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(-) Description

Title :  CARMINOMYCIN-4-O-METHYLTRANSFERASE (DNRK) VARIANT (298SER INSERT) IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEIN (SAH) AND ACLACINOMYCIN T
 
Authors :  M. Metsa-Ketela, L. Niiranen
Date :  13 Nov 14  (Deposition) - 29 Jul 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methyltransferase, Mono-Oxygenase, Sah Binding, Antibiotic Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Grocholski, P. Dinis, L. Niiranen, J. Niemi, M. Metsa-Ketela
Divergent Evolution Of An Atypical S-Adenosyl-L-Methionine-Dependent Monooxygenase Involved In Anthracycline Biosynthesis.
Proc. Natl. Acad. Sci. Usa V. 112 9866 2015
PubMed-ID: 26216966  |  Reference-DOI: 10.1073/PNAS.1501765112

(-) Compounds

Molecule 1 - CARMINOMYCIN 4-O-METHYLTRANSFERASE DNRK
    Chains: A, B
    EC Number: 2.1.1.292
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBHBDELTAHIS
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-356
    Gene: DNRK
    Organism Scientific: STREPTOMYCES PEUCETIUS
    Organism Taxid: 1950
    Other Details: 298S INSERT
    Synonym: COMT,ANTHRACYCLINE 4-O-METHYLTRANSFERASE

 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
13VL2Ligand/IonMETHYL (1R,2R,4S)-2-ETHYL-2,5,7-TRIHYDROXY-6,11-DIOXO-4-{[2,3,6-TRIDEOXY-3-(DIMETHYLAMINO)-ALPHA-L-LYXO-HEXOPYRANOSYL]OXY}-1,2,3,4,6,11-HEXAHYDROTETRACENE-1-CARBOXYLATE
2DTU1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4SO45Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:142 , ARG A:152 , PHE A:167 , GLY A:186 , GLU A:209 , MET A:210 , GLY A:235 , ASP A:236 , PHE A:237 , SER A:251 , PHE A:252 , ASN A:256 , 3VL A:402 , HOH A:517 , HOH A:570 , HOH A:588 , HOH A:631 , HOH A:640binding site for residue SAH A 401
2AC2SOFTWARETRP A:105 , PHE A:155 , LEU A:159 , CYS A:161 , ASP A:162 , PHE A:252 , ASN A:256 , GLU A:299 , LEU A:300 , ARG A:303 , MET A:304 , SAH A:401 , HOH A:655binding site for residue 3VL A 402
3AC3SOFTWAREPRO A:338 , THR A:339binding site for residue DTU A 403
4AC4SOFTWAREPRO A:258 , ASP A:259 , HIS A:260 , HOH A:539 , HOH A:610 , HOH A:612binding site for residue SO4 A 404
5AC5SOFTWAREARG A:114 , ARG A:148binding site for residue SO4 A 405
6AC6SOFTWARETYR B:142 , ARG B:152 , LEU B:159 , PHE B:167 , GLY B:186 , GLU B:209 , MET B:210 , GLY B:235 , ASP B:236 , PHE B:237 , SER B:251 , PHE B:252 , ASN B:256 , 3VL B:402 , HOH B:504 , HOH B:557 , HOH B:558 , HOH B:566 , HOH B:607binding site for residue SAH B 401
7AC7SOFTWAREPHE B:155 , LEU B:159 , CYS B:161 , ALA B:166 , PHE B:252 , ASN B:256 , GLU B:299 , LEU B:300 , ARG B:303 , ILE B:340 , SAH B:401 , HOH B:633binding site for residue 3VL B 402
8AC8SOFTWAREPRO B:258 , ASP B:259 , HIS B:260 , HOH B:572 , HOH B:574binding site for residue SO4 B 403
9AC9SOFTWAREARG B:114 , ARG B:148binding site for residue SO4 B 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WXH)

(-) 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:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee..eeee..hhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee.ee.....hhhhhhhhhhhhhhhhhh...eehhhhhhhhhhh.eeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxh A   9 RPQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFSTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 352
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348    


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..ee......ee..hhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxh B  11 QQIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLENSFNEQFSTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 352
                                    20        30        40        50        60        70        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281     ||292       302       312       322       332       342       352
                                                                                               79|                                                                                                                                                                                                           287|                                                               
                                                                                                81                                                                                                                                                                                                            289
   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 4WXH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  DNRK_STRPE | Q06528
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNRK_STRPE | Q06528: 1tw2 1tw3 5eeg 5eeh 5jr3

(-) Related Entries Specified in the PDB File

1tw2 1TW2 CONTAINS THE NATIVE FORM OF SAME PROTEIN COMPLEXED WITH SAH AND 4-METHOXY-E-RHODOMYCIN T
1tw3 1TW3 CONTAINS THE NATIVE FORM OF SAME PROTEIN COMPLEXED WITH SAH AND 4-METHOXY-E-RHODOMYCIN T