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(-) Description

Title :  CRYSTAL STRUCTURE OF IRIDOID SYNTHASE FROM CANTHARANTHUS ROSEUS IN COMPLEX WITH NADPH
 
Authors :  Y. M. Hu, W. D. Liu, Y. Y. Zheng, Z. X. Xu, T. P. Ko, C. C. Chen, R. T. Guo
Date :  21 Aug 15  (Deposition) - 04 Nov 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Metal-Binding, Substrate Binding, Acidocalcisomal Pyrophosphatase, Inhibitor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. M. Hu, W. D. Liu, S. R. Malwal, Y. Y. Zheng, X. X. Feng, T. P. Ko, C. C. Chen, Z. X. Xu, M. X. Liu, X. Han, J. Gao, E. Oldfield, R. T. Guo
Structures Of Iridoid Synthase From Cantharanthus Roseus With Bound Nad(+) , Nadph, Or Nad(+) /10-Oxogeranial: Reaction Mechanisms
Angew. Chem. Int. Ed. Engl. V. 54 15478 2015
PubMed-ID: 26768532  |  Reference-DOI: 10.1002/ANIE.201508310

(-) 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: PET32XA/LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 26-388
    Organism Common: MADAGASCAR PERIWINKLE
    Organism Scientific: CATHARANTHUS ROSEUS
    Organism Taxid: 4058

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
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 , HOH A:516 , HOH A:535binding site for residue NDP A 401
2AC2SOFTWAREGLY 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 , HOH B:511 , HOH B:552 , HOH B:569binding site for residue NDP B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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 5DBF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DBF)

(-) 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:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               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.eee........hhhhhhhhhhhhhhhh...ee...hhhhhhh...eeehhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhh...ee.........hhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhhhh......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dbf A  27 SYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKKPVEYIQCDVSDNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNILNSVIPNASNLQHVCLQTGIKHYFGIFEVPHDSPFTEDLPRLNVPNFYHDLEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHENKALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVFKWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLVPTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDKMRDYRFIPAS 390
                                    36        46        56        66        76        86        96       106       116       126       136       146      |161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
                                                                                                                                                        153|                                                                                                                                                                                                                                       
                                                                                                                                                         159                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               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.eee........hhhhhhhhhhhhhhhh...ee...hhhhhhh...eeehhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhh...ee.........hhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhhhh......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dbf B  27 SYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKKPVEYIQCDVSDNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNILNSVIPNASNLQHVCLQTGIKHYFGIFEEVPHDSPFTEDLPRLNVPNFYHDLEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHENKALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVFKWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLVPTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDKMRDYRFIPAS 390
                                    36        46        56        66        76        86        96       106       116       126       136       146       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390
                                                                                                                                                         154|                                                                                                                                                                                                                                       
                                                                                                                                                          159
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5DBF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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        IRIS_CATRO | K7WDL7: 5coa 5cob 5dbg 5dbi 5dcu 5dcw 5dcy 5df1 5emh

(-) Related Entries Specified in the PDB File

5dbg 5dbi