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(-) Description

Title :  CRYSTAL STRUCTURE OF ISOFLAVONE O-METHYLTRANSFERASE HOMOLOG IN COMPLEX WITH BIOCHANIN A AND SAH
 
Authors :  C. Wang, X. -H. Yu, C. -J. Liu
Date :  15 Aug 07  (Deposition) - 26 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isoflavone O-Methyltransferase 3, Surface Binding Site (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Wang, X. -H. Yu, C. -J. Liu
Crystal Structures Of Medicago Truncatula Isoflavone O-Methyltransferase Reveal Conserved Surface Binding Motifs Critical For Enzymatic Activity
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - O-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: MEDICAGO TRUNCATULA IOMT3 GENE
    Organism Common: BARREL MEDIC
    Organism Scientific: MEDICAGO TRUNCATULA
    Synonym: IOMT 3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1K13Ligand/IonPOTASSIUM ION
2QSO2Ligand/Ion5,7-DIHYDROXY-3-(4-METHOXYPHENYL)-4H-CHROMEN-4-ONE
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:262 , ASP A:293 , GLU A:323 , HOH A:703BINDING SITE FOR RESIDUE K A 358
2AC2SOFTWARETHR A:145 , LEU A:155BINDING SITE FOR RESIDUE K A 362
3AC3SOFTWAREGLU B:298 , HOH B:782BINDING SITE FOR RESIDUE K B 358
4AC4SOFTWAREHIS B:262 , ASP B:293 , GLU B:323 , HOH B:703BINDING SITE FOR RESIDUE K B 360
5AC5SOFTWAREGLY A:201 , THR A:207 , ASP A:224 , ARG A:225 , ASP A:244 , MET A:245 , PHE A:246 , LYS A:258 , ALA A:259 , TRP A:264 , HOH A:717 , HOH A:719BINDING SITE FOR RESIDUE SAH A 601
6AC6SOFTWARELEU A:128 , SER A:129 , PHE A:132 , TYR A:165 , HIS A:262 , ASP A:263 , ILE A:316BINDING SITE FOR RESIDUE QSO A 701
7AC7SOFTWAREGLY B:201 , THR B:207 , ASP B:224 , ARG B:225 , ASP B:244 , MET B:245 , PHE B:246 , LYS B:258 , TRP B:264 , HOH B:707 , HOH B:735 , HOH B:755BINDING SITE FOR RESIDUE SAH B 602
8AC8SOFTWARETYR A:25 , LEU B:128 , SER B:129 , PHE B:132 , HIS B:262BINDING SITE FOR RESIDUE QSO B 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QYO)

(-) 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:353
 aligned with Q06YR3_MEDTR | Q06YR3 from UniProtKB/TrEMBL  Length:357

    Alignment length:353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354   
         Q06YR3_MEDTR     5 INNRKPSEIFKAQALLYKNMYAFVDSMSLKWSIEMNIPNIIHNHGKPITLSNLVSILQIPSTKVDNVQRLMRYLAHNGFFEIITNQELENEEEAYALTVASELLVKGTELCLAPMVECVLDPTLSTSFHNLKKWVYEEDLTLFAVNLGCDLWEFLNKNPEYNTLYNDALASDSKMINLAMKDCNLVFEGLESIVDVGGGNGTTGKIICETFPKLTCVVFDRPKVVENLCGSNNLTYVGGDMFISVPKADAVLLKAVLHDWTDKDCIKILKKCKEAVTSDGKRGKVIVIDMVINEKKDENQLTQIKLLMNVTISCVNGKERNEEEWKKLFIEAGFQDYKISPFTGLMSLIEIYP 357
               SCOP domains d2qyoa1 A:5-113 automated matches                                                                            d2qyoa2 A:114-357 automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2qyoA01 A:5-108 'winged helix' repressor DNA binding domain                                             2qyoA02 A:109-357 Vaccinia Virus protein VP39                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeee..........eeeehhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...eeeee....hhhhhhhhhhh...eeeeeehhhhhh.......eeeee...........eeeee.hhhhhhhhhhhhhhhhhhhhhh......eeeeee.ee.....hhhhhhhhhhhhhhhhh.....eehhhhhhhhhhh...eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qyo A   5 INNRKPSEIFKAQALLYKNMYAFVDSMSLKWSIEMNIPNIIHNHGKPITLSNLVSILQIPSTKVDNVQRLMRYLAHNGFFEIITNQELENEEEAYALTVASELLVKGTELCLAPMVECVLDPTLSTSFHNLKKWVYEEDLTLFAVNLGCDLWEFLNKNPEYNTLYNDALASDSKMINLAMKDCNLVFEGLESIVDVGGGNGTTGKIICETFPKLTCVVFDRPKVVENLCGSNNLTYVGGDMFISVPKADAVLLKAVLHDWTDKDCIKILKKCKEAVTSDGKRGKVIVIDMVINEKKDENQLTQIKLLMNVTISCVNGKERNEEEWKKLFIEAGFQDYKISPFTGLMSLIEIYP 357
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354   


