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(-) Description

Title :  CRYSTAL STRUCTURE OF ELONGATION DOMAIN OF PHOMOPSIS AMYGDALI FUSICOCCADIENE SYNTHASE COMPLEXED WITH COBALT IONS AND PAMIDRONATE
 
Authors :  M. Chen, D. W. Christianson
Date :  14 Nov 15  (Deposition) - 20 Jan 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  A (1x),B (1x),C (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  C  (2x)
Keywords :  Diterpene Synthase, Lyase, Transferase (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, C
    EC Number: 2.5.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: GERANYLGERANYL DIPHOSPHATE SYNTHASE, RESIDUES 382-719
    Gene: PAFS
    Organism Scientific: PHOMOPSIS AMYGDALI
    Organism Taxid: 1214568

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC
Biological Unit 2 (1x): A (1x)B (1x)C (1x)
Biological Unit 3 (1x): AB 
Biological Unit 4 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
12103Ligand/IonPAMIDRONATE
2CO12Ligand/IonCOBALT (II) ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
12106Ligand/IonPAMIDRONATE
2CO-1Ligand/IonCOBALT (II) ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
12102Ligand/IonPAMIDRONATE
2CO-1Ligand/IonCOBALT (II) ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
12102Ligand/IonPAMIDRONATE
2CO-1Ligand/IonCOBALT (II) ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
12102Ligand/IonPAMIDRONATE
2CO-1Ligand/IonCOBALT (II) ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:605 , 210 A:804 , HOH A:918 , HOH A:923 , HOH A:926binding site for residue CO A 801
02AC2SOFTWAREASP A:474 , ASP A:478 , CO A:803 , 210 A:804 , HOH A:903 , HOH A:911 , HOH A:913binding site for residue CO A 802
03AC3SOFTWAREASP A:474 , ASP A:478 , CO A:802 , 210 A:804 , HOH A:905 , HOH A:928binding site for residue CO A 803
04AC4SOFTWARELEU A:471 , ASP A:474 , ASP A:478 , ARG A:483 , LYS A:561 , GLN A:602 , ASP A:605 , LYS A:619 , LYS A:629 , CO A:801 , CO A:802 , CO A:803 , HOH A:905 , HOH A:908 , HOH A:911 , HOH A:913 , HOH A:918 , HOH A:923 , HOH A:926 , HOH A:928binding site for residue 210 A 804
05AC5SOFTWAREASP A:447 , HOH A:965binding site for residue CO A 805
06AC6SOFTWAREASP B:605 , 210 B:804 , HOH B:915 , HOH B:922 , HOH B:930binding site for residue CO B 801
07AC7SOFTWAREASP B:474 , ASP B:478 , CO B:803 , 210 B:804 , HOH B:902 , HOH B:906 , HOH B:908binding site for residue CO B 802
08AC8SOFTWAREASP B:474 , ASP B:478 , CO B:802 , 210 B:804 , HOH B:903 , HOH B:907binding site for residue CO B 803
09AC9SOFTWAREASP B:474 , ASP B:478 , ARG B:483 , LYS B:561 , GLN B:602 , ASP B:605 , LYS B:619 , LYS B:629 , CO B:801 , CO B:802 , CO B:803 , HOH B:901 , HOH B:902 , HOH B:903 , HOH B:906 , HOH B:907 , HOH B:915 , HOH B:922 , HOH B:936binding site for residue 210 B 804
10AD1SOFTWAREASP B:447 , ASP B:453binding site for residue CO B 805
11AD2SOFTWAREASP C:605 , ASP C:624 , 210 C:804binding site for residue CO C 801
12AD3SOFTWAREASP C:474 , ASP C:478 , CO C:803 , 210 C:804binding site for residue CO C 802
13AD4SOFTWAREASP C:474 , ASP C:478 , GLU C:627 , CO C:802 , 210 C:804 , HOH C:902 , HOH C:907binding site for residue CO C 803
14AD5SOFTWAREASP C:474 , ASP C:478 , ARG C:483 , LYS C:561 , GLN C:602 , ASP C:605 , LYS C:619 , LYS C:629 , CO C:801 , CO C:802 , CO C:803 , HOH C:901binding site for residue 210 C 804
15AD6SOFTWAREASP C:447binding site for residue CO C 805

