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(-) Description

Title :  IRIDOID SYNTHASE G150A MUTANT FROM CATHARANTHUS ROSEUS - BINARY COMPLEX WITH NADP+
 
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) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
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: SOLUBL21
    Fragment: 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 AND BY A GLY TO ALA CHANGE AT POSITION 150. THE N-TERMINUS RETAINED TWO RESIDUES FROM THE NICKEL AFFINITY CLEAVAGE SITE.

 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, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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:86 , 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 , PGE A:901 , HOH A:1020 , HOH A:1036 , HOH A:1065 , HOH A:1073 , HOH A:1083 , HOH A:1143 , HOH A:1241binding site for residue NAP A 900
02AC2SOFTWAREGLU A:113 , LYS A:146 , ILE A:151 , ASN A:176 , PHE A:177 , TYR A:178 , MET A:213 , ILE A:345 , NAP A:900binding site for residue PGE A 901
03AC3SOFTWAREHIS A:147 , ARG A:171 , GLU A:182 , ARG A:200 , HOH A:1003 , HOH A:1051 , HOH A:1101binding site for residue EDO A 902
04AC4SOFTWAREILE A:225 , GLU A:229 , MET A:313 , LYS A:316 , HOH A:1121 , HOH A:1151binding site for residue EDO A 903
05AC5SOFTWAREGLY 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 , PGE B:901 , HOH B:1001 , HOH B:1008 , HOH B:1037 , HOH B:1040 , HOH B:1043 , HOH B:1049 , HOH B:1085 , HOH B:1173 , HOH B:1220binding site for residue NAP B 900
06AC6SOFTWAREGLU B:113 , LYS B:146 , ASN B:176 , PHE B:177 , TYR B:178 , MET B:213 , NAP B:900binding site for residue PGE B 901
07AC7SOFTWAREALA B:310 , ALA B:338 , ALA B:339 , PHE B:340 , TRP B:341 , HOH B:1077 , HOH B:1152 , HOH B:1252binding site for residue EDO B 902
08AC8SOFTWAREILE B:225 , CYS B:226 , GLU B:229 , MET B:313 , HOH B:1036 , HOH B:1059binding site for residue EDO B 903
09AC9SOFTWAREHIS B:147 , ARG B:171 , GLU B:182 , ARG B:200 , HOH B:1004 , HOH B:1050 , HOH B:1069binding site for residue EDO B 904
10AD1SOFTWAREASP B:250 , ASP B:252 , ARG B:368binding site for residue EDO B 905

(-) SS Bonds  (0, 0)

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

(-) 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 5DCY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DCY)

(-) 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:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee.....hhhhhhhhh.........eeeeeee.............eeee....hhhhhhhhhh......eeee.......hhhhhhhhhhhhhhhhh.......eeeee.hhhhhh.ee....ee.................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
                 5dcy A  23 GVCKSYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKKPVEYIQCDVSNNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNILNSVIPNASNLQHVCLQTGIKHYFAIFEEGSKVVPHDSPFTEDLPRLNVPNFYHDLEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHENKALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVFKWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLVPTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDKMRDYRFIP 388
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382      


Chain B from PDB  Type:PROTEIN  Length:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.....hhhhhhhhh.........eeeeeee....hhhhh....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
                 5dcy B  23 GVCKSYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKKPVEYIQCDVSNNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNILNSVIPNASNLQHVCLQTGIKHYFAPHDSPFTEDLPRLNVPNFYHDLEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHENKALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVFKWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLVPTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDKMRDYRFIP 388
                                    32        42        52        62        72        82        92       102       112       122       132       142       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       
                                                                                                                                                         150|                                                                                                                                                                                                                                    
                                                                                                                                                          160
   Legend:   → Mismatch (orange background)
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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 5DCY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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