVSPAIDHLDATDSDPLSLGLAVVGMLNKLQGVNGSKLAYLHVTQPR---------------EEEAKLMKSLRMAYNGTFMSSGGFNKELGMQAVQQGDADLVSYGRLFIANPDLVSRFKIDGELNKYNRKTFYTQDPVVGYTDYPFLAP 387
                                    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      |  -         -  |    307       317       327       337       347       357       367       377       387
                                                                                                                                                                                                                                                                                                              284             300                                                                                       

Chain B from PDB  Type:PROTEIN  Length:367
 aligned with OPR3_ARATH | Q9FUP0 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:377
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       
           OPR3_ARATH     9 NETLFSSYKMGRFDLSHRVVLAPMTRCRALNGVPNAALAEYYAQRTTPGGFLISEGTMVSPGSAGFPHVPGIYSDEQVEAWKQVVEAVHAKGGFIFCQLWHVGRASHAVYQPNGGSPISSTNKPISENRWRVLLPDGSHVKYPKPRALEASEIPRVVEDYCLSALNAIRAGFDGIEIHGAHGYLIDQFLKDGINDRTDQYGGSIANRCRFLKQVVEGVVSAIGASKVGVRVSPAIDHLDATDSDPLSLGLAVVGMLNKLQGVNGSKLAYLHVTQPRYHAYGQTESGRQGSDEEEAKLMKSLRMAYNGTFMSSGGFNKELGMQAVQQGDADLVSYGRLFIANPDLVSRFKIDGELNKYNRKTFYTQDPVVGYTDYPFL 385
               SCOP domains d1q45b_ B: 12-oxophytodienoate reductase (OPR, OYE homolog)                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1q45B00 B:9-385 Aldolase class I                                                                                                                                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) --Oxidored_FMN-1q45B01 B:11-363                                                                                                                                                                                                                                                                                                                                    ---------------------- Pfam domains (1)
           Pfam domains (2) --Oxidored_FMN-1q45B02 B:11-363                                                                                                                                                                                                                                                                                                                                    ---------------------- Pfam domains (2)
         Sec.struct. author .......eee..eee...eee.......hhhhh.hhhhhhhhhhh.....eeeeeeee...............hhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhh..ee............ee.....ee.....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee.......----------hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhh.......hhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q45 B   9 NETLFSSYKMGRFDLSHRVVLAPMTRCRALNGVPNAALAEYYAQRTTPGGFLISEGTMVSPGSAGFPHVPGIYSDEQVEAWKQVVEAVHAKGGFIFCQLWHVGRASHAVYQPNGGSPISSTNKPISENRWRVLLPDGSHVKYPKPRALEASEIPRVVEDYCLSALNAIRAGFDGIEIHGAHGYLIDQFLKDGINDRTDQYGGSIANRCRFLKQVVEGVVSAIGASKVGVRVSPAIDHLDATDSDPLSLGLAVVGMLNKLQGVNGSKLAYLHVTQPRYHAY----------DEEEAKLMKSLRMAYNGTFMSSGGFNKELGMQAVQQGDADLVSYGRLFIANPDLVSRFKIDGELNKYNRKTFYTQDPVVGYTDYPFL 385
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288         -|      308       318       328       338       348       358       368       378       
                                                                                                                                                                                                                                                                                                                 288        299                                                                                      

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (OPR3_ARATH | Q9FUP0)
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.
    GO:0009620    response to fungus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a fungus.
    GO:0010193    response to ozone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ozone stimulus.
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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        OPR3_ARATH | Q9FUP02g5w 2q3o

(-) Related Entries Specified in the PDB File

1q44 RELATED ID: GO.8210 RELATED DB: TARGETDB