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:519 -Glu A:520
2Gly B:519 -Glu B:520
3Val B:525 -Met B:526
4Ile B:581 -Pro B:582
5Ala C:613 -Asp C:614

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERO)

(-) 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:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ero A 413 DHIFFEKAVLEAPYDYIASMPSKGVRDQFIDALNDWLRVPDVKVGKIKDAVRVLHNSSLLLDDFQDNSPLRRGKPSTHNIFGSAQTVNTATYSIIKAIGQIMEFSAGEVQEVMNSIMILFQGQAMDLFWTYNGHVPSEEEYYRMIDQKTGQLFSIATSLLLNAARTKIQSCLHRLTRLLGRCFQIRDDYQNLVSADYTKQKGFCEDLDEGKWSLALIHMIHKQRSHMALLNVLSTGRKHGGMTLEQKQFVLDIIEEEKSLDYTRSVMMDLHVQLRAEIGRIEILLDSPNPAMRLLLELLRV 719
                                   422       432       442       452       462       472       482       492       502       512       523       533       543       553       563       573   ||  588       598       608       618       628       638       648       658       668       678       688       698       708       718 
                                                                                                                                     520|                                                    577|                                                                                                                                        
                                                                                                                                      522                                                     583                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ero B 414 HIFFEKAVLEAPYDYIASMPSKGVRDQFIDALNDWLRVPDVKVGKIKDAVRVLHNSSLLLDDFQDNSPLRRGKPSTHNIFGSAQTVNTATYSIIKAIGQIMEFSAGEEVMNSIMILFQGQAMDLFWTYNGHVPSEEEYYRMIDQKTGQLFSIATSLLLNAADNEIPRTKIQSCLHRLTRLLGRCFQIRDDYQNLVSADYTKQKGFCEDLDEGKWSLALIHMIHKQRSHMALLNVLSTGRKHGGMTLEQKQFVLDIIEEEKSLDYTRSVMMDLHVQLRAEIGRIEILLDSPNPAMRLLLEL 716
                                   423       433       443       453       463       473       483       493       503       513      |526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716
                                                                                                                                    520|                                                                                                                                                                                                
                                                                                                                                     524                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh..hhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ero C 415 IFFEKAVLEAPYDYIASMPSKGVRDQFIDALNDWLRVPDVKVGKIKDAVRVLHNSSLLLDDFQDNSPLRRGKPSTHNIFGSAQTVNTATYSIIKAIGQIMEFSAGESVQEVMNSIMILFQGQAMDLFWTYNGHVPSEEEYYRMIDQKTGQLFSIATSLLLNAADNEIPRTKIQSCLHRLTRLLGRCFQIRDDYQNLVSADYTKQKGFCEDLDEGKWSLALIHMISHMALLNVLSTGRKHGGMTLEQKQFVLDIIEEEKSLDYTRSVMMDLHVQLRAEIGRIEILLDSPNPAMRLLLELL 717
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634   ||  648       658       668       678       688       698       708         
                                                                                                                                                                                                                                                         638|                                                                          
                                                                                                                                                                                                                                                          643
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala C:613 - Asp C:614   [ RasMol ]  
    Gly A:519 - Glu A:520   [ RasMol ]  
    Gly B:519 - Glu B:520   [ RasMol ]  
    Ile B:581 - Pro B:582   [ RasMol ]  
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  2.5.1.29
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 Related Entries

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

UniProtKB/Swiss-Prot
        FUSS_PHOAM | A2PZA5: 5er8 5erm 5ern

(-) Related Entries Specified in the PDB File

5er8 5erm 5ern