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(-) Description

Title :  CRYSTAL STRUCTURE OF ENT-COPALYL DIPHOSPHATE SYNTHASE FROM ARABIDOPSIS THALIANA IN COMPLEX WITH (S)-15-AZA-14,15-DIHYDROGERANYLGERANYL THIOLODIPHOSPHATE
 
Authors :  M. Koksal, D. W. Christianson
Date :  12 Dec 10  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Class I And Ii Terpene Cyclase Fold, Class Ii Diterpene Cyclase, Dxxdd Motif, Gibberellin Biosynthesis, Biosynthesis Of Ent-Copalyl Diphosphate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Koksal, H. Hu, R. M. Coates, R. J. Peters, D. W. Christianson
Structure Of Ent-Copalyl Diphosphate Synthase From Arabidopsis Thaliana, A Protonation-Dependent Diterpene Cyclase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ENT-COPALYL DIPHOSPHATE SYNTHASE, CHLOROPLASTIC
    Chains: A
    EC Number: 5.5.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22BCV
    Expression System Strain: OVEREXPRESS C41 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT4G02780, GA1, T5J8.9, TPSGA1
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ATCPS, ENT-CDP SYNTHASE, ENT-KAURENE SYNTHASE A, KSA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2AG81Ligand/IonS-[(2E,6E,10E)-14-(DIMETHYLAMINO)-3,7,11-TRIMETHYLTETRADECA-2,6,10-TRIEN-1-YL] TRIHYDROGENTHIODIPHOSPHATE
3GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:208 , GLY A:209 , LYS A:245 , THR A:260 , HIS A:263 , TRP A:333 , TRP A:369 , ASP A:379 , ASP A:380 , ASN A:417 , LYS A:463 , TRP A:464 , TYR A:511 , HOH A:850BINDING SITE FOR RESIDUE AG8 A 901
2AC2SOFTWARELEU A:452 , GLU A:453 , GLU A:456 , ARG A:457BINDING SITE FOR RESIDUE GOL A 921
3AC3SOFTWAREHOH A:17 , TYR A:427 , SER A:430 , LYS A:444 , PRO A:481 , TYR A:483 , GLU A:749 , TYR A:781BINDING SITE FOR RESIDUE 1PE A 951

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:324 -Pro A:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PYA)

(-) 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:688
 aligned with KSA_ARATH | Q38802 from UniProtKB/Swiss-Prot  Length:802

    Alignment length:713
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 802 
                                   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       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800 | 
            KSA_ARATH    91 SNAFKEAVKSVKTILRNLTDGEITISAYDTAWVALIDAGDKTPAFPSAVKWIAENQLSDGSWGDAYLFSYHDRLINTLACVVALRSWNLFPHQCNKGITFFRENIGKLEDENDEHMPIGFEVAFPSLLEIARGINIDVPYDSPVLKDIYAKKELKLTRIPKEIMHKIPTTLLHSLEGMRDLDWEKLLKLQSQDGSFLFSPSSTAFAFMQTRDSNCLEYLRNAVKRFNGGVPNVFPVDLFEHIWIVDRLQRLGISRYFEEEIKECLDYVHRYWTDNGICWARCSHVQDIDDTAMAFRLLRQHGYQVSADVFKNFEKEGEFFCFVGQSNQAVTGMFNLYRASQLAFPREEILKNAKEFSYNYLLEKREREELIDKWIIMKDLPGEIGFALEIPWYASLPRVETRFYIDQYGGENDVWIGKTLYRMPYVNNNGYLELAKQDYNNCQAQHQLEWDIFQKWYEENRLSEWGVRRSELLECYYLAAATIFESERSHERMVWAKSSVLVKAISSSFGESSDSRRSFSDQFHEYIANARRSDHHFNDRNMRLDRPGSVQASRLAGVLIGTLNQMSFDLFMSHGRDVNNLLYLSWGDWMEKWKLYGDEGEGELMVKMIILMKNNDLTNFFTHTHFVRLAEIINRICLPRQYLKARRNDEKEKTIKSMEKEMGKMVELALSESDTFRDVSITFLDVAKAFYYFALCGDHLQTHISKVLFQKV-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Terpene_synth-3pyaA01 A:273-478                                                                                                                                                                               ------------------------------------------Terpene_synth_C-3pyaA02 A:521-769                                                                                                                                                                                                                        ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh........hhhhhhhhhh.........hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh....hhhhhhh.ee..ee.........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.......ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee...ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh-------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....------hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pya A  91 SNAFKEAVKSVKTILRNLTDGEITISAYDTAWVALIDAGDKTPAFPSAVKWIAENQLSDGSWGDAYLFSYHDRLINTLACVVALRSWNLFPHQCNKGITFFRENIGKLEDENDEHMPIGFEVAFPSLLEIARGINIDVPYDSPVLKDIYAKKELKLTRIPKEIMHKIPTTLLHSLEGMRDLDWEKLLKLQSQDGSFLFSPSSTAFAFMQTRDSNCLEYLRNAVKRFNGGVPNVFPVDLFEHIWIVDRLQRLGISRYFEEEIKECLDYVHRYWTDNGICWARCSHVQDIDDTAMAFRLLRQHGYQVSADVFKNFEKEGEFFCFVGQSNQAVTGMFNLYRASQLAFPREEILKNAKEFSYNYLLEKREREELIDKWIIMKDLPGEIGFALEIPWYASLPRVETRFYIDQYGGENDVWIGKTLYRMPYVNNNGYLELAKQDYNNCQAQHQLEWDIFQKWYEENRLSEWGVRRSELLECYYLAAATIFESERSHERMVWAKSSVLVKAISSSFGESSDSRRSFSDQFHEYI-------------------PGSVQASRLAGVLIGTLNQMSFDLFMSHGRDVNNLLYLSWGDWMEKWKLYGDEGEGELMVKMIILMKNNDLTNFFTHTHFVRLAEIINRICLPRQ------NDEKEKTIKSMEKEMGKMVELALSESDTFRDVSITFLDVAKAFYYFALCGDHLQTHISKVLFQKVG 803
                                   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       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610      |  -         -      |640       650       660       670       680       690       700       710       720       730|      740       750       760       770       780       790       800   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        617                 637                                                                                           731    738
   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  (0, 0)

(no "SCOP Domain" information available for 3PYA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PYA)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Terpene_synth] (17)
(-)
Clan: no clan defined [family: Terpene_synth_C] (19)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KSA_ARATH | Q38802)
molecular function
    GO:0009905    ent-copalyl diphosphate synthase activity    Catalysis of the reaction: all-trans-geranylgeranyl diphosphate = ent-copalyl diphosphate.
    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.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0010333    terpene synthase activity    Catalysis of the formation of cyclic terpenes through the cyclization of linear terpenes (e.g. isopentenyl-PP, geranyl-PP, farnesyl-PP and geranylgeranyl-PP) containing varying numbers of isoprene units.
biological process
    GO:0009740    gibberellic acid mediated signaling pathway    A series of molecular signals mediated by the detection of gibberellic acid.
    GO:0009686    gibberellin biosynthetic process    The chemical reactions and pathways resulting in the formation of gibberellin. Gibberellins are a class of highly modified terpenes that function as plant growth regulators.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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: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.

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        KSA_ARATH | Q38802: 3pyb 4lix

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