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(-) Description

Title :  MYCF MYCINAMICIN III 3'-O-METHYLTRANSFERASE (E35Q, M56A, E139A VARIANT) IN COMPLEX WITH MG, SAH AND MYCINAMICIN VI (MYCE 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 :  1.59
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, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1DMS4Ligand/IonDIMETHYL SULFOXIDE
2MG2Ligand/IonMAGNESIUM ION
3MVI2Ligand/IonMYCINAMICIN VI
4SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
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 , DMS A:302 , HOH A:463 , HOH A:524binding site for residue SAH A 301
02AC2SOFTWARETYR A:49 , ALA A:56 , VAL A:141 , LEU A:143 , SAH A:301 , MVI A:305 , HOH A:542binding site for residue DMS A 302
03AC3SOFTWAREHIS A:135 , GLN A:136 , ALA A:139 , HOH A:581 , HOH A:595binding site for residue DMS A 303
04AC4SOFTWAREASP A:189 , ASP A:216 , ASP A:217 , MVI A:305 , HOH A:543binding 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 , DMS A:302 , MG A:304 , HOH A:519 , HOH A:543binding site for residue MVI A 305
06AC6SOFTWARETHR 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 , DMS B:302 , HOH B:461 , HOH B:511binding site for residue SAH B 301
07AC7SOFTWARETYR B:49 , ALA B:56 , VAL B:141 , LEU B:143 , SAH B:301 , MVI B:305 , HOH B:538binding site for residue DMS B 302
08AC8SOFTWAREASN A:20 , TYR A:23 , ASN B:20 , TYR B:23 , HOH B:616binding site for residue DMS B 303
09AC9SOFTWAREASP B:189 , ASP B:216 , ASP B:217 , MVI B:305 , HOH B:599binding site for residue MG B 304
10AD1SOFTWARETYR B:49 , ARG B:74 , LEU B:134 , TYR B:137 , ASP B:189 , ASP B:191 , ASP B:216 , ASP B:217 , GLN B:246 , DMS B:302 , MG B:304 , HOH B:563 , HOH B:599binding site for residue MVI B 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X81)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X81)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X81)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X81)

(-) Exons   (0, 0)

(no "Exon" information available for 4X81)

(-) 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
                 4x81 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: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
                 4x81 B   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
   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 4X81)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X81)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X81)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4x81
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  MYCF_MICGR | Q49492
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  2.1.1.237
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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 4x7z 4xvy 4xvz

(-) Related Entries Specified in the PDB File

4x7u 4x7v 4x7w 4x7x 4x7y 4x7z