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(-) Description

Title :  DHPI-SAM COMPLEX
 
Authors :  B. Bae, S. K. Nair
Date :  14 Sep 10  (Deposition) - 27 Oct 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  O-Methyltransferase, Sam, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Lee, B. Bae, M. Kuemin, B. T. Circello, W. W. Metcalf, S. K. Nair, W. A. Van Der Donk
Characterization And Structure Of Dhpi, A Phosphonate O-Methyltransferase Involved In Dehydrophos Biosynthesis.
Proc. Natl. Acad. Sci. Usa V. 107 17557 2010
PubMed-ID: 20876132  |  Reference-DOI: 10.1073/PNAS.1006848107

(-) Compounds

Molecule 1 - SAM-DEPENDENT METHYLTRANSFERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET-28
    Gene: DHPI
    Organism Scientific: STREPTOMYCES LURIDUS
    Organism Taxid: 67320

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1SAM4Ligand/IonS-ADENOSYLMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:15 , TYR A:22 , ALA A:54 , SER A:55 , GLY A:56 , THR A:57 , TRP A:60 , ASP A:75 , GLY A:76 , SER A:77 , MET A:80 , GLN A:97 , ASP A:98 , LEU A:99 , PHE A:100 , ALA A:114 , TRP A:116 , HOH A:222 , HOH A:223 , HOH A:226 , HOH A:272 , SO4 A:301 , HOH A:504BINDING SITE FOR RESIDUE SAM A 300
2AC2SOFTWARETYR A:15 , ARG A:18 , HIS A:119 , ARG A:168 , LYS A:180 , HOH A:220 , HOH A:291 , SAM A:300BINDING SITE FOR RESIDUE SO4 A 301
3AC3SOFTWARETYR B:15 , TYR B:22 , ALA B:54 , SER B:55 , GLY B:56 , TRP B:60 , ASP B:75 , GLY B:76 , GLN B:97 , ASP B:98 , LEU B:99 , PHE B:100 , ALA B:114 , HIS B:115 , TRP B:116 , HOH B:223 , HOH B:225 , HOH B:245 , SO4 B:301BINDING SITE FOR RESIDUE SAM B 300
4AC4SOFTWARETYR B:15 , ARG B:18 , VAL B:27 , HIS B:119 , ARG B:168 , LYS B:180 , HOH B:285 , SAM B:300BINDING SITE FOR RESIDUE SO4 B 301
5AC5SOFTWARELEU C:12 , TYR C:15 , TYR C:22 , ALA C:54 , SER C:55 , GLY C:56 , TRP C:60 , ASP C:75 , GLY C:76 , SER C:77 , MET C:80 , GLN C:97 , ASP C:98 , LEU C:99 , PHE C:100 , ALA C:114 , HIS C:115 , TRP C:116 , HOH C:220 , HOH C:233 , HOH C:245 , HOH C:270 , SO4 C:301 , HOH C:496BINDING SITE FOR RESIDUE SAM C 300
6AC6SOFTWARETYR C:15 , ARG C:18 , HIS C:119 , ARG C:168 , LYS C:180 , HOH C:259 , HOH C:290 , SAM C:300BINDING SITE FOR RESIDUE SO4 C 301
7AC7SOFTWARETYR D:15 , TYR D:22 , ALA D:54 , SER D:55 , GLY D:56 , TRP D:60 , ASP D:75 , GLY D:76 , SER D:77 , MET D:80 , GLN D:97 , ASP D:98 , LEU D:99 , PHE D:100 , ALA D:114 , HIS D:115 , TRP D:116 , HOH D:252 , HOH D:341 , HOH D:497BINDING SITE FOR RESIDUE SAM D 300
8AC8SOFTWAREHOH A:267 , TYR D:15 , ARG D:18 , HIS D:119 , ARG D:168 , LYS D:180 , HOH D:250BINDING SITE FOR RESIDUE SO4 D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OU6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OU6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OU6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OU6)

(-) Exons   (0, 0)

(no "Exon" information available for 3OU6)

(-) 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:213
 aligned with D7PC21_9ACTN | D7PC21 from UniProtKB/TrEMBL  Length:218

