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(-) Description

Title :  SELINADIENE SYNTHASE IN COMPLEX WITH DIHYDROFARNESYL PYROPHOSPHATE
 
Authors :  P. Baer, P. Rabe, K. Fischer, C. A. Citron, T. Klapschinski, M. Groll, J. S. Dickschat
Date :  23 Jan 14  (Deposition) - 11 Jun 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Sesquiterpene, Cyclase, Terpenoid, Induced Fit, Closed Conformation, Dihydrofarnesyl Pyrophosphate, Pyrophosphate Sensor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Baer, P. Rabe, K. Fischer, C. A. Citron, T. A. Klapschinski, M. Groll J. S. Dickschat
Induced-Fit Mechanism In Class I Terpene Cyclases.
Angew. Chem. Int. Ed. Engl. V. 53 7652 2014
PubMed-ID: 24890698  |  Reference-DOI: 10.1002/ANIE.201403648

(-) Compounds

Molecule 1 - TERPENE SYNTHASE METAL-BINDING DOMAIN-CONTAINING PROTEIN
    Chains: A, B, C, D
    EC Number: 2.5.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SSDG_02809, ZP_06911744
    Organism Scientific: STREPTOMYCES PRISTINAESPIRALIS
    Organism Taxid: 457429

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
13E94Ligand/Ion(3S,6E)-3,7,11-TRIMETHYLDODECA-6,10-DIEN-1-YLTRIHYDROGEN DIPHOSPHATE
2MG12Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13E91Ligand/Ion(3S,6E)-3,7,11-TRIMETHYLDODECA-6,10-DIEN-1-YLTRIHYDROGEN DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13E91Ligand/Ion(3S,6E)-3,7,11-TRIMETHYLDODECA-6,10-DIEN-1-YLTRIHYDROGEN DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
13E91Ligand/Ion(3S,6E)-3,7,11-TRIMETHYLDODECA-6,10-DIEN-1-YLTRIHYDROGEN DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
13E91Ligand/Ion(3S,6E)-3,7,11-TRIMETHYLDODECA-6,10-DIEN-1-YLTRIHYDROGEN DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:82 , GLU A:87 , MG A:902 , 3E9 A:904 , HOH A:1231 , HOH A:1274 , HOH A:1281BINDING SITE FOR RESIDUE MG A 901
02AC2SOFTWAREASP A:82 , GLU A:87 , MG A:901 , 3E9 A:904 , HOH A:1015 , HOH A:1257 , HOH A:1258BINDING SITE FOR RESIDUE MG A 902
03AC3SOFTWAREASN A:224 , SER A:228 , GLU A:232 , 3E9 A:904 , HOH A:1267BINDING SITE FOR RESIDUE MG A 903
04AC4SOFTWARELEU A:78 , PHE A:79 , ASP A:82 , GLU A:87 , ARG A:178 , GLY A:182 , ALA A:183 , ASN A:224 , SER A:228 , LYS A:231 , GLU A:232 , ARG A:310 , TYR A:311 , MG A:901 , MG A:902 , MG A:903 , HOH A:1041 , HOH A:1045 , HOH A:1231 , HOH A:1257 , HOH A:1258 , HOH A:1267 , HOH A:1274 , HOH A:1281BINDING SITE FOR RESIDUE 3E9 A 904
05AC5SOFTWAREASP B:82 , GLU B:87 , MG B:902 , 3E9 B:904 , HOH B:1294 , HOH B:1310 , HOH B:1316BINDING SITE FOR RESIDUE MG B 901
06AC6SOFTWAREASP B:82 , GLU B:87 , MG B:901 , 3E9 B:904 , HOH B:1272 , HOH B:1308 , HOH B:1322BINDING SITE FOR RESIDUE MG B 902
07AC7SOFTWAREASN B:224 , SER B:228 , GLU B:232 , 3E9 B:904 , HOH B:1309BINDING SITE FOR RESIDUE MG B 903
08AC8SOFTWAREPHE B:55 , LEU B:78 , PHE B:79 , ASP B:82 , GLU B:87 , ARG B:178 , GLY B:182 , ALA B:183 , ASN B:224 , SER B:228 , LYS B:231 , GLU B:232 , ARG B:310 , TYR B:311 , MG B:901 , MG B:902 , MG B:903 , HOH B:1030 , HOH B:1294 , HOH B:1308 , HOH B:1309 , HOH B:1310 , HOH B:1316 , HOH B:1322BINDING SITE FOR RESIDUE 3E9 B 904
09AC9SOFTWAREASP C:82 , GLU C:87 , MG C:902 , 3E9 C:904 , HOH C:1014 , HOH C:1288 , HOH C:1293BINDING SITE FOR RESIDUE MG C 901
10BC1SOFTWAREASP C:82 , GLU C:87 , MG C:901 , 3E9 C:904 , HOH C:1273 , HOH C:1289 , HOH C:1298BINDING SITE FOR RESIDUE MG C 902
11BC2SOFTWAREASN C:224 , SER C:228 , GLU C:232 , 3E9 C:904 , HOH C:1294BINDING SITE FOR RESIDUE MG C 903
12BC3SOFTWAREPHE C:55 , LEU C:78 , PHE C:79 , ASP C:82 , GLU C:87 , TYR C:152 , ARG C:178 , GLY C:182 , ALA C:183 , ILE C:220 , ASN C:224 , SER C:228 , LYS C:231 , GLU C:232 , ARG C:310 , TYR C:311 , MG C:901 , MG C:902 , MG C:903 , HOH C:1014 , HOH C:1042 , HOH C:1288 , HOH C:1289 , HOH C:1293 , HOH C:1294 , HOH C:1298BINDING SITE FOR RESIDUE 3E9 C 904
13BC4SOFTWAREGLU D:87 , MG D:902 , 3E9 D:904 , HOH D:1213 , HOH D:1254 , HOH D:1263BINDING SITE FOR RESIDUE MG D 901
14BC5SOFTWAREASP D:82 , GLU D:87 , MG D:901 , 3E9 D:904 , HOH D:1227 , HOH D:1251 , HOH D:1264BINDING SITE FOR RESIDUE MG D 902
15BC6SOFTWAREASN D:224 , SER D:228 , GLU D:232 , 3E9 D:904 , HOH D:1262BINDING SITE FOR RESIDUE MG D 903
16BC7SOFTWAREPHE D:55 , PHE D:79 , ASP D:82 , GLU D:87 , TYR D:152 , ARG D:178 , GLY D:182 , ALA D:183 , ILE D:220 , ASN D:224 , SER D:228 , LYS D:231 , GLU D:232 , ARG D:310 , TYR D:311 , MG D:901 , MG D:902 , MG D:903 , HOH D:1082 , HOH D:1213 , HOH D:1251 , HOH D:1254 , HOH D:1262 , HOH D:1263BINDING SITE FOR RESIDUE 3E9 D 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OKZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OKZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OKZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OKZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4OKZ)

