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(-) Description

Title :  CRYSTAL STRUCTURE OF CARMINOMYCIN-4-O-METHYLTRANSFERASE DNRK IN COMPLEX WITH TETRAZOLE-SAH
 
Authors :  F. Wang, S. Singh, J. S. Thorson, G. N. Phillips Jr. , Enzyme Discovery Natural Product Biosynthesis (Natpro)
Date :  22 Oct 15  (Deposition) - 23 Dec 15  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Unnatural Substrate, Structural Genomics, Psi-Biology, Protein Structure Initiative, Enzyme Discovery For Natural Product Biosynthesis, Natpro, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. D. Huber, F. Wang, S. Singh, B. R. Johnson, J. Zhang, M. Sunkara, S. G. Van Lanen, A. J. Morris, G. N. Phillips, J. S. Thorson
Functional Adomet Isosteres Resistant To Classical Adomet Degradation Pathways.
Acs Chem. Biol. V. 11 2484 2016
PubMed-ID: 27351335  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00348

(-) Compounds

Molecule 1 - CARMINOMYCIN 4-O-METHYLTRANSFERASE DNRK
    Chains: A, B
    EC Number: 2.1.1.292
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: DNRK
    Organism Scientific: STREPTOMYCES PEUCETIUS
    Organism Taxid: 1950
    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  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1S8M2Ligand/Ion(2~{R},3~{R},4~{S},5~{S})-2-(6-AMINOPURIN-9-YL)-5-[[(3~{S})-3-AZANYL-3-(1~{H}-1,2,3,4-TETRAZOL-5-YL)PROPYL]SULFANYLMETHYL]OXOLANE-3,4-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:143 , ARG A:153 , LEU A:160 , PHE A:168 , GLY A:187 , GLY A:188 , GLY A:189 , GLU A:210 , MET A:211 , GLY A:236 , ASP A:237 , PHE A:238 , SER A:252 , PHE A:253 , ASN A:257 , HOH A:590 , HOH A:612 , HOH A:634 , HOH A:656binding site for residue S8M A 401
2AC2SOFTWARETYR B:143 , ARG B:153 , LEU B:160 , PHE B:168 , GLY B:187 , GLY B:188 , GLU B:210 , MET B:211 , GLY B:236 , ASP B:237 , PHE B:238 , SER B:252 , PHE B:253 , ASN B:257 , TRP B:258 , HOH B:542 , HOH B:610 , HOH B:617 , HOH B:643 , HOH B:650 , HOH B:656 , HOH B:683binding site for residue S8M B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EEG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EEG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EEG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EEG)

(-) Exons   (0, 0)

(no "Exon" information available for 5EEG)

(-) 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:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eee..hhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eeg A  15 DALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLYDLSLLVLAPA 352
                                    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||     350  
                                                                                                                                                                                                                                                                                                                                                          335|          
                                                                                                                                                                                                                                                                                                                                                           342          


Chain B from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eee..hhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eeg B  15 DALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSDLSLLVLAPA 352
                                    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  ||   349   
                                                                                                                                                                                                                                                                                                                                                            337|         
                                                                                                                                                                                                                                                                                                                                                             343
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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 5EEG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EEG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EEG)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  5eeg
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  DNRK_STRPE | Q06528
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  2.1.1.292
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNRK_STRPE | Q06528: 1tw2 1tw3 4wxh 5eeh 5jr3

(-) Related Entries Specified in the PDB File

5eeh