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(-) Description

Title :  MYCE METHYLTRANSFERASE FROM THE MYCINAMYCIN BIOSYNTHETIC PATHWAY IN COMPLEX WITH MG AND SAH, CRYSTAL FORM 1
 
Authors :  D. L. Akey, J. L. Smith
Date :  08 Jul 11  (Deposition) - 24 Aug 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Methyltransferase, Macrolide, Natural Product, Rossmann Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Akey, S. Li, J. R. Konwerski, L. A. Confer, S. M. Bernard, Y. Anzai, F. Kato, D. H. Sherman, J. L. Smith
A New Structural Form In The Sam/Metal-Dependent O‑ Methyltransferase Family: Myce From The Mycinamicin Biosynthetic Pathway.
J. Mol. Biol. V. 413 438 2011
PubMed-ID: 21884704  |  Reference-DOI: 10.1016/J.JMB.2011.08.040

(-) Compounds

Molecule 1 - METHYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MYCE
    Organism Scientific: MICROMONOSPORA GRISEORUBIDA
    Organism Taxid: 28040

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2SAH3Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:275 , GLU A:303 , ASP A:304BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWARETHR A:173 , PRO A:174 , LYS A:175 , GLU A:202 , GLY A:204 , GLY A:206 , TYR A:208 , SER A:217 , ASP A:234 , ILE A:235 , GLY A:251 , ASP A:252 , GLN A:253 , ASP A:275 , GLY A:276 , SER A:277 , HOH A:703 , HOH A:741 , PHE D:387BINDING SITE FOR RESIDUE SAH A 601
3AC3SOFTWAREASP C:275 , GLU C:303 , ASP C:304 , HOH C:713BINDING SITE FOR RESIDUE MG C 501
4AC4SOFTWAREPHE B:387 , THR C:173 , LYS C:175 , GLU C:202 , GLY C:204 , VAL C:205 , GLY C:206 , TYR C:208 , SER C:217 , ASP C:234 , ILE C:235 , GLY C:251 , ASP C:252 , GLN C:253 , ASP C:275 , GLY C:276 , SER C:277 , HIS C:282 , HOH C:498BINDING SITE FOR RESIDUE SAH C 601
5AC5SOFTWAREASP D:275 , GLU D:303 , ASP D:304 , HOH D:704BINDING SITE FOR RESIDUE MG D 501
6AC6SOFTWAREPHE A:387 , THR D:173 , LYS D:175 , GLU D:202 , GLY D:204 , GLY D:206 , TYR D:208 , SER D:217 , ASP D:234 , ILE D:235 , GLY D:251 , ASP D:252 , GLN D:253 , ASP D:275 , GLY D:276 , SER D:277 , HIS D:282 , HOH D:533 , HOH D:704 , HOH D:901BINDING SITE FOR RESIDUE SAH D 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:267 -Pro A:268
2Gly B:267 -Pro B:268
3Gly C:267 -Pro C:268
4Gly D:267 -Pro D:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SSM)

