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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ALLENE OXIDE CYCLASE 2 WITH BOUND INHIBITOR VERNOLIC ACID
 
Authors :  E. Hofmann, F. Schaller, P. Zerbe
Date :  30 Mar 06  (Deposition) - 21 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Beta Barrel, Inhibitor Complex, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Hofmann, P. Zerbe, F. Schaller
The Crystal Structure Of Arabidopsis Thaliana Allene Oxide Cyclase: Insights Into The Oxylipin Cyclization Reaction
Plant Cell V. 18 3201 2006
PubMed-ID: 17085685  |  Reference-DOI: 10.1105/TPC.106.043984

(-) Compounds

Molecule 1 - ALLENE OXIDE CYCLASE 2
    Chains: A, B, C
    EC Number: 5.3.99.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ALLENE OXIDE CYCLASE 2
    Gene: AT3G25770
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1EOD1Ligand/Ion11-[(2R,3S)-3-PENTYLOXIRAN-2-YL]UNDECANOIC ACID
2GOL5Ligand/IonGLYCEROL
3MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:23 , PRO B:32 , VAL B:49 , PHE B:51 , ASN B:53 , PHE B:85 , TYR B:89 , TYR B:105 , TYR B:136 , TYR B:142 , HOH B:530BINDING SITE FOR RESIDUE EOD B 401
2AC2SOFTWAREASN A:37 , ASN B:37 , LEU C:35 , ASN C:37 , HOH C:565 , HOH C:569 , HOH C:573BINDING SITE FOR RESIDUE GOL C 501
3AC3SOFTWAREASP B:28 , ARG B:29 , LYS B:54 , ASN B:188 , HOH B:602BINDING SITE FOR RESIDUE GOL B 502
4AC4SOFTWAREASP A:28 , ARG A:29 , LYS A:54 , ASN A:188BINDING SITE FOR RESIDUE GOL A 503
5AC5SOFTWAREGLU A:75 , HIS A:76 , PRO A:78 , GLU A:79 , HOH A:609 , HOH A:619 , ARG C:29 , ASN C:188 , GOL C:505BINDING SITE FOR RESIDUE GOL A 504
6AC6SOFTWAREGOL A:504 , ASP C:28 , ARG C:29 , LYS C:54 , ASN C:188 , HOH C:608BINDING SITE FOR RESIDUE GOL C 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DIO)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser A:31 -Pro A:32
2Tyr A:136 -Pro A:137
3Ser B:31 -Pro B:32
4Tyr B:136 -Pro B:137
5Ser C:31 -Pro C:32
6Tyr C:136 -Pro C:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DIO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DIO)

(-) Exons   (0, 0)

(no "Exon" information available for 2DIO)

(-) Sequences/Alignments

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:174
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:174
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
           AOC2_ARATH    80 KVQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2dioa_ A: Allene oxide cyclase, AOC                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.......................eeee..eeee.....eeeeeeeeeeeeeeehhhheeeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeeee......hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dio A  15 KVQELSVYEINELDRHSPKILKNAFSLmFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    24        34       |44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
                                                      42-MSE                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:174
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
           AOC2_ARATH    80 KVQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2diob_ B: Allene oxide cyclase, AOC                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.......................eeee..eeee.....eeeeeeeeeeeeeeehhhheeeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeeee......hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dio B  15 KVQELSVYEINELDRHSPKILKNAFSLmFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    24        34       |44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
                                                      42-MSE                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:174
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:174
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
           AOC2_ARATH    80 KVQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2dioc_ C: Allene oxide cyclase, AOC                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.......................eeee..eeee.....eeeeeeeeeeeeeeehhhheeeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeeee......hhhhh............hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dio C  15 KVQELSVYEINELDRHSPKILKNAFSLmFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    24        34       |44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
                                                      42-MSE
   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, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DIO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DIO)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (AOC2_ARATH | Q9LS02)
molecular function
    GO:0046423    allene-oxide cyclase activity    Catalysis of the reaction: (9Z,13S,15Z)-12,13-epoxyoctadeca-9,11,15-trienoate = (15Z)-12-oxophyto-10,15-dienoate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0009695    jasmonic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of jasmonic acid, a fatty acid derivative.
    GO:0009409    response to cold    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 cold stimulus, a temperature stimulus below the optimal temperature for that organism.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009941    chloroplast envelope    The double lipid bilayer enclosing the chloroplast and separating its contents from the rest of the cytoplasm; includes the intermembrane space.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0010319    stromule    Thin filamentous structure extending from the surface of all plastid types examined so far, including chloroplast, proplastid, etioplast, leucoplast, amyloplast, and chromoplast. In general, stromules are more abundant in tissues containing non-green plastids, and in cells containing smaller plastids. The primary function of stromules is still unresolved, although the presence of stromules markedly increases the plastid surface area, potentially increasing transport to and from the cytosol. Other functions of stromules, such as transfer of macromolecules between plastids and starch granule formation in cereal endosperm, may be restricted to particular tissues and cell types.

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 Related Entries

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UniProtKB/Swiss-Prot
        AOC2_ARATH | Q9LS02: 1z8k 2brj 2gin 2q4i 4cq6 4cq7

(-) Related Entries Specified in the PDB File

1z8k STRUCTURE OF AOC2 SOLVED BY THE CESG STRUCTURAL GENOMICS CONSORTIUM
2brj HIGHER RESOLUTION STRUCTURE OF SEMET LABELLED AOC2
2gin STRUCTURE OF UNLABELLED AOC2