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(-) Description

Title :  CRYSTAL STRUCTURE OF CARMINOMYCIN-4-O-METHYLTRANSFERASE DNRK IN COMPLEX WITH SAH AND 2-CHLORO-4-NITROPHENOL
 
Authors :  F. Wang, S. Singh, J. S. Thorson, G. N. Phillips Jr. , Enzyme Discovery Natural Product Biosynthesis (Natpro)
Date :  22 Oct 15  (Deposition) - 16 Dec 15  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B (1x),C (1x)
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, C
    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

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  B (1x)C (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 27)

Asymmetric Unit (3, 27)
No.NameCountTypeFull Name
1P9P15Ligand/Ion2-CHLORANYL-4-NITRO-PHENOL
2SAH3Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO49Ligand/IonSULFATE ION
Biological Unit 1 (3, 22)
No.NameCountTypeFull Name
1P9P12Ligand/Ion2-CHLORANYL-4-NITRO-PHENOL
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO48Ligand/IonSULFATE ION
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1P9P6Ligand/Ion2-CHLORANYL-4-NITRO-PHENOL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO44Ligand/IonSULFATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:143 , ARG A:153 , LEU A:160 , GLY A:187 , GLU A:210 , MET A:211 , GLY A:236 , ASP A:237 , PHE A:238 , SER A:252 , PHE A:253 , ASN A:257 , P9P A:404 , HOH A:534 , HOH A:535 , HOH A:638 , HOH A:662 , HOH A:677binding site for residue SAH A 401
02AC2SOFTWARETRP A:106 , VAL A:113 , PHE A:142 , PHE A:156 , LEU A:160 , ASN A:257 , ARG A:303 , MET A:304 , PHE A:307 , LEU A:308 , P9P A:403 , P9P A:404 , HOH A:504 , HOH A:635binding site for residue P9P A 402
03AC3SOFTWARETRP A:106 , ASP A:163 , TYR A:342 , P9P A:402 , P9P A:404 , P9P A:405 , HOH A:588binding site for residue P9P A 403
04AC4SOFTWARELEU A:160 , VAL A:166 , ALA A:167 , PHE A:253 , LEU A:300 , SAH A:401 , P9P A:402 , P9P A:403 , HOH A:667binding site for residue P9P A 404
05AC5SOFTWAREILE A:21 , ALA A:101 , GLN A:103 , ASP A:163 , THR A:339 , ILE A:340 , P9P A:403 , P9P A:406 , SO4 A:409 , P9P B:401binding site for residue P9P A 405
06AC6SOFTWAREARG A:18 , ILE A:21 , GLU A:295 , GLN A:296 , GLU A:299 , ILE A:340 , P9P A:405 , SO4 A:409 , HOH A:514 , HOH A:551 , HOH A:653binding site for residue P9P A 406
07AC7SOFTWAREALA A:173 , ARG A:200 , HOH A:625 , LEU B:94 , HIS B:99 , P9P B:406binding site for residue P9P A 407
08AC8SOFTWAREARG A:61 , ARG A:131 , HIS A:261 , HOH A:516 , HOH A:606 , HOH A:612 , HOH A:687 , HOH A:697 , ARG B:128binding site for residue SO4 A 408
09AC9SOFTWAREGLN A:103 , TRP A:106 , ARG A:303 , P9P A:405 , P9P A:406 , HOH A:670binding site for residue SO4 A 409
10AD1SOFTWAREARG A:115 , ARG A:149 , HOH A:502 , HOH A:521 , ARG B:265binding site for residue SO4 A 410
11AD2SOFTWAREHIS A:43 , ALA A:46 , HOH A:501 , HOH A:518binding site for residue SO4 A 411
12AD3SOFTWAREGLN A:13 , ILE A:14 , LEU A:17 , HIS A:99 , P9P A:405 , ARG B:200 , HOH B:638binding site for residue P9P B 401
13AD4SOFTWARETYR B:143 , ARG B:153 , LEU B:160 , GLY B:187 , 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 , P9P B:405 , HOH B:513 , HOH B:596 , HOH B:607 , HOH B:613 , HOH B:634 , HOH B:643 , HOH B:650binding site for residue SAH B 402
