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(-) Description

Title :  DMSP-DEPENDENT DEMETHYLASE FROM P. UBIQUE - WITH SUBSTRATE DMSP
 
Authors :  D. J. Schuller, C. R. Reisch, M. A. Moran, W. B. Whitman, W. N. Lanzilotta
Date :  15 Aug 11  (Deposition) - 28 Dec 11  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Demethylase, Thf, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Schuller, C. R. Reisch, M. A. Moran, W. B. Whitman, W. N. Lanzilott
Structures Of Dimethylsulfoniopropionate-Dependent Demethylase From The Marine Organism Pelagabacter Ubique.
Protein Sci. V. 21 289 2012
PubMed-ID: 22162093  |  Reference-DOI: 10.1002/PRO.2015

(-) Compounds

Molecule 1 - GCVT-LIKE AMINOMETHYLTRANSFERASE PROTEIN
    Chains: A, B
    EC Number: 2.1.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PABX101
    Expression System Strain: TOP10F'
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DMDA, SAR11_0246
    Organism Scientific: CANDIDATUS PELAGIBACTER UBIQUE
    Organism Taxid: 335992
    Strain: HTCC1062

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1DQY2Ligand/Ion3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC ACID
2GOL2Ligand/IonGLYCEROL
3NA2Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:32 , GLU A:63 , TRP A:197 , SER A:246 , HOH A:523 , HOH A:524 , HOH A:628 , HOH A:663BINDING SITE FOR RESIDUE DQY A 370
2AC2SOFTWARESER A:126 , TYR A:247 , HOH A:515 , HOH A:678 , HIS B:34 , GLU B:147 , HOH B:423BINDING SITE FOR RESIDUE GOL A 371
3AC3SOFTWARELEU A:36 , LEU A:37 , ASP A:59 , VAL A:60 , ALA A:61 , ALA A:62BINDING SITE FOR RESIDUE NA A 372
4AC4SOFTWARETYR B:32 , GLU B:63 , TRP B:197 , SER B:246 , HOH B:542 , HOH B:652 , HOH B:666 , HOH B:703BINDING SITE FOR RESIDUE DQY B 370
5AC5SOFTWAREHIS A:34 , ILE A:129 , GLU A:147 , HOH A:398 , TYR B:247 , HOH B:455 , HOH B:685 , HOH B:709BINDING SITE FOR RESIDUE GOL B 371
6AC6SOFTWARELEU B:36 , LEU B:37 , ASP B:59 , VAL B:60 , ALA B:61 , ALA B:62BINDING SITE FOR RESIDUE NA B 372

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:366 -Pro A:367
2Leu B:366 -Pro B:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TFI)

(-) 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:369
 aligned with DMDA_PELUB | Q4FP21 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:369
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360         
           DMDA_PELUB     1 MKNFSIAKSRRLRSTPYTSRIEKQGVTAYTIYNHMLLPAAFGSIEDSYKHLKEHVQIWDVAAERQVEISGKDSAELVQLMTCRDLSKSKIGRCYYCPIIDENGNLVNDPVVLKLDENKWWISIADSDVIFFAKGLASGHKFDVKIVEPVVDIMAIQGPKSFALMEKVFGKKITELKFFGFDYFDFEGTKHLIARSGWSKQGGYEVYVENTQSGQKLYDHLFEVGKEFNVGPGCPNLIERIESALLSYGNDFDNNDNPFECGFDQYVSLDSDINFLGKEKLKEIKLKGPQKKLRGVKIDIKEISLTGSKNIYDENNNVIGELRSACYSPHFQKVIGIAMIKKSHWEASQGFKIQINDNTINGNVCDLPFI 369
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..........hhhhhh.....eeeee..eeeeee..hhhhhhhhhhhh.eeee.....eeeee..hhhhhhhhhh...........eee..ee.....eee..eeeeee..eeeee....hhhhhhhhhhhhhh...eee....eeeeee..hhhhhhhhhhhhhhhhh....eeeeee..eeeeee........eeeeee.hhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhh.............hhhhh.hhhhh.........hhhhhhhhhhhh..eeeeeeee..........eeee.....eeeeeeeeeee....eeeeeeeee.hhh....eeeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfi A   1 MKNFSIAKSRRLRSTPYTSRIEKQGVTAYTIYNHMLLPAAFGSIEDSYKHLKEHVQIWDVAAERQVEISGKDSAELVQLMTCRDLSKSKIGRCYYCPIIDENGNLVNDPVVLKLDENKWWISIADSDVIFFAKGLASGHKFDVKIVEPVVDIMAIQGPKSFALMEKVFGKKITELKFFGFDYFDFEGTKHLIARSGWSKQGGYEVYVENTQSGQKLYDHLFEVGKEFNVGPGCPNLIERIESALLSYGNDFDNNDNPFECGFDQYVSLDSDINFLGKEKLKEIKLKGPQKKLRGVKIDIKEISLTGSKNIYDENNNVIGELRSACYSPHFQKVIGIAMIKKSHWEASQGFKIQINDNTINGNVCDLPFI 369
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360         


