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(-) Description

Title :  THE STRUCTURE OF 1,7 DIMETHYLXANTHINE METHYLTRANSFERASE
 
Authors :  A. A. Mccarthy, J. G. Mccarthy
Date :  22 Feb 07  (Deposition) - 01 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Sam-Dependant Methyltransferase, Sah, Theobromine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Mccarthy, J. G. Mccarthy
The Structure Of Two N-Methyltransferases From The Caffeine Biosynthetic Pathway
Plant Physiol. V. 144 879 2007
PubMed-ID: 17434991  |  Reference-DOI: 10.1104/PP.106.094854
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3,7-DIMETHYLXANTHINE METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEXHTB
    Expression System Strain: BL21 (RIL)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DXMT1
    Organism Scientific: COFFEA CANEPHORA
    Organism Taxid: 49390

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
137T1Ligand/IonTHEOBROMINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
137T2Ligand/IonTHEOBROMINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:7 , MET A:9 , TYR A:18 , GLY A:60 , CYS A:61 , ALA A:62 , ASN A:66 , ASN A:99 , ASP A:100 , GLY A:138 , SER A:139 , PHE A:140 , TYR A:141 , CYS A:156 , TYR A:157 , CYS A:158 , 37T A:502 , HOH A:510 , HOH A:517 , HOH A:520 , HOH A:547 , HOH A:647BINDING SITE FOR RESIDUE SAH A 501
2AC2SOFTWARETYR A:18 , LEU A:26 , PHE A:27 , TYR A:157 , HIS A:160 , TRP A:161 , ILE A:226 , SER A:237 , ILE A:332 , TYR A:368 , SAH A:501 , HOH A:509 , HOH A:587BINDING SITE FOR RESIDUE 37T A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2EFJ)

(-) 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:348
 aligned with DXMT1_COFCA | A4GE70 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:377
                                    12        22        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       
          DXMT1_COFCA     3 LQEVLHMNGGEGDTSYAKNSSYNLFLIRVKPVLEQCIQELLRANLPNINKCFKVGDLGCASGPNTFSTVRDIVQSIDKVGQEKKNELERPTIQIFLNDLFQNDFNSVFKLLPSFYRNLEKENGRKIGSCLIGAMPGSFYSRLFPEESMHFLHSCYCLHWLSQVPSGLVTELGISVNKGCIYSSKASRPPIQKAYLDQFTKDFTTFLRIHSEELISRGRMLLTFICKEDEFDHPNSMDLLEMSINDLVIEGHLEEEKLDSFNVPIYAPSTEEVKRIVEEEGSFEILYLETFNAPYDAGFSIDDDYQGRSHSPVSCDEHARAAHVASVVRSIYEPILASHFGEAILPDLSHRIAKNAAKVLRSGKGFYDSVIISLAKKP 379
               SCOP domains d2efja_ A    : automated matches                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------    -----2efjA02 A:21-163,A:196-229,A:264-295,A:365-379 Vaccinia Virus           protein VP39                                                           -----      ---------------------2efjA02                           ----------------------------------2efjA02                         -------         -----------------------------------------------------2efjA02         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........----.hhhhhh....hhhhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhhhh..----------.eeeeeee.....hhhhhhhhhhhhhhhhhhhh......eeeee..............eeeeeee............------..............hhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee.........hhhhhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhhh.eeeeeeeeeeee.......---------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2efj A   3 LQEVLHMNG----TSYAKNSSYNLFLIRVKPVLEQCIQELLRANLPNINKCFKVGDLGCASGPNTFSTVRDIVQSIDKV----------PTIQIFLNDLFQNDFNSVFKLLPSFYRNLEKENGRKIGSCLIGAMPGSFYSRLFPEESMHFLHSCYCLHWLSQVPSG------ISVNKGCIYSSKASRPPIQKAYLDQFTKDFTTFLRIHSEELISRGRMLLTFICKEDEFDHPNSMDLLEMSINDLVIEGHLEEEKLDSFNVPIYAPSTEEVKRIVEEEGSFEILYLETFNAPYDAGFSI---------SPVSCDEHARAAHVASVVRSIYEPILASHFGEAILPDLSHRIAKNAAKVLRSGKGFYDSVIISLAKKP 379
                                    |-   |    22        32        42        52        62        72        |-        92       102       112       122       132       142       152       162     |   -  |    182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       
                                   11   16                                                               81         92                                                                         168    175                                                                                                                            302       312
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EFJ)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (DXMT1_COFCA | A4GE70)
molecular function
    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: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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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(-) Related Entries Specified in the PDB File

2eg5 XANTHOSINE METHYLTRANSFERASE