Chain B from PDB  Type:PROTEIN  Length:352
 aligned with Q06YR3_MEDTR | Q06YR3 from UniProtKB/TrEMBL  Length:357

    Alignment length:352
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355  
         Q06YR3_MEDTR     6 NNRKPSEIFKAQALLYKNMYAFVDSMSLKWSIEMNIPNIIHNHGKPITLSNLVSILQIPSTKVDNVQRLMRYLAHNGFFEIITNQELENEEEAYALTVASELLVKGTELCLAPMVECVLDPTLSTSFHNLKKWVYEEDLTLFAVNLGCDLWEFLNKNPEYNTLYNDALASDSKMINLAMKDCNLVFEGLESIVDVGGGNGTTGKIICETFPKLTCVVFDRPKVVENLCGSNNLTYVGGDMFISVPKADAVLLKAVLHDWTDKDCIKILKKCKEAVTSDGKRGKVIVIDMVINEKKDENQLTQIKLLMNVTISCVNGKERNEEEWKKLFIEAGFQDYKISPFTGLMSLIEIYP 357
               SCOP domains d2qyob1 B:6-113 automated matches                                                                           d2qyob2 B:114-357 automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2qyoB01 B:6-108 'winged helix' repressor DNA binding domain                                            2qyoB02 B:109-357 Vaccinia Virus protein VP39                                                                                                                                                                                                             CATH domains
           Pfam domains (1) -------------------------Dimerisation-2qyoB01 B:31-79                     ----------Methyltransf_2-2qyoB03 B:90-334                                                                                                                                                                                                                      ----------------------- Pfam domains (1)
           Pfam domains (2) -------------------------Dimerisation-2qyoB02 B:31-79                     ----------Methyltransf_2-2qyoB04 B:90-334                                                                                                                                                                                                                      ----------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeee..........eeeehhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhh...eeeee....hhhhhhhhhhh...eeeeeehhhhhh.......eeeee...........eeeee.hhhhhhhhhhhhhhhhhhhhh.......eeeeee.ee.....hhhhhhhhhhhhhhhhh.....eehhhhhhhhhhh...eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qyo B   6 NNRKPSEIFKAQALLYKNMYAFVDSMSLKWSIEMNIPNIIHNHGKPITLSNLVSILQIPSTKVDNVQRLMRYLAHNGFFEIITNQELENEEEAYALTVASELLVKGTELCLAPMVECVLDPTLSTSFHNLKKWVYEEDLTLFAVNLGCDLWEFLNKNPEYNTLYNDALASDSKMINLAMKDCNLVFEGLESIVDVGGGNGTTGKIICETFPKLTCVVFDRPKVVENLCGSNNLTYVGGDMFISVPKADAVLLKAVLHDWTDKDCIKILKKCKEAVTSDGKRGKVIVIDMVINEKKDENQLTQIKLLMNVTISCVNGKERNEEEWKKLFIEAGFQDYKISPFTGLMSLIEIYP 357
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q06YR3_MEDTR | Q06YR3)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    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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