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(-) Description

Title :  CONVERSION OF A DISULFIDE BOND INTO A THIOACETAL GROUP DURING ECHINOMYCIN BIOSYNTHESIS
 
Authors :  K. Hotta, R. M. Keegan, S. Ranganathan, M. Fang, J. Bibby, M. D. Winn, M. S M. Lian, K. Watanabe, D. J. Rigden, C. -Y. Kim
Date :  29 Oct 13  (Deposition) - 15 Jan 14  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Methyltransferase, Sam-Dependent Methyltransferase, Transferase- Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hotta, R. M. Keegan, S. Ranganathan, M. Fang, J. Bibby, M. D. Winn, M. Sato, M. Lian, K. Watanabe, D. J. Rigden, C. -Y. Kim
Conversion Of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis
Angew. Chem. Int. Ed. Engl. 2013
PubMed-ID: 24302672  |  Reference-DOI: 10.1002/ANIE.201307404

(-) Compounds

Molecule 1 - PUTATIVE SAM-DEPENDENT METHYLTRANSFERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKW469
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET28
    Gene: ECM18
    Organism Scientific: STREPTOMYCES LASALIENSIS
    Organism Taxid: 324833
 
Molecule 2 - ECHINOMYCIN
    Chains: E, F, G, H
    Engineered: YES
    Organism Scientific: STREPTOMYCES ECHINATUS
    Organism Taxid: 67293
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A   E   
Biological Unit 2 (1x):  B   F  
Biological Unit 3 (1x):   C   G 
Biological Unit 4 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 44)

