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(-) Description

Title :  CRYSTAL STRUCTURE OF (+)-DELTA-CADINENE SYNTHASE FROM GOSSYPIUM ARBOREUM AND EVOLUTIONARY DIVERGENCE OF METAL BINDING MOTIFS FOR CATALYSIS
 
Authors :  H. A. Gennadios, L. Di Costanzo, D. J. Miller, R. K. Allemann, D. W. Chri
Date :  03 Feb 09  (Deposition) - 16 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cyclase, Lyase, Magnesium, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. A. Gennadios, V. Gonzalez, L. Di Costanzo, A. Li, F. Yu, D. J. Miller R. K. Allemann, D. W. Christianson
Crystal Structure Of (+)-Delta-Cadinene Synthase From Gossypium Arboreum And Evolutionary Divergence Of Metal Binding Motifs For Catalysis.
Biochemistry V. 48 6175 2009
PubMed-ID: 19489610  |  Reference-DOI: 10.1021/BI900483B

(-) Compounds

Molecule 1 - (+)-DELTA-CADINENE SYNTHASE ISOZYME XC1
    Chains: A, B
    EC Number: 4.2.3.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: TREE COTTON
    Organism Scientific: GOSSYPIUM ARBOREUM
    Organism Taxid: 29729
    Synonym: D-CADINENE SYNTHASE XC1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1BME3Ligand/IonBETA-MERCAPTOETHANOL
2GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1BME3Ligand/IonBETA-MERCAPTOETHANOL
2GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2GOL4Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:252 , BME A:1275BINDING SITE FOR RESIDUE BME A1273
2AC2SOFTWAREARG A:364 , GLY A:422 , HOH A:796BINDING SITE FOR RESIDUE BME A1274
3AC3SOFTWARECYS A:39 , LYS A:248 , SER A:251 , GLU A:252 , BME A:1273BINDING SITE FOR RESIDUE BME A1275
4AC4SOFTWAREASN B:518 , ARG B:521 , HOH B:604 , HOH B:630 , HOH B:631 , GOL B:2432BINDING SITE FOR RESIDUE GOL B2431
5AC5SOFTWAREGLN B:81 , ARG B:82 , GLU B:123 , ILE B:205 , HOH B:588 , HOH B:629 , HOH B:633 , GOL B:2431BINDING SITE FOR RESIDUE GOL B2432
6AC6SOFTWAREASP B:307 , ASP B:311 , GLU B:385 , THR B:407 , ARG B:448BINDING SITE FOR RESIDUE GOL B2433
7AC7SOFTWARETRP B:279 , SER B:304 , ASP B:307 , TYR B:382BINDING SITE FOR RESIDUE GOL B2434

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:408 -A:447
2B:408 -B:447

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Gln A:28 -Pro A:29
2Ala A:107 -Glu A:108
3His A:191 -Pro A:192
4Lys A:504 -Pro A:505
5Tyr A:535 -Val A:536
6His B:191 -Pro B:192
7Tyr B:221 -Gln B:222
8Gln B:222 -Asp B:223
9Lys B:504 -Pro B:505

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G4D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G4D)

(-) Exons   (0, 0)

(no "Exon" information available for 3G4D)

(-) 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:516
 aligned with DCS1_GOSAR | Q39761 from UniProtKB/Swiss-Prot  Length:554

    Alignment length:530
                                    34        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
           DCS1_GOSAR    25 ADFQPSIWGDLFLNCPDKNIDAETEKRHQQLKEEVRKMIVAPMANSTQKLAFIDSVQRLGVSYHFTKEIEDELENIYHNNNDAENDLYTTSIRFRLLREHGYNVSCDVFNKFKDEQGNFKSSVTSDVRGLLELYQASYLRVHGEDILDEAISFTTHHLSLAVASLDHPLSEEVSHALKQSIRRGLPRVEARHYLSVYQDIESHNKALLEFAKIDFNMLQFLHRKELSEICRWWKDLDFQRKLPYARDRVVEGYFWISGVYFEPQYSLGRKMLTKVIAMASIVDDTYDSYATYEELIPYTNAIERWDIKCIDEIPEYMKPSYKALLDVYEEMVQLVAEHGRQYRVEYAKNAMIRLAQSYLVEAKWTLQNYKPSFEEFKANALPTCGYAMLAITSFVGMGDIVTPETFKWAASDPKIIQASTIICRFMDDVAEHKFKHRREDDCSAIECYMEEYGVTAQEAYDVFNKHVESAWKDLNQEFLKPTEMPTEVLNRSLNLARVMDVLYREGDGYTYVGKAAKGGITSLLIEPIAL 554
               SCOP domains d3g4da1 A:25-226    automated matches                                                                                                                                                                     d3g4da2 A:227-554 automated matches                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3g4dA01 A:25-66,A   :227-553              3g4dA02 A:67-226 Isoprenoid Synthase - domain 1                                                                                                                 3g4dA01 A:25-66,A:227-553 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................---hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.------..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..-----..hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g4d A  25 ADFQPSIWGDLFLNCPD---DAETEKRHQQLKEEVRKMIVAPMANSTQKLAFIDSVQRLGVSYHFTKEIEDELENIYHNNNDAENDLYTTSIRFRLLREHGYNVSCDVFNKFKDEQGNFKSSVTSDVRGLLELYQASYLRVHGEDILDEAISFTTHHLSLAVASLDHPLSEEVSHALKQSIRRGLPRVEARHYLSVYQDIESHNKALLEFAKIDFNMLQFLHRKELSEICRWWKDLDFQRKLPYARDRVVEGYFWISGVYFEPQYSLGRKMLTKVIAMASIVDDTYDSYATYEELIPYTNAIERWDIKCIDEIPEYMKPSYKALLDVYEEMVQLVAEHGRQYRVEYAKNAMIRLAQSYLVEAKWTLQNYKPSFEEFKANALPTCGYAMLAITSFVGMGDIVTPETFKWAASDPKIIQASTIICRFMDDVAEHKF------DCSAIECYMEEYGVTAQEAYDVFNKHVESAWKDLNQEFLKPTEMPTEVLNRSLNLARVMDVLYRE-----YVGKAAKGGITSLLIEPIAL 554
                                    34      |  -|       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   |     -|      474       484       494       504       514       524    |    -|      544       554
                                           41  45                                                                                                                                                                                                                                                                                                                                                                                                                          458    465                                                             529   535                   


