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Title :  THE X-RAY STRUCTURE OF NORCOCLAURINE SYNTHASE FROM THALICTRUM FLAVUM
 
Authors :  A. Ilari, S. Franceschini, A. Boffi, A. Bonamore, A. Pasquo
Date :  04 Feb 08  (Deposition) - 05 Aug 08  (Release) - 13 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.72
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lyase, Norcoclaurine Synthase, Biosynthesis Of Benzylisoquinoline Alkaloids (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ilari, S. Franceschini, A. Bonamore, F. Arenghi, B. Botta, A. Macone, A. Pasquo, L. Bellucci, A. Boffi
Structural Basis Of Enzymatic S-Norcoclaurine Biosynthesis.
J. Biol. Chem. V. 284 897 2009
PubMed-ID: 19004827  |  Reference-DOI: 10.1074/JBC.M803738200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - S-NORCOCLAURINE SYNTHASE
    ChainsA, B
    EC Number4.2.1.78
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22-B
    Expression System StrainBL21DE3
    Expression System Taxid469008
    FragmentRESIDUES 16-210
    MutationYES
    Organism ScientificTHALICTRUM FLAVUM
    Organism Taxid150094
    Other DetailsTHE PROTEIN LACKS THE FIRST 15 RESIDUES AND IS HIS-TAGGED AT THE C-TERMINUS.
    SynonymNORCOCLAURINE SYNTHASE FROM THALICTRUM FLAVUM

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2VNE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VNE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VNE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VNE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VNE)

(-) Exons   (0, 0)

(no "Exon" information available for 2VNE)

(-) 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:173
 aligned with NCS_THLFG | Q67A25 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:176
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      
            NCS_THLFG    19 CQKLILTGRPFLHHQGIINQVSTVTKVIHHELEVAASADDIWTVYSWPGLAKHLPDLLPGAFEKLEIIGDGGVGTILDMTFVPGEFPHEYKEKFILVDNEHRLKKVQMIEGGYLDLGVTYYMDTIHVVPTGKDSCVIKSSTEYHVKPEFVKIVEPLITTGPLAAMADAISKLVLEH 194
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........---...........eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.......eeeeee.......eeeeeeeeee....eeeeeeeee.hhhh.eeeeeeeeeeeeee..eeeeeeeeeeee...hhhhhh....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vne A  19 SQKLILTGR---HHQGIINQVSTVTKVIHHELEVAASADDIWTVYSWPGLAKHLPDLLPGAFEKLEIIGDGGVGTILDmTFVPGEFPHEYKEKFILVDNEHRLKKVQmIEGGYLDLGVTYYmDTIHVVPTGKDSCVIKSSTEYHVKPEFVKIVEPLITTGPLAAmADAISKLVLEH 194
                                    |-  |     38        48        58        68        78        88        98       108       118       128       138 |     148       158       168       178    |  188      
                                   27  31                                                                97-MSE                      126-MSE       140-MSE                                    183-MSE       

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with NCS_THLFG | Q67A25 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:155
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189     
            NCS_THLFG    40 STVTKVIHHELEVAASADDIWTVYSWPGLAKHLPDLLPGAFEKLEIIGDGGVGTILDMTFVPGEFPHEYKEKFILVDNEHRLKKVQMIEGGYLDLGVTYYMDTIHVVPTGKDSCVIKSSTEYHVKPEFVKIVEPLITTGPLAAMADAISKLVLEH 194
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Bet_v_1-2vneB01 B:40-194                                                                                                                                    Pfam domains (1)
           Pfam domains (2) Bet_v_1-2vneB02 B:40-194                                                                                                                                    Pfam domains (2)
         Sec.struct. author ..eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.....eeeee.......eeeee........eeeeeeeeee....eeeeeeeee.hhhh.eeeeeeeeeeee.....eeeeeeeeeee...hhhhhh....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vne B  40 STVTKVIHHELEVAASADDIWTVYSWPGLAKHLPDLLPGAFEKLEIIGDGGVGTILDmTFVPGEFPHEYKEKFILVDNEHRLKKVQmIEGGYLDLGVTYYmDTIHVVPTGKDSCVIKSSTEYHVKPEFVKIVEPLITTGPLAAmADAISKLVLEH 194
                                    49        59        69        79        89       |99       109       119      |129       139|      149       159       169       179   |   189     
                                                                                    97-MSE                      126-MSE       140-MSE                                    183-MSE       

   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 2VNE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VNE)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NCS_THLFG | Q67A25)
molecular function
    GO:0050474    (S)-norcoclaurine synthase activity    Catalysis of the reaction: 4-(2-aminoethyl)benzene-1,2-diol + 4-hydroxyphenylacetaldehyde = (S)-norcoclaurine + H2O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0009820    alkaloid metabolic process    The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0009607    response to biotic stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCS_THLFG | Q67A252vq5

(-) Related Entries Specified in the PDB File

2vq5 X-RAY STRUCTURE OF NORCOCLAURINE SYNTHASE FROM THALICTRUM FLAVUM IN COMPLEX WITH DOPAMINE AND HYDROXYBENZALDEHYDE