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(-) Description

Title :  CRYSTAL STRUCTURE OF PERENNIAL RYEGRASS LPOMT1 BOUND TO SAH
 
Authors :  G. V. Louie, J. P. Noel, M. E. Bowman
Date :  17 Oct 10  (Deposition) - 12 Jan 11  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  S-Adenosylmethionine Dependent O-Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. V. Louie, M. E. Bowman, Y. Tu, A. Mouradov, G. Spangenberg, J. P. Noel
Structure-Function Analyses Of A Caffeic Acid O-Methyltransferase From Perennial Ryegrass Reveal The Molecular Basis For Substrate Preference.
Plant Cell V. 22 4114 2010
PubMed-ID: 21177481  |  Reference-DOI: 10.1105/TPC.110.077578

(-) Compounds

Molecule 1 - CAFFEIC ACID O-METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS8
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LPOMT1, OMT1
    Organism Common: PERENNIAL RYEGRASS
    Organism Scientific: LOLIUM PERENNE
    Organism Taxid: 4522

 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, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2DTV1Ligand/Ion(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3EDO3Ligand/Ion1,2-ETHANEDIOL
4SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2DTV2Ligand/Ion(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3EDO6Ligand/Ion1,2-ETHANEDIOL
4SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:205 , GLY A:207 , ASP A:228 , LEU A:229 , ASP A:248 , MET A:249 , PHE A:250 , LYS A:262 , TRP A:263 , HOH A:1007 , HOH A:1028 , HOH A:1037 , HOH A:1117 , HOH A:1123 , HOH A:1159 , HOH A:1174 , HOH A:1210 , HOH A:1284BINDING SITE FOR RESIDUE SAH A 401
2AC2SOFTWAREPHE A:19 , HOH A:1056 , HOH A:1128BINDING SITE FOR RESIDUE DTV A 900
3AC3SOFTWARELYS A:178 , SER A:181 , ILE A:182 , THR A:185 , ALA A:210 , HOH A:1052 , HOH A:1290BINDING SITE FOR RESIDUE ACT A 901
4AC4SOFTWAREPRO A:114 , SER A:120 , ALA A:123 , ASN A:179 , HOH A:1208BINDING SITE FOR RESIDUE EDO A 902
5AC5SOFTWAREARG A:76 , ARG A:79 , ARG A:325 , TYR A:328 , HOH A:1014 , HOH A:1017 , HOH A:1233BINDING SITE FOR RESIDUE EDO A 903
6AC6SOFTWAREARG A:98 , LEU A:99 , ARG A:101 , TYR A:328BINDING SITE FOR RESIDUE EDO A 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P9C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P9C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P9C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P9C)

(-) Exons   (0, 0)

(no "Exon" information available for 3P9C)

(-) 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:352
 aligned with Q9ZTU2_LOLPR | Q9ZTU2 from UniProtKB/TrEMBL  Length:360

    Alignment length:352
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358  
         Q9ZTU2_LOLPR     9 AASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAGGKSLTPTEVAAKLPSAANPEAPDMVDRILRLLASYNVVTCLVEEGKDGRLSRSYGAAPVCKFLTPNEDGVSMAALALMNQDKVLMESWYYLKDAVLDGGIPFNKAYGMSAFEYHGTDPRFNRVFNEGMKNHSIIITKKLLELYHGFEGLGTLVDVGGGVGATVAAIAAHYPTIKGVNFDLPHVISEAPQFPGVTHVGGDMFKEVPSGDTILMKWILHDWSDQHCATLLKNCYDALPAHGKVVLVQCILPVNPEANPSSQGVFHVDMIMLAHNPGGRERYEREFQALARGAGFTGVKSTYIYANAWAIEFTK 360
               SCOP domains d3p9ca1 A:9-116 automated matches                                                                           d3p9ca2 A:117-360 automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------Dimerisation-3p9cA01 A:31-82                        ---------Methyltransf_2-3p9cA02 A:92-337                                                                                                                                                                                                                       ----------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.......hhhhhhhhhhhhhhhh..eeeeeee.....eeeeeee.hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhh...eeeeeehhhhhh.......eeeee...........eeeee.hhhhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p9c A   9 AASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAGGKSLTPTEVAAKLPSAANPEAPDMVDRILRLLASYNVVTCLVEEGKDGRLSRSYGAAPVCKFLTPNEDGVSMAALALMNQDKVLMESWYYLKDAVLDGGIPFNKAYGMSAFEYHGTDPRFNRVFNEGMKNHSIIITKKLLELYHGFEGLGTLVDVGGGVGATVAAIAAHYPTIKGVNFDLPHVISEAPQFPGVTHVGGDMFKEVPSGDTILMKWILHDWSDQHCATLLKNCYDALPAHGKVVLVQCILPVNPEANPSSQGVFHVDMIMLAHNPGGRERYEREFQALARGAGFTGVKSTYIYANAWAIEFTK 360
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P9C)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9ZTU2_LOLPR | Q9ZTU2)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0016206    catechol O-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol.
    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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 Related Entries

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

UniProtKB/TrEMBL
        Q9ZTU2_LOLPR | Q9ZTU2: 3p9i 3p9k

(-) Related Entries Specified in the PDB File

3p9c CRYSTAL STRUCTURE OF PERENNIAL RYEGRASS LPOMT1 BOUND TO S- ADENOSYL-L-HOMOCYSTEINE
3p9i CRYSTAL STRUCTURE OF PERENNIAL RYEGRASS LPOMT1 COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE AND SINAPALDEHYDE
3p9k CRYSTAL STRUCTURE OF PERENNIAL RYEGRASS LPOMT1 COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE AND CONIFERALDEHYDE