Chain B from PDB  Type:PROTEIN  Length:512
 aligned with DCS1_GOSAR | Q39761 from UniProtKB/Swiss-Prot  Length:554

    Alignment length:527
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       
           DCS1_GOSAR    28 QPSIWGDLFLNCPDKNIDAETEKRHQQLKEEVRKMIVAPMANSTQKLAFIDSVQRLGVSYHFTKEIEDELENIYHNNNDAENDLYTTSIRFRLLREHGYNVSCDVFNKFKDEQGNFKSSVTSDVRGLLELYQASYLRVHGEDILDEAISFTTHHLSLAVASLDHPLSEEVSHALKQSIRRGLPRVEARHYLSVYQDIESHNKALLEFAKIDFNMLQFLHRKELSEICRWWKDLDFQRKLPYARDRVVEGYFWISGVYFEPQYSLGRKMLTKVIAMASIVDDTYDSYATYEELIPYTNAIERWDIKCIDEIPEYMKPSYKALLDVYEEMVQLVAEHGRQYRVEYAKNAMIRLAQSYLVEAKWTLQNYKPSFEEFKANALPTCGYAMLAITSFVGMGDIVTPETFKWAASDPKIIQASTIICRFMDDVAEHKFKHRREDDCSAIECYMEEYGVTAQEAYDVFNKHVESAWKDLNQEFLKPTEMPTEVLNRSLNLARVMDVLYREGDGYTYVGKAAKGGITSLLIEPIAL 554
               SCOP domains d3g4db1 B:28-226  automated matches                                                                                                                                                                    d3g4db2 B:227-554 automated matches                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3g4dB01 B:28-66,B :227-553             3g4dB02 B:67-226 Isoprenoid Synthase      - domain 1                                                                                                            3g4dB01 B:28-66,B:227-553 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................-hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..-----.hhhhhhhhhhhhhhh....hhhhhhhhh............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..-----..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....h----hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g4d B  28 QPSIWGDLFLNCPDKNI-AETEKRHQQLKEEVRKMIVAPMANSTQKLAFIDSVQRLGVSYHFTKEIEDELENIYHN-----NDLYTTSIRFRLLREHGYNVSCDVFNKFKDEQGNFKSSVTSDVRGLLELYQASYLRVHGEDILDEAISFTTHHLSLAVASLDHPLSEEVSHALKQSIRRGLPRVEARHYLSVYQDIESHNKALLEFAKIDFNMLQFLHRKELSEICRWWKDLDFQRKLPYARDRVVEGYFWISGVYFEPQYSLGRKMLTKVIAMASIVDDTYDSYATYEELIPYTNAIERWDIKCIDEIPEYMKPSYKALLDVYEEMVQLVAEHGRQYRVEYAKNAMIRLAQSYLVEAKWTLQNYKPSFEEFKANALPTCGYAMLAITSFVGMGDIVTPETFKWAASDPKIIQASTIICRFMDDVAEHKFK-----DCSAIECYMEEYGVTAQEAYDVFNKHVESAWKDLNQEFLKPTEMPTEVLNRSLNLARVMDVLYREGDG----GKAAKGGITSLLIEPIAL 554
                                    37      | 47        57        67        77        87        97     |   - |     117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457 |     467       477       487       497       507       517       527    |  537       547       
                                           44 |                                                      103   109                                                                                                                                                                                                                                                                                                                                                           459   465                                                                532  537                 
                                             46
   Legend:   → Mismatch (orange background)
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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, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G4D)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DCS1_GOSAR | Q39761)
molecular function
    GO:0047461    (+)-delta-cadinene synthase activity    Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate = diphosphate + (+)-delta-cadinene.
    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.

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 Related Entries

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

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        DCS1_GOSAR | Q39761: 3g4f

(-) Related Entries Specified in the PDB File

3g4f