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(-) Description

Title :  IRIDOID SYNTHASE FROM CATHARANTHUS ROSEUS - TERNARY COMPLEX WITH NADP+ AND TRIETHYLENE GLYCOL CARBOXYLIC ACID
 
Authors :  L. Caputi, H. Kries, C. E. M. Stevenson, M. O. Kamileen, N. H. Sherden, F. Flores, D. M. Lawson, S. E. O'Connor
Date :  24 Aug 15  (Deposition) - 28 Oct 15  (Release) - 30 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Iridoid Synthase, Short Chain Dehydrogenase, Nadph-Dependent, Catharanthus Roseus, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kries, L. Caputi, C. E. Stevenson, M. O. Kamileen, N. H. Sherden, F. Geu-Flores, D. M. Lawson, S. E. O'Connor
Structural Determinants Of Reductive Terpene Cyclization In Iridoid Biosynthesis.
Nat. Chem. Biol. V. 12 6 2016
PubMed-ID: 26551396  |  Reference-DOI: 10.1038/NCHEMBIO.1955

(-) Compounds

Molecule 1 - IRIDOID SYNTHASE
    Chains: A, B
    EC Number: 1.3.1.99
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: POPIN-F
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-388
    Organism Common: MADAGASCAR PERIWINKLE
    Organism Scientific: CATHARANTHUS ROSEUS
    Organism Taxid: 4058
    Other Details: THE CRYSTALLISED PROTEIN CONTAINED RESIDUES 23-388 OF THE WILD-TYPE AMINO ACID SEQUENCE. THE SEQUENCE DIFFERED FROM DATABASE ENTRY K7WDL7 BY AN ASP TO ASN CHANGE AT POSITION 87. THE N- TERMINUS RETAINED TWO RESIDUES FROM THE NICKEL AFFINITY CLEAVAGE SITE. THE C-TERMINUS HAD AN ADDITIONAL THREE VECTOR-DERIVED RESIDUES.

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3TEG2Ligand/Ion[2-(2-HYDROXYETHOXY)ETHOXY]ACETIC ACID
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3TEG2Ligand/Ion[2-(2-HYDROXYETHOXY)ETHOXY]ACETIC ACID
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3TEG2Ligand/Ion[2-(2-HYDROXYETHOXY)ETHOXY]ACETIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:36 , THR A:38 , GLY A:39 , ILE A:40 , ALA A:65 , ARG A:66 , ARG A:67 , CYS A:83 , ASP A:84 , VAL A:85 , SER A:108 , TRP A:109 , MET A:121 , GLN A:142 , THR A:143 , TYR A:178 , PRO A:201 , ALA A:202 , VAL A:204 , SER A:211 , MET A:212 , MET A:213 , TEG A:902 , HOH A:1003 , HOH A:1017 , HOH A:1026 , HOH A:1032 , HOH A:1045 , HOH A:1054 , HOH A:1066 , HOH A:1140 , HOH A:1345binding site for residue NAP A 900
2AC2SOFTWAREHIS A:147 , ARG A:171 , GLU A:182 , ARG A:200 , HOH A:1004 , HOH A:1027 , HOH A:1072binding site for residue EDO A 901
3AC3SOFTWAREGLY A:144 , ILE A:145 , LYS A:146 , TYR A:178 , PRO A:201 , ALA A:346 , SER A:349 , NAP A:900binding site for residue TEG A 902
4AC4SOFTWAREILE A:225 , GLU A:229 , MET A:313 , LYS A:316 , HOH A:1103 , HOH A:1115binding site for residue EDO A 903
5AC5SOFTWAREGLY B:36 , THR B:38 , GLY B:39 , ILE B:40 , ALA B:65 , ARG B:66 , ARG B:67 , CYS B:83 , ASP B:84 , VAL B:85 , SER B:108 , TRP B:109 , MET B:121 , GLN B:142 , THR B:143 , TYR B:178 , PRO B:201 , ALA B:202 , VAL B:204 , SER B:211 , MET B:212 , MET B:213 , TEG B:902 , HOH B:1005 , HOH B:1053 , HOH B:1062 , HOH B:1083 , HOH B:1084 , HOH B:1099 , HOH B:1102binding site for residue NAP B 900
6AC6SOFTWAREHIS B:147 , ARG B:171 , GLU B:182 , ARG B:200 , HOH B:1008 , HOH B:1052 , HOH B:1054binding site for residue EDO B 901
7AC7SOFTWAREGLY B:144 , ILE B:145 , LYS B:146 , TYR B:178 , PRO B:201 , ALA B:346 , SER B:349 , NAP B:900binding site for residue TEG B 902
8AC8SOFTWAREGLU B:229 , MET B:313 , LYS B:316 , HOH B:1038 , HOH B:1181binding site for residue EDO B 903

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 5)

Asymmetric Unit
No.Residues
1Gly A:57 -Pro A:58
2Ser A:163 -Pro A:164
3Gly B:57 -Pro B:58
4Ser B:163 -Pro B:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DCU)

(-) 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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.....hhhhhhhhh.........eeeeeee....hhhhhh...eeee....hhhhhhhhhh......eeee.......hhhhhhhhhhhhhhhhh.......eeeee..hhhhhh....................hhhhhhhhhhhhhhhhh..eeeeeee..ee........hhhhhhhhhhhhhhhh...ee...hhhhhhh....eehhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhh..ee.........hhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhhhh......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dcu A  23 GVCKSYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKKPVEYIQCDVSNNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNILNSVIPNASNLQHVCLQTGIKHYFGIFEVPHDSPFTEDLPRLNVPNFYHDLEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHENKALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVFKWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLVPTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDKMRDYRFIPKAF 391
                                    32        42        52        62        72        82        92       102       112       122       132       142       152||     167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387    
                                                                                                                                                            153|                                                                                                                                                                                                                                        
                                                                                                                                                             159                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.....hhhhhhhhh.........eeeeeee....hhhhhh...eeee....hhhhhhhhhh......eeee.......hhhhhhhhhhhhhhhhh.......eeeee..hhhhhh....................hhhhhhhhhhhhhhhhh..eeeeeee..ee........hhhhhhhhhhhhhhhh...ee...hhhhhhh....eehhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhh..ee.........hhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhh........hhhhhhh......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dcu B  23 GVCKSYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKKPVEYIQCDVSNNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNILNSVIPNASNLQHVCLQTGIKHYFGIFEVPHDSPFTEDLPRLNVPNFYHDLEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHENKALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVFKWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLVPTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDKMRDYRFIPKAF 391
                                    32        42        52        62        72        82        92       102       112       122       132       142       152||     167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387    
                                                                                                                                                            153|                                                                                                                                                                                                                                        
                                                                                                                                                             159
   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 5DCU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        IRIS_CATRO | K7WDL7: 5coa 5cob 5dbf 5dbg 5dbi 5dcw 5dcy 5df1 5emh

(-) Related Entries Specified in the PDB File

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