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(-) Description

Title :  CRYSTAL STRUCTURE OF PFOMT, PHENYLPROPANOID AND FLAVONOID O-METHYLTRANSFERASE FROM M. CRYSTALLINUM
 
Authors :  J. G. Kopycki, D. Rauh, P. Neumann, M. T. Stubbs
Date :  29 Jan 08  (Deposition) - 01 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.37
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plant Secondary Metabolism, O-Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. G. Kopycki, D. Rauh, A. A. Chumanevich, P. Neumann, T. Vogt, M. T. Stubbs
Biochemical And Structural Analysis Of Substrate Promiscuity In Plant Mg(2+)-Dependent O-Methyltransferases
J. Mol. Biol. V. 378 154 2008
PubMed-ID: 18342334  |  Reference-DOI: 10.1016/J.JMB.2008.02.019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - O-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.104
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: M15 PREP4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: COMMON ICEPLANT
    Organism Scientific: MESEMBRYANTHEMUM CRYSTALLINUM
    Organism Taxid: 3544
    Synonym: PFOMT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:154 , ASP A:180 , ASN A:181 , HOH A:470 , HOH A:693 , HOH A:694BINDING SITE FOR RESIDUE CA A 238
2AC2SOFTWAREGLU A:106 , GLU A:109 , GLU A:204 , GLU A:208 , HOH A:700 , HOH A:703BINDING SITE FOR RESIDUE CA A 239
3AC3SOFTWAREASP B:154 , ASP B:180 , ASN B:181 , HOH B:694 , HOH B:695 , HOH B:696BINDING SITE FOR RESIDUE CA B 238
4AC4SOFTWAREMET A:52 , SER A:53 , THR A:54 , GLY A:78 , VAL A:79 , PHE A:80 , SER A:84 , ASP A:102 , PHE A:103 , ASP A:104 , SER A:129 , ASP A:130 , ALA A:131 , ASP A:154 , ALA A:155 , ASP A:156 , HOH A:466 , HOH A:513 , HOH A:532 , HOH A:643BINDING SITE FOR RESIDUE SAH A 464
5AC5SOFTWAREMET B:52 , SER B:53 , THR B:54 , GLY B:78 , VAL B:79 , PHE B:80 , SER B:84 , ASP B:102 , PHE B:103 , ASP B:104 , SER B:129 , ASP B:130 , ALA B:131 , ASP B:154 , ALA B:155 , ASP B:156 , HOH B:480 , HOH B:559 , HOH B:583 , HOH B:636BINDING SITE FOR RESIDUE SAH B 465

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C3Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C3Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3C3Y)

(-) Sequences/Alignments

Asymmetric/Biological 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:225
 aligned with Q6YI95_MESCR | Q6YI95 from UniProtKB/TrEMBL  Length:237

    Alignment length:225
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     
         Q6YI95_MESCR    13 GLLQSEELCQYILRTSVYPREAGFLKELREANESHPDSYMSTSPLAGQLMSFVLKLVNAKKTIEVGVFTGYSLLLTALSIPDDGKITAIDFDREAYEIGLPFIRKAGVEHKINFIESDAMLALDNLLQGQESEGSYDFGFVDADKPNYIKYHERLMKLVKVGGIVAYDNTLWGGTVAQPESEVPDFMKENREAVIELNKLLAADPRIEIVHLPLGDGITFCRRLY 237
               SCOP domains d3c3ya_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains 3c3yA00 A:13-237 Vaccinia Virus protein VP39                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c3y A  13 GLLQSEELCQYILRTSVYPREAGFLKELREANESHPDSYMSTSPLAGQLMSFVLKLVNAKKTIEVGVFTGYSLLLTALSIPDDGKITAIDFDREAYEIGLPFIRKAGVEHKINFIESDAMLALDNLLQGQESEGSYDFGFVDADKPNYIKYHERLMKLVKVGGIVAYDNTLWGGTVAQPESEVPDFMKENREAVIELNKLLAADPRIEIVHLPLGDGITFCRRLY 237
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with Q6YI95_MESCR | Q6YI95 from UniProtKB/TrEMBL  Length:237

    Alignment length:225
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     
         Q6YI95_MESCR    13 GLLQSEELCQYILRTSVYPREAGFLKELREANESHPDSYMSTSPLAGQLMSFVLKLVNAKKTIEVGVFTGYSLLLTALSIPDDGKITAIDFDREAYEIGLPFIRKAGVEHKINFIESDAMLALDNLLQGQESEGSYDFGFVDADKPNYIKYHERLMKLVKVGGIVAYDNTLWGGTVAQPESEVPDFMKENREAVIELNKLLAADPRIEIVHLPLGDGITFCRRLY 237
               SCOP domains d3c3yb_ B: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains 3c3yB00 B:13-237 Vaccinia Virus protein VP39                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh........eeeeee..hhhhhhhhhhhhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c3y B  13 GLLQSEELCQYILRTSVYPREAGFLKELREANESHPDSYMSTSPLAGQLMSFVLKLVNAKKTIEVGVFTGYSLLLTALSIPDDGKITAIDFDREAYEIGLPFIRKAGVEHKINFIESDAMLALDNLLQGQESEGSYDFGFVDADKPNYIKYHERLMKLVKVGGIVAYDNTLWGGTVAQPESEVPDFMKENREAVIELNKLLAADPRIEIVHLPLGDGITFCRRLY 237
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C3Y)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6YI95_MESCR | Q6YI95)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0042409    caffeoyl-CoA O-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + caffeoyl-CoA = S-adenosyl-L-homocysteine + feruloyl-CoA.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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