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(-) Description

Title :  THE CRYSTAL STRUCTURE OF 5-EPI-ARISTOLOCHENE SYNTHASE COMPLEXED WITH (2-TRANS,6-TRANS)-2-FLUOROFARNESYL DIPHOSPHATE
 
Authors :  J. P. Noel, N. Dellas, J. A. Faraldos, M. Zhao, B. A. Hess Jr. , L. Smentek R. M. Coates, P. E. O'Maille
Date :  02 Mar 10  (Deposition) - 07 Jul 10  (Release) - 07 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Plant Terpenoid Cyclase, 5-Epi-Aristolochene Synthase, Lyase, Metal- Binding Domain, (2-Trans, 6-Trans)-2-Fluorofarnesyl Diphosphate, Magnesium, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Noel, N. Dellas, J. A. Faraldos, M. Zhao, B. A. Hess, L. Smentek, R. M. Coates, P. E. O'Maille
Structural Elucidation Of Cisoid And Transoid Cyclization Pathways Of A Sesquiterpene Synthase Using 2-Fluorofarnesyl Diphosphates.
Acs Chem. Biol. V. 5 377 2010
PubMed-ID: 20175559  |  Reference-DOI: 10.1021/CB900295G

(-) Compounds

Molecule 1 - ARISTOLOCHENE SYNTHASE
    Chains: A
    EC Number: 4.2.3.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS9GW
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EAS3, EAS4
    Organism Common: AMERICAN TOBACCO,TOBACCO
    Organism Scientific: NICOTIANA TABACUM
    Organism Taxid: 4097
    Synonym: 5-EPI-ARISTOLOCHENE SYNTHASE, EAS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FPF1Ligand/Ion(2Z,6E)-2-FLUORO-3,7,11-TRIMETHYLDODECA-2,6,10-TRIEN-1-YL TRIHYDROGEN DIPHOSPHATE
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:264 , TRP A:273 , SER A:298 , ASP A:301 , ASP A:444 , TYR A:520 , HOH A:637 , HOH A:646 , HOH A:675 , HOH A:694 , HOH A:703 , HOH A:704 , HOH A:705 , MG A:853 , MG A:854 , MG A:855BINDING SITE FOR RESIDUE FPF A 549
2AC2SOFTWAREASP A:444 , THR A:448 , GLU A:452 , FPF A:549 , HOH A:675 , HOH A:690 , HOH A:705BINDING SITE FOR RESIDUE MG A 853
3AC3SOFTWAREASP A:301 , ASP A:305 , FPF A:549 , HOH A:703 , MG A:855BINDING SITE FOR RESIDUE MG A 854
4AC4SOFTWAREASP A:301 , ASP A:305 , FPF A:549 , HOH A:694 , HOH A:704 , HOH A:706 , MG A:854BINDING SITE FOR RESIDUE MG A 855
5AC5SOFTWARELYS A:200 , GLN A:481 , GLU A:485 , TRP A:488 , GLU A:517BINDING SITE FOR RESIDUE ACT A 707
6AC6SOFTWARESER A:154 , HIS A:155 , ARG A:157 , LYS A:200 , GLU A:485 , TRP A:488 , ASN A:492BINDING SITE FOR RESIDUE ACT A 708

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M01)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:184 -Pro A:185
2Arg A:497 -Pro A:498

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M01)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M01)

(-) Exons   (0, 0)

(no "Exon" information available for 3M01)

(-) 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:530
 aligned with 5EAS_TOBAC | Q40577 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:535
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543     
           5EAS_TOBAC    14 VRPVADFSPSLWGDQFLSFSIKNQVAEKYAKEIEALKEQTRNMLLATGMKLADTLNLIDTIERLGISYHFEKEIDDILDQIYNQNSNCNDLCTSALQFRLLRQHGFNISPEIFSKFQDENGKFKESLASDVLGLLNLYEASHVRTHADDILEDALAFSTIHLESAAPHLKSPLREQVTHALEQCLHKGVPRVETRFFISSIYDKEQSKNNVLLRFAKLDFNLLQMLHKQELAQVSRWWKDLDFVTTLPYARDRVVECYFWALGVYFEPQYSQARVMLVKTISMISIVDDTFDAYGTVKELEAYTDAIQRWDINEIDRLPDYMKISYKAILDLYKDYEKELSSAGRSHIVCHAIERMKEVVRNYNVESTWFIEGYTPPVSEYLSNALATTTYYYLATTSYLGMKSATEQDFEWLSKNPKILEASVIICRVIDDTATYEVEKSRGQIATGIECCMRDYGISTKEAMAKFQNMAETAWKDINEGLLRPTPVSTEFLTPILNLARIVEVTYIHNLDGYTHPEKVLKPHIINLLVDSIKI 548
               SCOP domains d3m01a1 A:14-220 automated matches                                                                                                                                                                             d3m01a2 A:221-548 automated matches                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Terpene_synth-3m01A01 A:25-194                                                                                                                                            ------------------------------Terpene_synth_C-3m01A02 A:225-492                                                                                                                                                                                                                                           -------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..-----.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m01 A  14 VRPVADFSPSLWGDQFLSFSIKNQVAEKYAKEIEALKEQTRNMLLATGMKLADTLNLIDTIERLGISYHFEKEIDDILDQIYNQNSNCNDLCTSALQFRLLRQHGFNISPEIFSKFQDENGKFKESLASDVLGLLNLYEASHVRTHADDILEDALAFSTIHLESAAPHLKSPLREQVTHALEQCLHKGVPRVETRFFISSIYDKEQSKNNVLLRFAKLDFNLLQMLHKQELAQVSRWWKDLDFVTTLPYARDRVVECYFWALGVYFEPQYSQARVMLVKTISMISIVDDTFDAYGTVKELEAYTDAIQRWDINEIDRLPDYMKISYKAILDLYKDYEKELSSAGRSHIVCHAIERMKEVVRNYNVESTWFIEGYTPPVSEYLSNALATTTYYYLATTSYLGMKSATEQDFEWLSKNPKILEASVIICRVIDDTATYEVEKSRGQIATGIECCMRDYGISTKEAMAKFQNMAETAWKDINEGLLRPTPVSTEFLTPILNLARIVEVTYIH-----THPEKVLKPHIINLLVDSIKI 548
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513        |-    |  533       543     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      522   528
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M01)

(-) 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  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (5EAS_TOBAC | Q40577)
molecular function
    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.
    GO:0016114    terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
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

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

UniProtKB/Swiss-Prot
        5EAS_TOBAC | Q40577: 1hx9 1hxa 1hxc 1hxg 3lz9 3m00 3m02 4di5 4rnq 5dhi 5dhk 5eas 5eat 5eau 5ik0 5ik6 5ik9 5ika 5ikh 5il3 5il8 5ild 5ilh 5ili 5ilj 5ilk 5ily 5ilz 5im1

(-) Related Entries Specified in the PDB File

3m00 3m02