(-) 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:387
 aligned with MYCE_MICGR | Q83WF2 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:390
                                    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       365       375       385       395
           MYCE_MICGR     6 EFDEATVQDVVRLAGGHDSELRELTQKYDPAMISRLLVAEILSRCPPPSNDTPVLVELAIVHGSERFRHFLRVVRDSPIRPVGADEGFVGMLVEYELTELLRELFGVTHERPAGVRGTKLFPYLTDDEEAVEQIGTYLLAAQQGTEAVLAGCGSRKPDLSELSSRYFTPKFGFLHWFTPHYDRHFRDYRNQQVRVLEIGVGGYKHPEWGGGSLRMWKSFFPRGQIYGLDIMDKSHVDELRIRTIQGDQNDAEFLDRIARRYGPFDIVIDDGSHINAHVRTSFAALFPHVRPGGLYVIEDMWTAYWPGFGGQADPQECSGTSLGLLKSLIDAIQHQELPSDPNRSPGYVDRNIVGLHVYHNVAFVEKGRNDEGGIPTWIPRDFESLVQASS 395
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee......eee......eeeeeeeehhhhhhhhhh..........eeee......---hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhh....eeeee...........hhhhhhhhhhh...eeeeee...hhhhh...eeeee....hhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhh..eeeeeeeeee.hhhhhhhhhh..........hhhhhhhhhhhhhhhhhh........hhhhhheeeeeee..eeeeee..............hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ssm A   6 EFDEATVQDVVRLAGGHDSELRELTQKYDPAMISRLLVAEILSRCPPPSNDTPVLVELAIVHGSERFRHFLRVVRDSPIRPVGADEGFVGMLVEYELTELLRELFGVTHERPAGVRGTKLFPYLTD---AVEQIGTYLLAAQQGTEAVLAGCGSRKPDLSELSSRYFTPKFGFLHWFTPHYDRHFRDYRNQQVRVLEIGVGGYKHPEWGGGSLRMWKSFFPRGQIYGLDIMDKSHVDELRIRTIQGDQNDAEFLDRIARRYGPFDIVIDDGSHINAHVRTSFAALFPHVRPGGLYVIEDMWTAYWPGFGGQADPQECSGTSLGLLKSLIDAIQHQELPSDPNRSPGYVDRNIVGLHVYHNVAFVEKGRNDEGGIPTWIPRDFESLVQASS 395
                                    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       365       375       385       395
                                                                                                                                                       131 135                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:354
 aligned with MYCE_MICGR | Q83WF2 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:392
                                    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       365       375       385       395  
           MYCE_MICGR     6 EFDEATVQDVVRLAGGHDSELRELTQKYDPAMISRLLVAEILSRCPPPSNDTPVLVELAIVHGSERFRHFLRVVRDSPIRPVGADEGFVGMLVEYELTELLRELFGVTHERPAGVRGTKLFPYLTDDEEAVEQIGTYLLAAQQGTEAVLAGCGSRKPDLSELSSRYFTPKFGFLHWFTPHYDRHFRDYRNQQVRVLEIGVGGYKHPEWGGGSLRMWKSFFPRGQIYGLDIMDKSHVDELRIRTIQGDQNDAEFLDRIARRYGPFDIVIDDGSHINAHVRTSFAALFPHVRPGGLYVIEDMWTAYWPGFGGQADPQECSGTSLGLLKSLIDAIQHQELPSDPNRSPGYVDRNIVGLHVYHNVAFVEKGRNDEGGIPTWIPRDFESLVQASSGG 397
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee......eee......eeeeeeeehhhhhhhhhh..........eeee........hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.---------hhhhhhhhhhhhh....eeeee..--------.hhhhhhhhhhh...eeeeee...........eeeee....hhhhhhhhhhhhh.eeeeeee...---hhhhhhhhhh..eeeeeeeeee.------------------hhhhhhhhhhhhhhhhhhhh........hhhhhheeeeeee..eeeeee..............hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ssm B   6 EFDEATVQDVVRLAGGHDSELRELTQKYDPAMISRLLVAEILSRCPPPSNDTPVLVELAIVHGSERFRHFLRVVRDSPIRPVGADEGFVGMLVEYELTELLRELFGVTHERPAGVRGTKLFPYLTDDEEAVEQIGTYLLAAQQGTEAVLAGCGSRKPDLSELSSRYF---------FTPHYDRHFRDYRNQQVRVLEIGV--------GGGSLRMWKSFFPRGQIYGLDIMDKSHVDELRIRTIQGDQNDAEFLDRIARRYGPFDIVIDDGSH---HVRTSFAALFPHVRPGGLYVIED------------------SGTSLGLLKSLIDAIQHQELPSDPNRSPGYVDRNIVGLHVYHNVAFVEKGRNDEGGIPTWIPRDFESLVQASSGG 397
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165      |  -      |185       195       205       215       225       235       245       255       265       275  |   |285       295        |-         -       325       335       345       355       365       375       385       395  
                                                                                                                                                                                                172       182                    205      214                                                             278 282                   304                323                                                                          


