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(-) Description

Title :  FUNCTIONAL AND STRUCTURAL CHARACTERIZATION OF A CATIONDEPENDENT O-METHYLTRANSFERASE FROM THE CYANOBACTERIUM SYNECHOCYSTIS SP. STRAIN PCC 6803
 
Authors :  J. G. Kopycki, P. Neumann, M. T. Stubbs
Date :  22 Feb 08  (Deposition) - 10 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  O-Methyltransferase, Cyanobacterium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. G. Kopycki, M. T. Stubbs, W. Brandt, M. Hagemann, A. Porzel, J. Schmidt, W. Schliemann, M. H. Zenk, T. Vogt
Functional And Structural Characterization Of A Cation-Dependent O-Methyltransferase From The Cyanobacterium Synechocystis Sp. Strain Pcc 6803
J. Biol. Chem. V. 283 20888 2008
PubMed-ID: 18502765  |  Reference-DOI: 10.1074/JBC.M801943200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - O-METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.-
    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 Scientific: SYNECHOCYSTIS SP.
    Organism Taxid: 1148
    Strain: PCC 6803

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
14FE1Ligand/Ion(2E)-3-(3-HYDROXY-4-METHOXYPHENYL)PROP-2-ENOIC ACID
2FER1Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
3MG1Ligand/IonMAGNESIUM ION
4SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
14FE2Ligand/Ion(2E)-3-(3-HYDROXY-4-METHOXYPHENYL)PROP-2-ENOIC ACID
2FER2Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:42 , ASP A:143 , ASP A:169 , ASN A:170 , HOH A:1128BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREGLN A:43 , ILE A:44 , GLY A:68 , PHE A:70 , TYR A:73 , SER A:74 , ASP A:92 , GLN A:93 , PRO A:120 , ALA A:121 , ASP A:143 , ALA A:144 , ASP A:145 , TYR A:152 , HOH A:1141 , HOH A:1142 , HOH A:1258 , HOH A:1259BINDING SITE FOR RESIDUE SAH A 301
3AC3SOFTWAREMET A:42 , ASP A:143 , LYS A:146 , ASN A:170 , HIS A:174BINDING SITE FOR RESIDUE FER A 501
4AC4SOFTWARELYS A:3 , MET A:42 , ASP A:143 , LYS A:146 , ASN A:170 , HIS A:174BINDING SITE FOR RESIDUE 4FE A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:132 -Pro A:133

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CBG)

(-) 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:218
 aligned with Q55813_SYNY3 | Q55813 from UniProtKB/TrEMBL  Length:220

    Alignment length:218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
         Q55813_SYNY3     3 KGITGFDPSLYSYLQSISADDSFYLAQLRRETAHLPGAPMQISPEQAQFLGLLISLTGAKQVLEIGVFRGYSALAMALQLPPDGQIIACDQDPNATAIAKKYWQKAGVAEKISLRLGPALATLEQLTQGKPLPEFDLIFIDADKRNYPRYYEIGLNLLRRGGLMVIDNVLWHGKVTEVDPQEAQTQVLQQFNRDLAQDERVRISVIPLGDGMTLALKK 220
               SCOP domains d3cbga_ A: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh....hhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhheeeeeeeeee..hhhhhhhh....hhhhhhhhhhhhhhh....eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cbg A   3 KGITGFDPSLYSYLQSISADDSFYLAQLRRETAHLPGAPMQISPEQAQFLGLLISLTGAKQVLEIGVFRGYSALAMALQLPPDGQIIACDQDPNATAIAKKYWQKAGVAEKISLRLGPALATLEQLTQGKPLPEFDLIFIDADKRNYPRYYEIGLNLLRRGGLMVIDNVLWHGKVTEVDPQEAQTQVLQQFNRDLAQDERVRISVIPLGDGMTLALKK 220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CBG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q55813_SYNY3 | Q55813)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    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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(-) Related Entries Specified in the PDB File

3c3y O-METHYLTRANSFERASE FROM M. CRYSTALLINUM