    Alignment length:213
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   
         D7PC21_9ACTN     3 TSHGLIESQLSYYRARASEYDATFVPYMDSAAPAALERLRAGNIRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGLDNVEFRQQDLFDWTPDRQWDAVFFAHWLAHVPDDRFEAFWESVRSAVAPGGVVEFVDVTDHERRLEQQDDSEPEVAVRRTLQDGRSFRIVKVFRSPAELTERLTALGWSCSVDEVHPGFLYATCRP 215
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhh.....eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhh......eeeee.....eeeee....hhhhhhhhhhhh..eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ou6 A   3 TSHGLIESQLSYYRARASEYDATFVPYMDSAAPAALERLRAGNIRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGLDNVEFRQQDLFDWTPDRQWDAVFFAHWLAHVPDDRFEAFWESVRSAVAPGGVVEFVDVTDHERRLEQQDDSEPEVAVRRTLQDGRSFRIVKVFRSPAELTERLTALGWSCSVDEVHPGFLYATCRP 215
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with D7PC21_9ACTN | D7PC21 from UniProtKB/TrEMBL  Length:218

    Alignment length:211
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 
         D7PC21_9ACTN     5 HGLIESQLSYYRARASEYDATFVPYMDSAAPAALERLRAGNIRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGLDNVEFRQQDLFDWTPDRQWDAVFFAHWLAHVPDDRFEAFWESVRSAVAPGGVVEFVDVTDHERRLEQQDDSEPEVAVRRTLQDGRSFRIVKVFRSPAELTERLTALGWSCSVDEVHPGFLYATCRP 215
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhh.....eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhh......eeeee.....eeeee....hhhhhhhhhhhh..eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ou6 B   5 HGLIESQLSYYRARASEYDATFVPYMDSAAPAALERLRAGNIRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGLDNVEFRQQDLFDWTPDRQWDAVFFAHWLAHVPDDRFEAFWESVRSAVAPGGVVEFVDVTDHERRLEQQDDSEPEVAVRRTLQDGRSFRIVKVFRSPAELTERLTALGWSCSVDEVHPGFLYATCRP 215
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 


Chain C from PDB  Type:PROTEIN  Length:208
 aligned with D7PC21_9ACTN | D7PC21 from UniProtKB/TrEMBL  Length:218

    Alignment length:208
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        
         D7PC21_9ACTN     7 LIESQLSYYRARASEYDATFVPYMDSAAPAALERLRAGNIRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGLDNVEFRQQDLFDWTPDRQWDAVFFAHWLAHVPDDRFEAFWESVRSAVAPGGVVEFVDVTDHERRLEQQDDSEPEVAVRRTLQDGRSFRIVKVFRSPAELTERLTALGWSCSVDEVHPGFLYATCR 214
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhh...eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhh......eeeee.....eeeee....hhhhhhhhhhh...eeeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ou6 C   7 LIESQLSYYRARASEYDATFVPYMDSAAPAALERLRAGNIRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGLDNVEFRQQDLFDWTPDRQWDAVFFAHWLAHVPDDRFEAFWESVRSAVAPGGVVEFVDVTDHERRLEQQDDSEPEVAVRRTLQDGRSFRIVKVFRSPAELTERLTALGWSCSVDEVHPGFLYATCR 214
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        


Chain D from PDB  Type:PROTEIN  Length:213
 aligned with D7PC21_9ACTN | D7PC21 from UniProtKB/TrEMBL  Length:218

    Alignment length:213
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   
         D7PC21_9ACTN     3 TSHGLIESQLSYYRARASEYDATFVPYMDSAAPAALERLRAGNIRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGLDNVEFRQQDLFDWTPDRQWDAVFFAHWLAHVPDDRFEAFWESVRSAVAPGGVVEFVDVTDHERRLEQQDDSEPEVAVRRTLQDGRSFRIVKVFRSPAELTERLTALGWSCSVDEVHPGFLYATCRP 215
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhh.....eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhh......eeeee.....eeeee....hhhhhhhhhhhh..eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ou6 D   3 TSHGLIESQLSYYRARASEYDATFVPYMDSAAPAALERLRAGNIRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGLDNVEFRQQDLFDWTPDRQWDAVFFAHWLAHVPDDRFEAFWESVRSAVAPGGVVEFVDVTDHERRLEQQDDSEPEVAVRRTLQDGRSFRIVKVFRSPAELTERLTALGWSCSVDEVHPGFLYATCRP 215
                                    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)
  - → 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 3OU6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OU6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OU6)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (D7PC21_9ACTN | D7PC21)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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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  3ou6
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 Related Entries

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

UniProtKB/TrEMBL
        D7PC21_9ACTN | D7PC21: 3ou2 3ou7

(-) Related Entries Specified in the PDB File

3ou2 DHPI-SAH COMPLEX STRUCTURE
3ou7 DHPI-SAM-HEP COMPLEX