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(-) Description

Title :  CRYSTAL STRUCTURE OF CYCLIZATION DOMAIN OF PHOMOPSIS AMYGDALI FUSICOCCADIENE SYNTHASE COMPLEXED WITH MANGANESE IONS AND NERIDRONATE
 
Authors :  M. Chen, D. W. Christianson
Date :  13 Nov 15  (Deposition) - 20 Jan 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Diterpene Cyclase, Terpenoids, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Chen, W. K. Chou, T. Toyomasu, D. E. Cane, D. W. Christianson
Structure And Function Of Fusicoccadiene Synthase, A Hexameric Bifunctional Diterpene Synthase.
Acs Chem. Biol. V. 11 889 2016
PubMed-ID: 26734760  |  Reference-DOI: 10.1021/ACSCHEMBIO.5B00960

(-) Compounds

Molecule 1 - FUSICOCCADIENE SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: FUSICOCCA-2,10(14)-DIENE SYNTHASE, RESIDUES 1-344
    Gene: PAFS
    Organism Scientific: PHOMOPSIS AMYGDALI
    Organism Taxid: 1214568
    Other Details: NERIDRONATE

 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  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MN9Ligand/IonMANGANESE (II) ION
3NRD2Ligand/Ion(6-AZANYL-1-OXIDANYL-1-PHOSPHONO-HEXYL)PHOSPHONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MN-1Ligand/IonMANGANESE (II) ION
3NRD1Ligand/Ion(6-AZANYL-1-OXIDANYL-1-PHOSPHONO-HEXYL)PHOSPHONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MN-1Ligand/IonMANGANESE (II) ION
3NRD1Ligand/Ion(6-AZANYL-1-OXIDANYL-1-PHOSPHONO-HEXYL)PHOSPHONIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:92 , ASP A:96 , LYS A:239 , GLU A:240 , MN A:702 , NRD A:704 , HOH A:803 , HOH A:806binding site for residue MN A 701
02AC2SOFTWAREASP A:92 , ASP A:96 , MN A:701 , NRD A:704 , HOH A:801 , HOH A:804 , HOH A:807 , HOH A:813binding site for residue MN A 702
03AC3SOFTWAREARG A:188 , ASN A:232 , SER A:236 , GLU A:240 , NRD A:704 , HOH A:802binding site for residue MN A 703
04AC4SOFTWAREPHE A:65 , ASP A:92 , ASP A:96 , ARG A:188 , ASP A:191 , ASN A:232 , SER A:236 , LYS A:239 , GLU A:240 , ARG A:325 , TYR A:326 , MN A:701 , MN A:702 , MN A:703 , HOH A:801 , HOH A:802 , HOH A:803 , HOH A:804 , HOH A:806 , HOH A:813 , HOH A:820binding site for residue NRD A 704
05AC5SOFTWARETHR A:16 , GLU A:17 , HOH A:822 , THR B:265binding site for residue CL A 705
06AC6SOFTWAREHOH A:821 , HOH A:822 , HOH A:830 , HOH B:838binding site for residue MN A 706
07AC7SOFTWAREASP B:92 , ASP B:96 , LYS B:239 , MN B:702 , NRD B:704 , HOH B:803 , HOH B:821binding site for residue MN B 701
08AC8SOFTWAREASP B:92 , ASP B:96 , MN B:701 , NRD B:704 , HOH B:809 , HOH B:818 , HOH B:823binding site for residue MN B 702
09AC9SOFTWAREARG B:188 , ASN B:232 , SER B:236 , GLU B:240 , NRD B:704 , HOH B:802binding site for residue MN B 703
10AD1SOFTWAREASP B:92 , ASP B:96 , ARG B:188 , ASP B:191 , VAL B:192 , TRP B:225 , ASN B:232 , SER B:236 , LYS B:239 , GLU B:240 , ARG B:325 , TYR B:326 , MN B:701 , MN B:702 , MN B:703 , HOH B:803 , HOH B:809 , HOH B:810 , HOH B:821binding site for residue NRD B 704
11AD2SOFTWARETHR A:265 , TYR B:15 , THR B:16 , GLU B:17 , HOH B:814binding site for residue CL B 705
12AD3SOFTWAREHOH A:829 , HOH B:812 , HOH B:814 , HOH B:833 , HOH B:842binding site for residue MN B 706
13AD4SOFTWAREHIS B:212 , GLU B:213 , SER B:297 , HOH B:824binding site for residue MN B 707

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ER8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5ER8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ER8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ER8)

(-) Exons   (0, 0)

(no "Exon" information available for 5ER8)

(-) 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeehhhhh..........eee..hhhhhhhhhhhhhhhhhhhh..............hhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5er8 A   2 EFKYSEVVEPSTYYTEGLCEGIDVRKSKFTTLEDRGAIRAHEDWNKHIGPCREYRGTLGPRFSFISVAVPECIPERLEVISYANEFAFLHDDVTDGKKRIQSQLFLEMLAIDPECAKTTMKSWARTRFVELAKYIPYRIMDVGEMFWFGLVTFGLGLHIPDHELELCRELMANAWIAVGLQNDIWSWPKERDAATLHGKDHVVNAIWVLMQEHQTDVDGAMQICRKLIVEYVAKYLEVIEATKNDESISLDLRKYLDAMLYSISGNVVWSLECPRYNPDVSFNKTQLEWMRQGL 344
                                    11        21        31        41        51        61        71        81        91    || 139       149       159    || 180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
                                                                                                                         96|                          164|                                                                                                                                                                        
                                                                                                                         135                           176                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhh...........eee.hhhhhhhhhhhhhhhhhhhh..............hhhhhhh...hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5er8 B   2 EFKYSEVVEPSTYYTEGLCEGIDVRKSKFTTLEDRGAIRAHEDWNKHIGPCREYRGTLGPRFSFISVAVPECIPERLEVISYANEFAFLHDDVTDAGKKRIQSQLFLEMLAIDPECAKTTMKSWARFVEVGSSRETRFVELAKYIPYRIMDVGEMFWFGLVTFGLGLHIPDHELELCRELMANAWIAVGLQNDIWSWPKERDAATLHGKDHVVNAIWVLMQEHQTDVDGAMQICRKLIVEYVAKYLEVIEATKNDESISLDLRKYLDAMLYSISGNVVWSLECPRYNPDVSFNKTQLEWMRQGL 344
                                    11        21        31        41        51        61        71        81        91    || 138       148       158       168   ||  180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
                                                                                                                         96|                                   172|                                                                                                                                                                         
                                                                                                                         134                                    175
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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  (0, 0)

(no "SCOP Domain" information available for 5ER8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ER8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ER8)

(-) Gene Ontology  (7, 7)

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 Related Entries

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UniProtKB/Swiss-Prot
        FUSS_PHOAM | A2PZA5: 5erm 5ern 5ero

(-) Related Entries Specified in the PDB File

5ern 5ero