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(-) Description

Title :  (+)-BORNYL DIPHOSPHATE SYNTHASE: COCRYSTAL WITH MG AND 3-AZA-2,3-DIHYDROGERANYL DIPHOSPHATE
 
Authors :  D. A. Whittington, M. L. Wise, M. Urbansky, R. M. Coates, R. B. Croteau, D. W. Christianson
Date :  21 Oct 02  (Deposition) - 27 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Terpene Synthase Fold, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Whittington, M. L. Wise, M. Urbansky, R. M. Coates, R. B. Croteau, D. W. Christianson
Bornyl Diphosphate Synthase: Structure And Strategy For Carbocation Manipulation By A Terpenoid Synthase
Proc. Natl. Acad. Sci. Usa V. 99 15375 2002
PubMed-ID: 12432096  |  Reference-DOI: 10.1073/PNAS.232591099
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - (+)-BORNYL DIPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 5.5.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSBET
    Expression System Strain: BLR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUE 50-598
    Organism Common: GARDEN SAGE
    Organism Scientific: SALVIA OFFICINALIS
    Organism Taxid: 38868

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
13AG1Ligand/Ion2-[METHYL-(4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
13AG2Ligand/Ion2-[METHYL-(4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:351 , ASP A:355 , GLU A:429 , MG A:703 , 3AG A:900 , HOH A:921 , HOH A:922BINDING SITE FOR RESIDUE MG A 701
2AC2SOFTWAREASP A:496 , THR A:500 , GLU A:504 , 3AG A:900 , HOH A:919BINDING SITE FOR RESIDUE MG A 702
3AC3SOFTWAREASP A:351 , ASP A:355 , MG A:701 , 3AG A:900 , HOH A:920 , HOH A:921 , HOH A:923BINDING SITE FOR RESIDUE MG A 703
4AC4SOFTWAREARG A:314 , ILE A:344 , ASP A:351 , ASP A:355 , ILE A:457 , LEU A:492 , ARG A:493 , ASP A:496 , THR A:500 , GLU A:504 , LYS A:512 , TYR A:572 , PHE A:578 , MG A:701 , MG A:702 , MG A:703 , HOH A:919 , HOH A:920 , HOH A:921 , HOH A:922 , HOH A:923 , HOH A:925 , HOH A:926BINDING SITE FOR RESIDUE 3AG A 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N21)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N21)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N21)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N21)

(-) Exons   (0, 0)

(no "Exon" information available for 1N21)

(-) 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:535
 aligned with BPPS_SALOF | O81192 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:546
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592      
           BPPS_SALOF    53 QIRRSGNYQPALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKCFHNNEVEKMDLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLDEGGNEIDENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGTSYFELARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEPYA 598
               SCOP domains d1n21a1 A:53-270 (+)-bornyl diphosphate synthase                                                                                                                                                                          d1n21a2 A:271-598 (+)-bornyl diphosphate synthase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------1n21A01 A:80-285 Isoprenoid Synthase - domain 1                                                                                                                                                               1n21A02 A:286-598 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------Terpene_synth-1n21A01 A:65-245                                                                                                                                                       -----------------------------Terpene_synth_C-1n21A02 A:275-544                                                                                                                                                                                                                                             ------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....-----..hhhhhhhhhhhhhhh....hhhhhhhhh.......hhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n21 A  53 QIRRSGNYQPALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKCFH-----KMDLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLD------DENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGTSYFELARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEPYA 598
                                    62        72        82        92       102       112       122       132        |-    |  152       162       172       182       192       202       212       222    |    - |     242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592      
                                                                                                                  141   147                                                                             227    234
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (BPPS_SALOF | O81192)
molecular function
    GO:0047926    geranyl-diphosphate cyclase activity    Catalysis of the reaction: geranyl diphosphate = (2S)-bornyl 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: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:0046211    (+)-camphor biosynthetic process    The chemical reactions and pathways resulting in the formation of (+)-camphor, a bicyclic monoterpene ketone.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        BPPS_SALOF | O81192: 1n1b 1n1z 1n20 1n22 1n23 1n24

(-) Related Entries Specified in the PDB File

1n1b CRYSTAL STRUCTURE OF (+)-BORNYL DIPHOSPHATE SYNTHASE FROM SAGE
1n1z (+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG AND PYROPHOSPHATE
1n20 (+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG AND 3-AZA- 2,3-DIHYDROGERANYL DIPHOSPHATE
1n22 (+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4R)-7-AZA-7,8-DIHYDROLIMONENE
1n23 (+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (1R,4S)-2-AZABORNANE
1n24 (+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG AND PRODUCT