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(-) Description

Title :  MYCF MYCINAMICIN III 3'-O-METHYLTRANSFERASE (E35Q, M56A, E139A VARIANT) IN COMPLEX WITH MG, SAH AND MYCINAMICIN III (SUBSTRATE)
 
Authors :  S. M. Bernard, J. L. Smith
Date :  09 Dec 14  (Deposition) - 04 Mar 15  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Macrolide, Methyltransferase, Antibiotic, Natural Product, Transferase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Bernard, D. L. Akey, A. Tripathi, S. R. Park, J. R. Konwerski, Y. Anzai, S. Li, F. Kato, D. H. Sherman, J. L. Smith
Structural Basis Of Substrate Specificity And Regiochemistr In The Mycf/Tylf Family Of Sugar O-Methyltransferases.
Acs Chem. Biol. V. 10 1340 2015
PubMed-ID: 25692963  |  Reference-DOI: 10.1021/CB5009348

(-) Compounds

Molecule 1 - MYCINAMICIN III 3''-O-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.237
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B-MYCF
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: MYCF
    Mutation: YES
    Organism Scientific: MICROMONOSPORA GRISEORUBIDA
    Organism Taxid: 28040
    Synonym: MYCINAMICIN BIOSYNTHESIS PROTEIN F

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1DMS2Ligand/IonDIMETHYL SULFOXIDE
2MG5Ligand/IonMAGNESIUM ION
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZM32Ligand/IonMYCINAMICIN III

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:55 , ALA A:56 , ILE A:57 , GLU A:83 , GLY A:85 , VAL A:86 , TRP A:87 , ALA A:91 , ASP A:113 , SER A:114 , GLY A:117 , PHE A:118 , GLY A:169 , TRP A:170 , PHE A:171 , ASP A:189 , ASP A:191 , HOH A:489 , HOH A:750 , HOH A:775binding site for residue SAH A 301
02AC2SOFTWAREASP A:189 , ASP A:216 , ASP A:217 , ZM3 A:305 , HOH A:755binding site for residue MG A 302
03AC3SOFTWAREHOH A:405 , HOH A:425 , HOH A:471 , HOH B:413 , HOH B:422 , HOH B:482binding site for residue MG A 303
04AC4SOFTWAREASP A:123 , HOH A:403 , HOH A:410 , HOH B:418binding site for residue MG A 304
05AC5SOFTWARETYR A:49 , LEU A:134 , TYR A:137 , ASP A:189 , ASP A:191 , ASP A:216 , ASP A:217 , GLN A:246 , MG A:302 , HOH A:656 , HOH A:682 , HOH A:694 , HOH A:699 , HOH A:755 , HOH A:757binding site for residue ZM3 A 305
06AC6SOFTWAREHIS A:135 , GLN A:136 , TYR A:137 , ASN A:138 , ALA A:139 , HOH A:515 , HOH A:609binding site for residue DMS A 306
07AC7SOFTWARETHR B:55 , ALA B:56 , ILE B:57 , GLU B:83 , GLY B:85 , VAL B:86 , TRP B:87 , ALA B:91 , ASP B:113 , SER B:114 , GLY B:117 , PHE B:118 , GLY B:169 , TRP B:170 , PHE B:171 , ASP B:189 , ASP B:191 , HOH B:496 , HOH B:515 , HOH B:803binding site for residue SAH B 301
08AC8SOFTWAREASP B:189 , ASP B:216 , ASP B:217 , ZM3 B:304 , HOH B:765binding site for residue MG B 302
09AC9SOFTWAREHOH A:418 , HOH A:469 , HOH B:410 , HOH B:433 , HOH B:477binding site for residue MG B 303
10AD1SOFTWARETYR B:49 , ARG B:74 , TYR B:137 , ASP B:189 , ASP B:191 , ASP B:216 , ASP B:217 , GLN B:246 , MG B:302 , HOH B:407 , HOH B:522 , HOH B:604 , HOH B:690 , HOH B:723 , HOH B:765binding site for residue ZM3 B 304
11AD2SOFTWARELEU B:73 , ARG B:74 , TYR B:102 , HOH B:738binding site for residue DMS B 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X7Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X7Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X7Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X7Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4X7Z)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...................hhhhhhh...........hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh......eeeee............hhhhhhhhhhhhh.......hhhhhhhhhhhh......eeeee.hhhhhh.......eeeeee...hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhh.....ee.....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x7z A   4 STGVELYLDLLKRTVSNFIYQDATHVAGLITQAAFVEEARESGEDYPTVAHTAIGMKRLNNLQHCVESALRDGVPGDVLETGVWRGGACIFARGILKAYDVRDRTVWVADSFQGFPKITDDDHPMDAEMNLHQYNAAVDLPTSLATVQRNFSRYGLLDDQVRFLPGWFKDTMPTAPFERLAVLRMDGDSYGATMDVLTHAYPRLSPGGFAIIDDYCIPACREAVHEYRDRHGISDEIVEIDRQGVYWRRS 253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253


Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...................hhhhhhh...........hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh......eeeee............hhhhhhhhhhhhh.......hhhhhhhhhhhh......eeeee.hhhhhh.......eeeeee...hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhh.....ee.....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x7z B   4 STGVELYLDLLKRTVSNFIYQDATHVAGLITQAAFVEEARESGEDYPTVAHTAIGMKRLNNLQHCVESALRDGVPGDVLETGVWRGGACIFARGILKAYDVRDRTVWVADSFQGFPKITDDDHPMDAEMNLHQYNAAVDLPTSLATVQRNFSRYGLLDDQVRFLPGWFKDTMPTAPFERLAVLRMDGDSYGATMDVLTHAYPRLSPGGFAIIDDYCIPACREAVHEYRDRHGISDEIVEIDRQGVYWRRSA 254
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
   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 4X7Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X7Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X7Z)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  MYCF_MICGR | Q49492
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 Related Entries

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

UniProtKB/Swiss-Prot
        MYCF_MICGR | Q49492: 4x7u 4x7v 4x7w 4x7x 4x7y 4x81 4xvy 4xvz

(-) Related Entries Specified in the PDB File

4x7u 4x7v 4x7w 4x7x 4x7y 4x81