Asymmetric Unit (10, 44)
No.NameCountTypeFull Name
115P2Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2ACT1Ligand/IonACETATE ION
3DSN8Mod. Amino AcidD-SERINE
4MVA8Mod. Amino AcidN-METHYLVALINE
5N2C4Mod. Amino AcidN,S-DIMETHYLCYSTEINE
6NA3Ligand/IonSODIUM ION
7NCY4Mod. Amino AcidN-METHYLCYSTEINE
8PGE2Ligand/IonTRIETHYLENE GLYCOL
9QUI8Ligand/Ion2-CARBOXYQUINOXALINE
10SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (7, 10)
No.NameCountTypeFull Name
115P-1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2ACT-1Ligand/IonACETATE ION
3DSN2Mod. Amino AcidD-SERINE
4MVA2Mod. Amino AcidN-METHYLVALINE
5N2C1Mod. Amino AcidN,S-DIMETHYLCYSTEINE
6NA-1Ligand/IonSODIUM ION
7NCY1Mod. Amino AcidN-METHYLCYSTEINE
8PGE1Ligand/IonTRIETHYLENE GLYCOL
9QUI2Ligand/Ion2-CARBOXYQUINOXALINE
10SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (7, 10)
No.NameCountTypeFull Name
115P-1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2ACT1Ligand/IonACETATE ION
3DSN2Mod. Amino AcidD-SERINE
4MVA2Mod. Amino AcidN-METHYLVALINE
5N2C1Mod. Amino AcidN,S-DIMETHYLCYSTEINE
6NA-1Ligand/IonSODIUM ION
7NCY1Mod. Amino AcidN-METHYLCYSTEINE
8PGE-1Ligand/IonTRIETHYLENE GLYCOL
9QUI2Ligand/Ion2-CARBOXYQUINOXALINE
10SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 3 (6, 9)
No.NameCountTypeFull Name
115P-1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2ACT-1Ligand/IonACETATE ION
3DSN2Mod. Amino AcidD-SERINE
4MVA2Mod. Amino AcidN-METHYLVALINE
5N2C1Mod. Amino AcidN,S-DIMETHYLCYSTEINE
6NA-1Ligand/IonSODIUM ION
7NCY1Mod. Amino AcidN-METHYLCYSTEINE
8PGE-1Ligand/IonTRIETHYLENE GLYCOL
9QUI2Ligand/Ion2-CARBOXYQUINOXALINE
10SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 4 (8, 12)
No.NameCountTypeFull Name
115P2Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2ACT-1Ligand/IonACETATE ION
3DSN2Mod. Amino AcidD-SERINE
4MVA2Mod. Amino AcidN-METHYLVALINE
5N2C1Mod. Amino AcidN,S-DIMETHYLCYSTEINE
6NA-1Ligand/IonSODIUM ION
7NCY1Mod. Amino AcidN-METHYLCYSTEINE
8PGE1Ligand/IonTRIETHYLENE GLYCOL
9QUI2Ligand/Ion2-CARBOXYQUINOXALINE
10SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:5 , TYR A:9 , TRP A:21 , GLY A:47 , CYS A:48 , GLY A:49 , ASP A:68 , LEU A:69 , ALA A:93 , ASP A:94 , ALA A:95 , SER A:111 , GLY A:112 , LEU A:113 , HOH A:503 , HOH A:543 , HOH A:545 , HOH A:548 , HOH A:550 , N2C E:3BINDING SITE FOR RESIDUE SAH A 401
02AC2SOFTWAREGLU A:91 , VAL A:92 , ALA A:93 , ASP A:94 , ASP A:97 , LEU A:98 , THR A:99 , TRP A:101 , SER C:228BINDING SITE FOR RESIDUE PGE A 402
03AC3SOFTWAREALA A:157 , ILE A:160 , ASP A:161 , ILE A:163BINDING SITE FOR RESIDUE NA A 403
04AC4SOFTWAREPHE B:5 , TYR B:9 , TRP B:21 , GLY B:47 , CYS B:48 , GLY B:49 , ASP B:68 , LEU B:69 , ALA B:93 , ASP B:94 , ALA B:95 , SER B:111 , GLY B:112 , LEU B:113 , HOH B:503 , HOH B:565 , HOH B:569 , HOH B:571 , HOH B:574 , HOH B:576 , N2C F:3BINDING SITE FOR RESIDUE SAH B 401
05AC5SOFTWAREALA B:114 , PHE B:117 , LEU B:122 , ARG B:178 , HIS B:182 , LEU B:183 , HOH B:532BINDING SITE FOR RESIDUE ACT B 402
06AC6SOFTWAREPHE C:5 , TYR C:9 , TRP C:21 , GLY C:47 , CYS C:48 , GLY C:49 , ASP C:68 , LEU C:69 , ALA C:93 , ASP C:94 , ALA C:95 , SER C:111 , GLY C:112 , LEU C:113 , HOH C:558 , HOH C:559 , HOH C:563 , HOH C:564 , HOH C:566 , HOH C:572 , HOH C:576 , N2C G:3BINDING SITE FOR RESIDUE SAH C 401
07AC7SOFTWAREALA C:157 , ILE C:160 , ASP C:161 , ILE C:163BINDING SITE FOR RESIDUE NA C 402
08AC8SOFTWAREMET D:1 , PHE D:5 , TYR D:9 , TRP D:21 , GLY D:47 , CYS D:48 , GLY D:49 , ASP D:68 , LEU D:69 , ALA D:93 , ASP D:94 , ALA D:95 , SER D:111 , GLY D:112 , LEU D:113 , PGE D:404 , HOH D:579 , HOH D:581 , HOH D:583 , HOH D:588 , HOH D:591 , N2C H:3BINDING SITE FOR RESIDUE SAH D 401
09AC9SOFTWAREGLU D:3 , VAL D:4 , ALA D:7 , ARG D:10 , HOH D:592 , MVA H:8BINDING SITE FOR RESIDUE 15P D 402
10BC1SOFTWAREGLU A:210 , LEU A:211 , GLY D:41 , ALA D:42 , GLY D:61 , ALA D:63 , VAL D:64 , THR D:65 , ASP D:106 , HOH D:574BINDING SITE FOR RESIDUE 15P D 403
11BC2SOFTWAREASP D:45 , ALA D:46 , GLY D:47 , ASP D:110 , SER D:111 , GLY D:112 , LEU D:113 , SAH D:401 , HOH D:588BINDING SITE FOR RESIDUE PGE D 404
12BC3SOFTWAREMET A:1 , PHE A:5 , PHE A:15 , TRP A:21 , HIS A:115 , THR A:116 , GLU A:118 , ILE A:144 , GLN A:153 , PRO A:164 , SAH A:401 , GLY D:119 , ASP D:120 , THR D:175BINDING SITE FOR LINKED RESIDUES E 1 to 102
13BC4SOFTWAREMET B:1 , PHE B:15 , PRO B:20 , TRP B:21 , HIS B:115 , THR B:116 , ILE B:144 , SER B:149 , GLN B:153 , ILE B:163 , ALA B:165 , LEU B:167 , LEU B:176 , ARG B:178 , SAH B:401 , HOH B:523 , HOH B:557 , ASP C:161 , GLU C:162 , HOH F:201BINDING SITE FOR LINKED RESIDUES F 1 to 102
14BC5SOFTWAREGLU B:118 , ASP B:120 , THR B:175 , MET C:1 , PHE C:15 , PRO C:20 , TRP C:21 , HIS C:115 , THR C:116 , ILE C:144 , SER C:149 , GLN C:153 , ILE C:163 , ARG C:178 , SAH C:401 , HOH G:201 , HOH G:202BINDING SITE FOR LINKED RESIDUES G 1 to 102
15BC6SOFTWAREASP A:161 , VAL D:4 , PHE D:5 , PHE D:15 , PRO D:20 , TRP D:21 , HIS D:115 , THR D:116 , SER D:149 , GLN D:153 , ILE D:163 , PRO D:164 , ALA D:165 , LEU D:176 , ARG D:178 , SAH D:401 , 15P D:402 , HOH D:506 , HOH H:201BINDING SITE FOR LINKED RESIDUES H 1 to 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ala E:2 -N2c E:3
2Ala F:2 -N2c F:3
3Ala F:6 -Ncy F:7
4Ala G:2 -N2c G:3
5Ala H:2 -N2c H:3

