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(-) Description

Title :  X-RAY STRUCTURE OF THE WT ALLENE OXIDE CYCLASE 2 FROM ARABIDOPSIS THALIANA
 
Authors :  E. Hofmann, F. Schaller, P. Zerbe
Date :  29 Mar 06  (Deposition) - 21 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Beta Barrel, 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
    ChainsA, B, C, D, E, F
    EC Number5.3.99.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE-30
    Expression System StrainM15
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentALLENE OXIDE CYCLASE 2
    GeneAT3G25770
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:37 , HOH A:1000 , HOH A:1001 , LEU B:35 , ASN B:37 , LEU C:35 , ASN C:37BINDING SITE FOR RESIDUE GOL A 901
2AC2SOFTWARELEU D:35 , ASN D:37 , HOH D:951 , HOH D:982 , ASN E:37 , HOH E:294 , ASN F:37BINDING SITE FOR RESIDUE GOL D 902
3AC3SOFTWAREPRO F:32 , CYS F:71 , TYR F:136 , HOH F:986 , HOH F:1000BINDING SITE FOR RESIDUE GOL F 903
4AC4SOFTWAREASN B:53 , HOH B:980BINDING SITE FOR RESIDUE GOL B 904
5AC5SOFTWAREASP D:28 , ARG D:29 , LYS D:54 , ASN D:188BINDING SITE FOR RESIDUE GOL D 905

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric 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
7Ser D:31 -Pro D:32
8Tyr D:136 -Pro D:137
9Ser E:31 -Pro E:32
10Tyr E:136 -Pro E:137
11Ser F:31 -Pro F:32
12Tyr F:136 -Pro F:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GIN)

(-) 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:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2gina_ 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
                 2gin A  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2ginb_ 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
                 2gin B  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   

Chain C from PDB  Type:PROTEIN  Length:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2ginc_ C: Allene oxide cyclase, AOC                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......................eeee..eeee.....eeeeeeeeeeeeeee....eeeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeeee......hhhhh............hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gin C  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   

Chain D from PDB  Type:PROTEIN  Length:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2gind_ D: 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
                 2gin D  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   

Chain E from PDB  Type:PROTEIN  Length:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2gine_ E: 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............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gin E  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   

Chain F from PDB  Type:PROTEIN  Length:173
 aligned with AOC2_ARATH | Q9LS02 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:173
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           AOC2_ARATH    81 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 253
               SCOP domains d2ginf_ F: 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......hhhhhh...........hhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gin F  16 VQELSVYEINELDRHSPKILKNAFSLMFGLGDLVPFTNKLYTGDLKKRVGITAGLCVVIEHVPEKKGERFEATYSFYFGDYGHLSVQGPYLTYEDSFLAITGGAGIFEGAYGQVKLQQLVYPTKLFYTFYLKGLANDLPLELTGTPVPPSKDIEPAPEAKALEPSGVISNYTN 188
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   

   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, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (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

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

UniProtKB/Swiss-Prot
        AOC2_ARATH | Q9LS021z8k 2brj 2dio 2q4i 4cq6 4cq7

(-) Related Entries Specified in the PDB File

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2dio THE SAME PROTEIN COMPLEXED WITH INHIBITOR VERNOLIC ACID