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(-) Description

Title :  Y305F TRICHODIENE SYNTHASE COMPLEXED WITH PYROPHOSPHATE
 
Authors :  L. S. Vedula, M. J. Rynkiewicz, H. J. Pyun, R. M. Coates, D. E. Cane, D. W. Christianson
Date :  25 Feb 05  (Deposition) - 29 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Terpenoid Cyclase Fold, Site-Directed Mutant, Pyrophosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. S. Vedula, M. J. Rynkiewicz, H. J. Pyun, R. M. Coates, D. E. Cane, D. W. Christianson
Molecular Recognition Of The Substrate Diphosphate Group Governs Product Diversity In Trichodiene Synthase Mutants.
Biochemistry V. 44 6153 2005
PubMed-ID: 15835903  |  Reference-DOI: 10.1021/BI050059O
(for further references see the PDB file header)

(-) 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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2POP1Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:225 , SER B:229 , GLU B:233 , POP B:700 , HOH B:800BINDING SITE FOR RESIDUE MG B 701
2AC2SOFTWAREASP B:100 , POP B:700 , MG B:703 , HOH B:803 , HOH B:804 , HOH B:805BINDING SITE FOR RESIDUE MG B 702
3AC3SOFTWAREASP B:100 , POP B:700 , MG B:702 , HOH B:801 , HOH B:802 , HOH B:803 , HOH B:806BINDING SITE FOR RESIDUE MG B 703
4AC4SOFTWAREASP B:100 , ARG B:182 , ASN B:225 , SER B:229 , LYS B:232 , GLU B:233 , ARG B:304 , PHE B:305 , MG B:701 , MG B:702 , MG B:703 , HOH B:772 , HOH B:801 , HOH B:802 , HOH B:803 , HOH B:804 , HOH B:805BINDING SITE FOR RESIDUE POP B 700

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological 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 1YYQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YYQ)

(-) 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: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 d1yyqa_ A: Trichodiene synthase                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1yyqA00 A:2-354 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yyq A   2 ENFPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRRFRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 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   


Chain B from PDB  Type:PROTEIN  Length:351
 aligned with TRI5_FUSSP | P13513 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:351
                                    13        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 
           TRI5_FUSSP     4 FPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRRYRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 354
               SCOP domains d1yyqb_ B: Trichodiene synthase                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1yyqB00 B:4-354 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) TRI5-1yyqB01 B:4-354                                                                                                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) TRI5-1yyqB02 B:4-354                                                                                                                                                                                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yyq B   4 FPTEYFLNTTVRLLEYIRYRDSNYTREERIENLHYAYNKAAHHFAQPRQQQLLKVDPKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRRMNGLGHCVGASLWPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAVFSDKDPQVMDTIECFMHGYVTWHLCDRRFRLSEIYEKVKEEKTEDAQKFCKFYEQAANVGAVSPSEWAYPPVAQLANV 354
                                    13        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
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: TRI5] (16)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological 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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  Cis Peptide Bonds
    Tyr A:345 - Pro A:346   [ RasMol ]  
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  1yyq
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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 1yyr 1yys 1yyt 1yyu 2aek 2ael 2aet 2ps4 2ps5 2ps6 2ps7 2ps8 2q9y 2q9z

(-) Related Entries Specified in the PDB File

1jfa TRICHODIENE SYNTHASE FROM FUSARIUM SPOROTRICHIOIDES
1jfg TRICHODIENE SYNTHASE FROM FUSARIUM SPOROTRICHIOIDES COMPLEXED WITH DIPHOSPHATE
1kiy D100E TRICHODIENE SYNTHASE
1kiz D100E TRICHODIENE SYNTHASE COMPLEXED WITH PYROPHOSPHATE
1yj4 Y305F TRICHODIENE SYNTHASE
1yyr Y305F TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4R)-7-AZABISABOLENE
1yys Y305F TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4S)-7-AZABISABOLENE
1yyt D100E TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4R)-7-AZABISABOLENE
1yyu D100E TRICHODIENE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4S)-7-AZABISABOLENE