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(-) Description

Title :  CRYSTAL STRUCTURE OF PRFA-DNA BINARY COMPLEX
 
Authors :  Y. Wang, H. Feng, Y. L. Zhu, P. Gao
Date :  21 Feb 17  (Deposition) - 12 Apr 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,M,N,O,P
Biol. Unit 1:  M,N,O,P  (1x)
Biol. Unit 2:  A,B,C,D  (1x)
Biol. Unit 3:  E,F,G,H  (1x)
Keywords :  Dna Complex, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Wang, H. Feng, Y. Zhu, P. Gao
Structural Insights Into Glutathione-Mediated Activation Of The Master Regulator Prfa In Listeria Monocytogenes
Protein Cell V. 8 308 2017
PubMed-ID: 28271443  |  Reference-DOI: 10.1007/S13238-017-0390-X

(-) Compounds

Molecule 1 - LISTERIOLYSIN POSITIVE REGULATORY FACTOR A
    ChainsM, N, A, B, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePRFA, AJL40_05990, AJN46_04535, M643_11230
    Organism ScientificLISTERIA MONOCYTOGENES
    Organism Taxid1639
    SynonymLISTERIOLYSIN POSITIVE REGULATORY PROTEIN,LISTERIOLYSIN REGULATORY PROTEIN,PLEITROPHIC REGULATORY FACTOR A,POSITIVE REGULATORY FACTOR A,PRFA,TRANSCRIPTIONAL REGULATOR
 
Molecule 2 - DNA (29-MER)
    ChainsO, C, G
    EngineeredYES
    Organism ScientificLISTERIA MONOCYTOGENES
    Organism Taxid1639
    SyntheticYES
 
Molecule 3 - DNA (28-MER)
    ChainsP, D, H
    EngineeredYES
    Organism ScientificLISTERIA MONOCYTOGENES
    Organism Taxid1639
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHMNOP
Biological Unit 1 (1x)        MNOP
Biological Unit 2 (1x)ABCD        
Biological Unit 3 (1x)    EFGH    

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1GSH6Ligand/IonGLUTATHIONE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GSH2Ligand/IonGLUTATHIONE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GSH2Ligand/IonGLUTATHIONE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GSH2Ligand/IonGLUTATHIONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN M:61 , TYR M:62 , LYS M:64 , ALA M:66 , PHE M:67 , LYS M:122 , TYR M:126 , GLN M:146 , ILE M:149 , CYS M:229binding site for residue GSH M 301
2AC2SOFTWAREGLN N:61 , TYR N:62 , LYS N:64 , ALA N:66 , PHE N:67 , LYS N:122 , GLN N:123 , TYR N:126 , ILE N:149 , CYS N:229binding site for residue GSH N 301
3AC3SOFTWAREGLN A:61 , TYR A:62 , TYR A:63 , LYS A:64 , ALA A:66 , PHE A:67 , LYS A:122 , TYR A:126 , ILE A:149 , CYS A:229binding site for residue GSH A 301
4AC4SOFTWAREGLN B:61 , TYR B:62 , TYR B:63 , LYS B:64 , ALA B:66 , PHE B:67 , LYS B:122 , GLN B:123 , TYR B:126 , ILE B:149 , TYR B:154 , CYS B:229binding site for residue GSH B 301
5AC5SOFTWAREGLN E:61 , TYR E:62 , TYR E:63 , LYS E:64 , ALA E:66 , PHE E:67 , LYS E:122 , TYR E:126 , GLN E:146 , ILE E:149binding site for residue GSH E 301
6AC6SOFTWAREGLN F:61 , TYR F:62 , LYS F:64 , ALA F:66 , PHE F:67 , LYS F:122 , GLN F:123 , TYR F:126 , ILE F:149 , TYR F:154 , CYS F:229 , THR F:232binding site for residue GSH F 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X6E)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn M:2 -Ala M:3
2Asp M:167 -Asn M:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X6E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X6E)

(-) Exons   (0, 0)

(no "Exon" information available for 5X6E)

(-) 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:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh............................eeeeeee.eeeeeee.....eeeeeeee..eeee.............eeee.....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.......hhhhhhhhh...hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6e A   2 NAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN 237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      

Chain B from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh........................eeeee...eeeeeee.....eeeeeeee..eeee.............eeee......eeeee.hhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeee.....hhhhhhhhh...hhhhhhh.hhhhhh...ee......ee..hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6e B   2 NAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN 237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      

Chain C from PDB  Type:DNA  Length:29
                                                             
                 5x6e C   1 CATCGTCGTTAACAAATGTTAATGCCTAC  29
                                    10        20         

Chain D from PDB  Type:DNA  Length:29
                                                             
                 5x6e D   1 GGTAGGCATTAACATTTGTTAACGACGAT  29
                                    10        20         

Chain E from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.........eeee.............eeeeeee.eeeeee.......eeeeeee..eeee.............eeee...eeeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheeee..eeee.....hhhhhhhhh...hhhhhhhhhhhhh....eee....eee..hhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6e E   2 NAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN 237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      

Chain F from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eee...............eeeeeeeeeeeeeee.....eeeeeeee..eeee.............eeeeeeeeeeeeeeehhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh...hhhhhhhhh........eeee..eeee..hhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6e F   2 NAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN 237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      

Chain G from PDB  Type:DNA  Length:28
                                                            
                 5x6e G   2 ATCGTCGTTAACAAATGTTAATGCCTAC  29
                                    11        21        

Chain H from PDB  Type:DNA  Length:29
                                                             
                 5x6e H   1 GGTAGGCATTAACATTTGTTAACGACGAT  29
                                    10        20         

Chain M from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....eeee...eee.......eeeeeee.eeeeeee.....eeeeeeee..eeee.............eeee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeee.....hhhhhhhhh...hhhhhhhhhh.........ee..eeee..hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6e M   2 NAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN 237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      

Chain N from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.........ee...............eeeeeee.eeeeeee.....eeeeeeee..eeee.............eeee.....eeeeeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee......ee.....hhhhhhhhh...hhhhhhhhhhhhh....eehhhhh.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x6e N   2 NAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN 237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      

Chain O from PDB  Type:DNA  Length:29
                                                             
                 5x6e O   1 CATCGTCGTTAACAAATGTTAATGCCTAC  29
                                    10        20         

Chain P from PDB  Type:DNA  Length:28
                                                            
                 5x6e P   2 GTAGGCATTAACATTTGTTAACGACGAT  29
                                    11        21        

   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 5X6E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X6E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X6E)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q4TVQ0_LISMN | Q4TVQ05lrr 5lrs 5x6d

(-) Related Entries Specified in the PDB File

5x6d