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NEC)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...............hhhhhhhhhh......eeee....hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh...eeee............eeeeeee.hhhhh.hhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhhhh................hhhhhhhhh...eeeeeeeeeeeeee......eeeeeeeeeeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nec A   0 HMTEVFDAVYRGESPFGKRPPWDIGAPQPAYVALEKAGLIQGAVLDAGCGTGEDALHLAGLGYAVTGLDLSPTAISVARDKADARGLGAVFEVADALDLTGWEERFDTVIDSGLAHTFEGDRLRAYATALHRACRPGAVAHILSISDRGSAEMQARLAEAIDEIPAPLPDDDPTLKRSADHLRDGFAEGWTIESIDESLMRGVIPTTSELLDVHAWLGRFRRDWNSSSVDKLAAALEH 239
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 ||    181       191       201       211       221       231        
                                                                                                                                                                                                     171|                                                                 
                                                                                                                                                                                                      174                                                                 


Chain B from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...............hhhhhhhhhh......eeee....hhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh...eeee............eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhhhh............hhhhh.hhhhhhhhh...eeeeeeeeeeeeee......eeeeeeeeeeeee...hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nec B   0 HMTEVFDAVYRGESPFGKRPPWDIGAPQPAYVALEKAGLIQGAVLDAGCGTGEDALHLAGLGYAVTGLDLSPTAISVARDKADARGLGAVFEVADALDLTGWEERFDTVIDSGLAHTFEGDRLRAYATALHRACRPGAVAHILSISDRGSAEMQARLAEAIDEIPAPLPDDDESPTLKRSADHLRDGFAEGWTIESIDESLMRGVIPTTSELLDVHAWLGRFRRDWNSSSVDKLAAALEHHHHH 243
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    


Chain C from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh................hhhhhhhhhh.....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeee............eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhhhh...........hhhhhhhhh...eeeeeeeeeeeeee......eeeeeeeeeeeee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nec C   1 MTEVFDAVYRGESPFGKRPPWDIGAPQPAYVALEKAGLIQGAVLDAGCGTGEDALHLAGLGYAVTGLDLSPTAISVARDKADARGLGAVFEVADALDLTGWEERFDTVIDSGLAHTFEGDRLRAYATALHRACRPGAVAHILSISDRGSAEMQARLAEAIDEIPAPLPDKRSADHLRDGFAEGWTIESIDESLMRGVIPTTSELLDVHAWLGRFRRDWNSSSVDKLAAALEHH 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       177       187       197       207       217       227       237   
                                                                                                                                                                                                  169|                                                               
                                                                                                                                                                                                   177                                                               


Chain D from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh................hhhhhhhhhh.....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeee............eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhhh...eeeeeeeeeeeeee......eeeeeeeeeeeee...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nec D   0 HMTEVFDAVYRGESPFGKRPPWDIGAPQPAYVALEKAGLIQGAVLDAGCGTGEDALHLAGLGYAVTGLDLSPTAISVARDKADARGLGAVFEVADALDLTGWEERFDTVIDSGLAHTFEGDRLRAYATALHRACRPGAVAHILSISDRGSAEMQARLAEAIDEIPAPLPDSPTLKRSADHLRDGFAEGWTIESIDESLMRGVIPTTSELLDVHAWLGRFRRDWNSSSVDKLAAALEHHH 241
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169|      182       192       202       212       222       232         
                                                                                                                                                                                                   169|                                                                    
                                                                                                                                                                                                    173                                                                    


Chain E from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4nec E   1 xAxvxAxv   8
                            | ||| ||
                            1-DSN ||
                              3-N2C|
                               4-MVA
                                5-DSN
                                  7-NCY
                                   8-MVA


Chain F from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4nec F   1 xAxvxAxv   8
                            | ||| ||
                            | ||| ||
                            1-DSN ||
                              3-N2C|
                               4-MVA
                                5-DSN
                                  7-NCY
                                   8-MVA


Chain G from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4nec G   1 xAxvxAxv   8
                            | ||| ||
                            | ||| ||
                            1-DSN ||
                              3-N2C|
                               4-MVA
                                5-DSN
                                  7-NCY
                                   8-MVA


Chain H from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4nec H   1 xAxvxAxv   8
                            | ||| ||
                            | ||| ||
                            1-DSN ||
                              3-N2C|
                               4-MVA
                                5-DSN
                                  7-NCY
                                   8-MVA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4NEC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

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  4nec
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 Related Entries

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