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(-) Description

Title :  STRUCTURE OF A THREE-DOMAIN SESQUITERPENE SYNTHASE: A PROSPECTIVE TARGET FOR ADVANCED BIOFUELS PRODUCTION
 
Authors :  R. P. Mcandrew, P. P. Peralta-Yahya, A. Degiovanni, J. H. Pereira, M. Z. J. D. Keasling, P. D. Adams
Date :  09 Jun 11  (Deposition) - 14 Dec 11  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase, Terpene Synthase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Mcandrew, P. P. Peralta-Yahya, A. Degiovanni, J. H. Pereira, M. Z. Hadi, J. D. Keasling, P. D. Adams
Structure Of A Three-Domain Sesquiterpene Synthase: A Prospective Target For Advanced Biofuels Production.
Structure V. 19 1876 2011
PubMed-ID: 22153510  |  Reference-DOI: 10.1016/J.STR.2011.09.013

(-) Compounds

Molecule 1 - ALPHA-BISABOLENE SYNTHASE
    Chains: A
    EC Number: 4.2.3.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSKB33
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: AG1
    Organism Common: GRAND FIR,LOWLAND FIR,LOWLAND WHITE FIR,SILVER FIR, WHITE FIR,YELLOW FIR
    Organism Scientific: ABIES GRANDIS
    Organism Taxid: 46611
    Synonym: (E)-ALPHA-BISABOLENE SYNTHASE, AGFEABIS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
12101Ligand/IonPAMIDRONATE
2CL1Ligand/IonCHLORIDE ION
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:125 , GLN A:439 , ARG A:470BINDING SITE FOR RESIDUE CL A 818
2AC2SOFTWAREASP A:566 , ASP A:570 , MG A:821 , 210 A:822 , HOH A:1320 , HOH A:1321BINDING SITE FOR RESIDUE MG A 819
3AC3SOFTWAREASP A:713 , 210 A:822 , HOH A:1317 , HOH A:1318 , HOH A:1319BINDING SITE FOR RESIDUE MG A 820
4AC4SOFTWAREASP A:566 , ASP A:570 , MG A:819 , 210 A:822 , HOH A:1322 , HOH A:1323 , HOH A:1324BINDING SITE FOR RESIDUE MG A 821
5AC5SOFTWAREASP A:566 , ASP A:570 , ARG A:710 , ASP A:713 , MG A:819 , MG A:820 , MG A:821 , HOH A:1317 , HOH A:1318 , HOH A:1319 , HOH A:1320 , HOH A:1321 , HOH A:1322 , HOH A:1324BINDING SITE FOR RESIDUE 210 A 822

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:294 -Pro A:295

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SDR)

(-) 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:775
 aligned with TPSD1_ABIGR | O81086 from UniProtKB/Swiss-Prot  Length:817

    Alignment length:783
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814   
          TPSD1_ABIGR    35 WGYDLVHSLKSPYIDSSYRERAEVLVSEIKAMLNPAITGDGESMITPSAYDTAWVARVPAIDGSARPQFPQTVDWILKNQLKDGSWGIQSHFLLSDRLLATLSCVLVLLKWNVGDLQVEQGIEFIKSNLELVKDETDQDSLVTDFEIIFPSLLREAQSLRLGLPYDLPYIHLLQTKRQERLAKLSREEIYAVPSPLLYSLEGIQDIVEWERIMEVQSQDGSFLSSPASTACVFMHTGDAKCLEFLNSVMIKFGNFVPCLYPVDLLERLLIVDNIVRLGIYRHFEKEIKEALDYVYRHWNERGIGWGRLNPIADLETTALGFRLLRLHRYNVSPAIFDNFKDANGKFICSTGQFNKDVASMLNLYRASQLAFPGENILDEAKSFATKYLREALEKSETSSAWNNKQNLSQEIKYALKTSWHASVPRVEAKRYCQVYRPDYARIAKCVYKLPYVNNEKFLELGKLDFNIIQSIHQEEMKNVTSWFRDSGLPLFTFARERPLEFYFLVAAGTYEPQYAKCRFLFTKVACLQTVLDDMYDTYGTLDELKLFTEAVRRWDLSFTENLPDYMKLCYQIYYDIVHEVAWEAEKEQGRELVSFFRKGWEDYLLGYYEEAEWLAAEYVPTLDEYIKNGITSIGQRILLLSGVLIMDGQLLSQEALEKVDYPGRRVLTELNSLISRLADDTKTYKAEKARGELASSIECYMKDHPECTEEEALDHIYSILEPAVKELTREFLKPDDVPFACKKMLFEETRVTMVIFKDGDGFGVSKLEVKDHIKECLIEPLPL 817
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh...........hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhh.......hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh....hhhhhhhhh..--.......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.......ee...ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.......hhhhhhhhhhhhhhhhhh...------..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sdr A  35 WGYDLVHSLKSPYIDSSYRERAEVLVSEIKAMLNPAITGDGESMITPSAYDTAWVARVPAIDGSARPQFPQTVDWILKNQLKDGSWGIQSHFLLSDRLLATLSCVLVLLKWNVGDLQVEQGIEFIKSNLELVKDETDQDSLVTDFEIIFPSLLREAQSLRLGLPYDLPYIHLLQTKRQERLAKLSREEIYAVPSPLLYSLEGIQDIVEWERIMEVQSQDGSFLSSPASTACVFMHTGDAKCLEFLNSVMIKFGNFVPCLYPVDLLERLLIVDNIVRLGIYRHFEKEIKEALDYVYRHWNERGIGWGRLNPIADLETTALGFRLLRLHRYNVSPAIFDNFKDA--KFICSTGQFNKDVASMLNLYRASQLAFPGENILDEAKSFATKYLREALEKSETSSAWNNKQNLSQEIKYALKTSWHASVPRVEAKRYCQVYRPDYARIAKCVYKLPYVNNEKFLELGKLDFNIIQSIHQEEMKNVTSWFRDSGLPLFTFARERPLEFYFLVAAGTYEPQYAKCRFLFTKVACLQTVLDDMYDTYGTLDELKLFTEAVRRWDLSFTENLPDYMKLCYQIYYDIVHEVAWEAEKEQGRELVSFFRKGWEDYLLGYYEEAEWLAAEYVPTLDEYIKNGITSIGQRILLLSGVLIMDGQLLSQEALEKVDYPGRRVLTELNSLISRLADDTKTYKA------LASSIECYMKDHPECTEEEALDHIYSILEPAVKELTREFLKPDDVPFACKKMLFEETRVTMVIFKDGDGFGVSKLEVKDHIKECLIEPLPL 817
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374 |  |  384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714     |   -  |    734       744       754       764       774       784       794       804       814   
                                                                                                                                                                                                                                                                                                                                                                               376  |                                                                                                                                                                                                                                                                                                                                                  720    727                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                  379
   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 3SDR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TPSD1_ABIGR | O81086)
molecular function
    GO:0052681    alpha-bisabolene synthase activity    Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate = (E,R)-alpha-bisabolene + diphosphate.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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UniProtKB/Swiss-Prot
        TPSD1_ABIGR | O81086: 3sae 3sdq 3sdt 3sdu 3sdv

(-) Related Entries Specified in the PDB File

3sae 3sdq 3sdt 3sdu 3sdv