Chain B from PDB  Type:PROTEIN  Length:369
 aligned with DMDA_PELUB | Q4FP21 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:369
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360         
           DMDA_PELUB     1 MKNFSIAKSRRLRSTPYTSRIEKQGVTAYTIYNHMLLPAAFGSIEDSYKHLKEHVQIWDVAAERQVEISGKDSAELVQLMTCRDLSKSKIGRCYYCPIIDENGNLVNDPVVLKLDENKWWISIADSDVIFFAKGLASGHKFDVKIVEPVVDIMAIQGPKSFALMEKVFGKKITELKFFGFDYFDFEGTKHLIARSGWSKQGGYEVYVENTQSGQKLYDHLFEVGKEFNVGPGCPNLIERIESALLSYGNDFDNNDNPFECGFDQYVSLDSDINFLGKEKLKEIKLKGPQKKLRGVKIDIKEISLTGSKNIYDENNNVIGELRSACYSPHFQKVIGIAMIKKSHWEASQGFKIQINDNTINGNVCDLPFI 369
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..........hhhhhh.....eeeee..eeeeee..hhhhhhhhhhhh.eeee.....eeeee..hhhhhhhhhh...........eee..ee.....eee..eeeeee..eeeee....hhhhhhhhhhhhhh...eee....eeeeee..hhhhhhhhhhhhhhhhh....eeeeee..eeeeee........eeeeee.hhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhh.............hhhhh.hhhhh.........hhhhhhhhhhhh..eeeeeeee..........eeee.....eeeeeeeeeee....eeeeeeeee.hhh....eeeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfi B   1 MKNFSIAKSRRLRSTPYTSRIEKQGVTAYTIYNHMLLPAAFGSIEDSYKHLKEHVQIWDVAAERQVEISGKDSAELVQLMTCRDLSKSKIGRCYYCPIIDENGNLVNDPVVLKLDENKWWISIADSDVIFFAKGLASGHKFDVKIVEPVVDIMAIQGPKSFALMEKVFGKKITELKFFGFDYFDFEGTKHLIARSGWSKQGGYEVYVENTQSGQKLYDHLFEVGKEFNVGPGCPNLIERIESALLSYGNDFDNNDNPFECGFDQYVSLDSDINFLGKEKLKEIKLKGPQKKLRGVKIDIKEISLTGSKNIYDENNNVIGELRSACYSPHFQKVIGIAMIKKSHWEASQGFKIQINDNTINGNVCDLPFI 369
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
   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  (0, 0)

(no "SCOP Domain" information available for 3TFI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DMDA_PELUB | Q4FP21)
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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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  Cis Peptide Bonds
    Leu A:366 - Pro A:367   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        DMDA_PELUB | Q4FP21: 3tfh 3tfj

(-) Related Entries Specified in the PDB File

3tfh DMSP-DEPENDENT DEMETHYLASE FROM P. UBIQUE - APO
3tfj DMSP-DEPENDENT DEMETHYLASE FROM P. UBIQUE - WITH COFACTOR THF