Chain C from PDB  Type:PROTEIN  Length:363
 aligned with MYCE_MICGR | Q83WF2 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:377
                                    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       365       375       
           MYCE_MICGR     6 EFDEATVQDVVRLAGGHDSELRELTQKYDPAMISRLLVAEILSRCPPPSNDTPVLVELAIVHGSERFRHFLRVVRDSPIRPVGADEGFVGMLVEYELTELLRELFGVTHERPAGVRGTKLFPYLTDDEEAVEQIGTYLLAAQQGTEAVLAGCGSRKPDLSELSSRYFTPKFGFLHWFTPHYDRHFRDYRNQQVRVLEIGVGGYKHPEWGGGSLRMWKSFFPRGQIYGLDIMDKSHVDELRIRTIQGDQNDAEFLDRIARRYGPFDIVIDDGSHINAHVRTSFAALFPHVRPGGLYVIEDMWTAYWPGFGGQADPQECSGTSLGLLKSLIDAIQHQELPSDPNRSPGYVDRNIVGLHVYHNVAFVEKGRNDEGGIPTW 382
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee......eeehhhhh.eeeeeeeehhhhhhhhhh..........eeee....--..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..........hhhhhhhhhhhhh....eeeee...........hhhhhhhhhhh...eeeeee...........eeeee....hhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhh..eeeeeeeeee.hhhhhhhhhh..........hhhhhhhhhhhhhh------------hhhhhheeeeeee..eeeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ssm C   6 EFDEATVQDVVRLAGGHDSELRELTQKYDPAMISRLLVAEILSRCPPPSNDTPVLVELAIVHGSERFRHFLRVVRDSPIRPVGADEGFVGMLVEYELTELLRELFGVTHERPAGVRGTKLFPYL--DEEAVEQIGTYLLAAQQGTEAVLAGCGSRKPDLSELSSRYFTPKFGFLHWFTPHYDRHFRDYRNQQVRVLEIGVGGYKHPEWGGGSLRMWKSFFPRGQIYGLDIMDKSHVDELRIRTIQGDQNDAEFLDRIARRYGPFDIVIDDGSHINAHVRTSFAALFPHVRPGGLYVIEDMWTAYWPGFGGQADPQECSGTSLGLLKSLIDAIQ------------GYVDRNIVGLHVYHNVAFVEKGRNDEGGIPTW 382
                                    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  |      -     | 355       365       375       
                                                                                                                                                     129  |                                                                                                                                                                                                           338          351                               
                                                                                                                                                        132                                                                                                                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:393
 aligned with MYCE_MICGR | Q83WF2 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:393
                                    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       364       374       384       394   
           MYCE_MICGR     5 TEFDEATVQDVVRLAGGHDSELRELTQKYDPAMISRLLVAEILSRCPPPSNDTPVLVELAIVHGSERFRHFLRVVRDSPIRPVGADEGFVGMLVEYELTELLRELFGVTHERPAGVRGTKLFPYLTDDEEAVEQIGTYLLAAQQGTEAVLAGCGSRKPDLSELSSRYFTPKFGFLHWFTPHYDRHFRDYRNQQVRVLEIGVGGYKHPEWGGGSLRMWKSFFPRGQIYGLDIMDKSHVDELRIRTIQGDQNDAEFLDRIARRYGPFDIVIDDGSHINAHVRTSFAALFPHVRPGGLYVIEDMWTAYWPGFGGQADPQECSGTSLGLLKSLIDAIQHQELPSDPNRSPGYVDRNIVGLHVYHNVAFVEKGRNDEGGIPTWIPRDFESLVQASSGG 397
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee......eee......eeeeeeeehhhhhhhhhh..........eeee........hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..........hhhhhhhhhhhhh....eeeee...........hhhhhhhhhhh...eeeeee...hhhhh...eeeee....hhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhh..eeeeeeeeee.hhhhhhhhhh..........hhhhhhhhhhhhhhhhhh........hhhhhheeeeeee..eeeeee..............hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ssm D   5 TEFDEATVQDVVRLAGGHDSELRELTQKYDPAMISRLLVAEILSRCPPPSNDTPVLVELAIVHGSERFRHFLRVVRDSPIRPVGADEGFVGMLVEYELTELLRELFGVTHERPAGVRGTKLFPYLTDDEEAVEQIGTYLLAAQQGTEAVLAGCGSRKPDLSELSSRYFTPKFGFLHWFTPHYDRHFRDYRNQQVRVLEIGVGGYKHPEWGGGSLRMWKSFFPRGQIYGLDIMDKSHVDELRIRTIQGDQNDAEFLDRIARRYGPFDIVIDDGSHINAHVRTSFAALFPHVRPGGLYVIEDMWTAYWPGFGGQADPQECSGTSLGLLKSLIDAIQHQELPSDPNRSPGYVDRNIVGLHVYHNVAFVEKGRNDEGGIPTWIPRDFESLVQASSGG 397
                                    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       364       374       384       394
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (MYCE_MICGR | Q83WF2)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MYCE_MICGR | Q83WF2: 3ssn 3sso

(-) Related Entries Specified in the PDB File

3ssn 3sso