14AD5SOFTWARETRP B:106 , VAL B:113 , PHE B:142 , PHE B:156 , LEU B:160 , ASN B:257 , ARG B:303 , MET B:304 , PHE B:307 , LEU B:308 , P9P B:404 , P9P B:405 , HOH B:504 , HOH B:602binding site for residue P9P B 403
15AD6SOFTWARETRP B:106 , ASP B:163 , TYR B:342 , P9P B:403 , P9P B:405 , P9P B:406 , P9P B:407 , HOH B:587 , HOH B:608binding site for residue P9P B 404
16AD7SOFTWARELEU B:160 , ALA B:167 , PHE B:253 , LEU B:300 , SAH B:402 , P9P B:403 , P9P B:404binding site for residue P9P B 405
17AD8SOFTWAREP9P A:407 , ALA B:101 , GLN B:103 , ASP B:163 , THR B:339 , ILE B:340 , P9P B:404 , P9P B:407 , SO4 B:409binding site for residue P9P B 406
18AD9SOFTWAREGLU B:295 , GLU B:299 , ILE B:340 , P9P B:404 , P9P B:406 , SO4 B:409 , HOH B:510 , HOH B:608binding site for residue P9P B 407
19AE1SOFTWAREARG B:131 , PRO B:259 , HIS B:261 , HOH B:509 , HOH B:522 , HOH B:597 , HOH B:656 , HOH B:672binding site for residue SO4 B 408
20AE2SOFTWAREGLN B:103 , TRP B:106 , ARG B:303 , P9P B:406 , P9P B:407 , HOH B:519 , HOH B:683binding site for residue SO4 B 409
21AE3SOFTWAREARG B:115 , ARG B:149binding site for residue SO4 B 410
22AE4SOFTWAREARG B:61 , PRO B:62 , GLU B:63binding site for residue SO4 B 411
23AE5SOFTWARETYR C:143 , ARG C:153 , LEU C:160 , PHE C:168 , GLY C:187 , GLY C:189 , GLU C:210 , MET C:211 , GLY C:236 , ASP C:237 , PHE C:238 , SER C:252 , PHE C:253 , ASN C:257 , P9P C:403 , HOH C:594 , HOH C:614binding site for residue SAH C 401
24AE6SOFTWARETRP C:106 , VAL C:113 , PHE C:142 , PHE C:156 , ASN C:257 , ARG C:303 , MET C:304 , PHE C:307 , LEU C:308 , P9P C:403 , P9P C:404 , HOH C:502 , HOH C:616binding site for residue P9P C 402
25AE7SOFTWARELEU C:160 , PHE C:168 , PHE C:253 , LEU C:300 , SAH C:401 , P9P C:402 , P9P C:404 , HOH C:646binding site for residue P9P C 403
26AE8SOFTWARETYR C:342 , P9P C:402 , P9P C:403 , HOH C:616 , HOH C:646binding site for residue P9P C 404
27AE9SOFTWAREARG C:115 , ARG C:149binding site for residue SO4 C 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EEH)

(-) Sequences/Alignments

Asymmetric 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee..eeee..hhhhhh.....hhhhhh...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
                 5eeh A  11 PQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 352
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eee..hhhhhh.....hhhhhh...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
                 5eeh B  13 QIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 352
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352


Chain C from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eee..hhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhh.......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eeh C  11 PQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPAA 353
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350
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  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 5EEH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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 Related Entries

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        DNRK_STRPE | Q06528: 1tw2 1tw3 4wxh 5eeg 5jr3

(-) Related Entries Specified in the PDB File

5eeg