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(-) Description

Title :  R304K TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4R)-7-AZABISABOLENE
 
Authors :  L. S. Vedula, D. E. Cane, D. W. Christianson
Date :  22 Jul 05  (Deposition) - 04 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Terpenoid Cyclase Fold, Site-Directed Mutant, Pyrophosphate, (4R)-7- Azabisabolene, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. S. Vedula, D. E. Cane, D. W. Christianson
Role Of Arginine-304 In The Diphosphate-Triggered Active Site Closure Mechanism Of Trichodiene Synthase.
Biochemistry V. 44 12719 2005
PubMed-ID: 16171386  |  Reference-DOI: 10.1021/BI0510476

(-) Compounds

Molecule 1 - TRICHODIENE SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TRI5
    Mutation: YES
    Organism Scientific: FUSARIUM SPOROTRICHIOIDES
    Organism Taxid: 5514
    Synonym: SESQUITERPENE CYCLASE, TS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MG3Ligand/IonMAGNESIUM ION
3POP1Ligand/IonPYROPHOSPHATE 2-
4SAZ1Ligand/Ion(1S)-N,4-DIMETHYL-N-(4-METHYLPENT-3-ENYL)CYCLOHEX-3-ENAMINIUM
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3POP-1Ligand/IonPYROPHOSPHATE 2-
4SAZ-1Ligand/Ion(1S)-N,4-DIMETHYL-N-(4-METHYLPENT-3-ENYL)CYCLOHEX-3-ENAMINIUM
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3POP1Ligand/IonPYROPHOSPHATE 2-
4SAZ1Ligand/Ion(1S)-N,4-DIMETHYL-N-(4-METHYLPENT-3-ENYL)CYCLOHEX-3-ENAMINIUM
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3POP1Ligand/IonPYROPHOSPHATE 2-
4SAZ1Ligand/Ion(1S)-N,4-DIMETHYL-N-(4-METHYLPENT-3-ENYL)CYCLOHEX-3-ENAMINIUM

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:182 , ASN B:225 , ASP B:226 , SER B:229 , GLU B:233 , POP B:700BINDING SITE FOR RESIDUE MG B 701
2AC2SOFTWAREASP B:100 , ASP B:239 , POP B:700BINDING SITE FOR RESIDUE MG B 702
3AC3SOFTWAREASP B:100 , GLU B:164 , POP B:700BINDING SITE FOR RESIDUE MG B 703
4AC4SOFTWAREMET B:73 , THR B:96 , LEU B:97 , PHE B:157 , ASN B:185 , GLY B:186 , LEU B:187 , MET B:221 , ASN B:225 , TYR B:295 , TRP B:298 , LYS B:304 , TYR B:305 , POP B:700BINDING SITE FOR RESIDUE SAZ B 704
5AC5SOFTWAREASP B:100 , ARG B:182 , ASN B:225 , SER B:229 , LYS B:232 , GLU B:233 , LYS B:304 , TYR B:305 , MG B:701 , MG B:702 , MG B:703 , SAZ B:704BINDING SITE FOR RESIDUE POP B 700
6AC6SOFTWARETYR A:113 , TRP A:128 , ASN A:132 , HOH A:773 , PHE B:114BINDING SITE FOR RESIDUE EDO A 750
7AC7SOFTWARETYR B:113 , TRP B:128 , ASN B:132 , PHE B:135 , HOH B:769BINDING SITE FOR RESIDUE EDO B 751
8AC8SOFTWAREMET A:73 , MET A:221 , TYR A:295 , HOH A:839BINDING SITE FOR RESIDUE EDO A 752

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AEL)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:345 -Pro A:346
2Tyr B:345 -Pro B:346

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AEL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AEL)

(-) Exons   (0, 0)

(no "Exon" information available for 2AEL)

(-) 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:352
 aligned with TRI5_FUSSP | P13513 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:352
                                    12        22        32        42        52        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  
           TRI5_FUSSP     3 NFPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRRYRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 354
               SCOP domains d2aela_ A: Trichodiene synthase                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2aelA00 A:3-354 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ael A   3 NFPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRKYRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 354
                                    12        22        32        42        52        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  


Chain B from PDB  Type:PROTEIN  Length:353
 aligned with TRI5_FUSSP | P13513 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:353
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351   
           TRI5_FUSSP     2 ENFPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRRYRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 354
               SCOP domains d2aelb_ B: Trichodiene synthase                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2aelB00 B:2-354 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ael B   2 ENFPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRKYRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 354
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AEL)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRI5_FUSSP | P13513)
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:0045482    trichodiene synthase activity    Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate = diphosphate + trichodiene.
biological process
    GO:0016106    sesquiterpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of sesquiterpenoid compounds, terpenoids with three isoprene units.

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  2ael
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  TRI5_FUSSP | P13513
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  4.2.3.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRI5_FUSSP | P13513: 1jfa 1jfg 1kiy 1kiz 1yj4 1yyq 1yyr 1yys 1yyt 1yyu 2aek 2aet 2ps4 2ps5 2ps6 2ps7 2ps8 2q9y 2q9z

(-) Related Entries Specified in the PDB File

1jfa TRICHODIENE SYNTHASE FROM FUSARIUM SPOROTRICHIODES
1jfg TRICHODIENE SYNTHASE FROM FUSARIUM SPOROTRICHIOIDES COMPLEXED WITH DIPHOSPHATE
1yyr Y305F TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4R)-7-AZABISABOLENE
1yyt D100E TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4R)-7-AZABISABOLENE
2aek R304K TRICHODIENE SYNTHASE