(-) 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:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...........................hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4okz A   4 ELTVPPLFSPIRQAIHPKHADIDVQTAAWAETFRIGSEELRGKLVTQDIGTFSARILPEGREEVVSLLADFILWLFGVDDGHCEEGELGHRPGDLAGLLHRLIRVAQNPEAPMMQDDPLAAGLRDLRMRVDRFGTAGQTARWVDALREYFFSVVWEAAHRRAGTVPDLNDYTLMRLYDGATSVVLPMLEMGHGYELQPYERDRTAVRAVAEMASFIITWDNDIFSYHKERRGSGYYLNALRVLEQERGLTPAQALDAAISQRDRVMCLFTTVSEQLAEQGSPQLRQYLHSLRCFIRGAQDWGISSVRYTTPDDPANMPSVFTDVPTDDSTEPLDIPAVSWWWDLLA 349
                                    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      


Chain B from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...........................hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4okz B   4 ELTVPPLFSPIRQAIHPKHADIDVQTAAWAETFRIGSEELRGKLVTQDIGTFSARILPEGREEVVSLLADFILWLFGVDDGHCEEGELGHRPGDLAGLLHRLIRVAQNPEAPMMQDDPLAAGLRDLRMRVDRFGTAGQTARWVDALREYFFSVVWEAAHRRAGTVPDLNDYTLMRLYDGATSVVLPMLEMGHGYELQPYERDRTAVRAVAEMASFIITWDNDIFSYHKERRGSGYYLNALRVLEQERGLTPAQALDAAISQRDRVMCLFTTVSEQLAEQGSPQLRQYLHSLRCFIRGAQDWGISSVRYTTPDDPANMPSVFTDVPTDDSTEPLDIPAVSWWWDLL 348
                                    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     


Chain C from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...........................hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4okz C   4 ELTVPPLFSPIRQAIHPKHADIDVQTAAWAETFRIGSEELRGKLVTQDIGTFSARILPEGREEVVSLLADFILWLFGVDDGHCEEGELGHRPGDLAGLLHRLIRVAQNPEAPMMQDDPLAAGLRDLRMRVDRFGTAGQTARWVDALREYFFSVVWEAAHRRAGTVPDLNDYTLMRLYDGATSVVLPMLEMGHGYELQPYERDRTAVRAVAEMASFIITWDNDIFSYHKERRGSGYYLNALRVLEQERGLTPAQALDAAISQRDRVMCLFTTVSEQLAEQGSPQLRQYLHSLRCFIRGAQDWGISSVRYTTPDDPANMPSVFTDVPTDDSTEPLDIPAVSWWWDLL 348
                                    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     


Chain D from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...........................hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4okz D   4 ELTVPPLFSPIRQAIHPKHADIDVQTAAWAETFRIGSEELRGKLVTQDIGTFSARILPEGREEVVSLLADFILWLFGVDDGHCEEGELGHRPGDLAGLLHRLIRVAQNPEAPMMQDDPLAAGLRDLRMRVDRFGTAGQTARWVDALREYFFSVVWEAAHRRAGTVPDLNDYTLMRLYDGATSVVLPMLEMGHGYELQPYERDRTAVRAVAEMASFIITWDNDIFSYHKERRGSGYYLNALRVLEQERGLTPAQALDAAISQRDRVMCLFTTVSEQLAEQGSPQLRQYLHSLRCFIRGAQDWGISSVRYTTPDDPANMPSVFTDVPTDDSTEPLDIPAVSWWWDLLA 349
                                    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
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4OKZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OKZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OKZ)

(-) Gene Ontology  (1, 1)

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        B5HDJ6_STRPR | B5HDJ6: 4okm

(-) Related Entries Specified in the PDB File

1ps1 PENTALENENE SYNTHASE
4mc0 HEDYCARYOL APO
4mc3 HEDYCARYOL SYNTHASE IN COMPLEX WITH NEROLIDOL
4okm SELINADIENE SYNTHASE APO AND IN COMPLEX WITH DIPHOSPHATE