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(-) Description

Title :  CRYSTAL STRUCTURE OF SCO3205, A MARR FAMILY TRANSCRIPTIONAL REGULATOR FROM STREPTOMYCES COELICOLOR, IN COMPLEX WITH DNA
 
Authors :  C. E. M. Stevenson, A. Assaad, D. M. Lawson
Date :  28 Feb 13  (Deposition) - 17 Jul 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Transcription-Dna Complex, Transcription, Winged Helix Motif, Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. E. M. Stevenson, A. Assaad, G. Chandra, T. B. K. Le, S. J. Greive, M. J. Bibb, D. M. Lawson
Investigation Of Dna Sequence Recognition By A Streptomycete Marr Family Transcriptional Regulator Through Surface Plasmon Resonance And X-Ray Crystallography.
Nucleic Acids Res. V. 41 7009 2013
PubMed-ID: 23748564  |  Reference-DOI: 10.1093/NAR/GKT523

(-) Compounds

Molecule 1 - PUTATIVE MARR-FAMILY TRANSCRIPTIONAL REPRESSOR
    Atcc: BAA-471
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A-SCO3205
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET21A
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 1902
    Other Details: SYNTHETIC GENE WITH OPTIMISED CODON USAGE FOR E.COLI EXPRESSION. INCLUDES N-TERMINAL HIS-TAG OF SEQUENCE MHHHHHHENLYFQG APPENDED TO WILD-TYPE SEQUENCE. SEQUENCE NUMBERING IS RELATIVE TO THE WILD-TYPE SEQUENCE.
    Strain: M145
    Synonym: SCO3205
 
Molecule 2 - 5'-D(*AP*AP*AP*GP*AP*TP*TP*GP*AP*GP*AP*TP*CP*TP *CP*AP*AP*TP*CP*TP*TP*DT)-3'
    Chains: C, D, G, H
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synonym: SYMMETRISED SCO3204 OPERATOR
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPO4 A:1165 , ASP E:92 , GLN E:100BINDING SITE FOR RESIDUE PO4 A1164
2AC2SOFTWAREASP A:92 , GLN A:100 , PO4 A:1164 , ASP E:92BINDING SITE FOR RESIDUE PO4 A1165
3AC3SOFTWAREDT C:18 , DA D:3 , DG D:4BINDING SITE FOR RESIDUE PO4 D1023
4AC4SOFTWAREDT C:18 , DC C:19 , DT D:6 , DT D:7BINDING SITE FOR RESIDUE PO4 C1023

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZPL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZPL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZPL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZPL)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZPL)

(-) 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:159
 aligned with Q9KYU1_STRCO | Q9KYU1 from UniProtKB/TrEMBL  Length:163

    Alignment length:159
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154         
         Q9KYU1_STRCO     5 PRWLTAEEQLVWRSYIEAATLLEDHLDRQLQRDAGMPHVYYGLLVKLAESPRRRLRMTELAKYAKITRSRLSHAVARLEKNGWVRREDCPSDKRGQFAILTDEGYEVLRRTAPGHVDAVRQAVFDRLTPEQQKSLGEIMRIVAEGLQPSEAGADLPWLR 163
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.eeehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zpl A   5 PRWLTAEEQLVWRSYIEAATLLEDHLDRQLQRDAGMPHVYYGLLVKLAESPRRRLRMTELAKYAKITRSRLSHAVARLEKNGWVRREDCPSDKRGQFAILTDEGYEVLRRTAPGHVDAVRQAVFDRLTPEQQKSLGEIMRIVAEGLQPSEAGADLPWLR 163
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154         


Chain B from PDB  Type:PROTEIN  Length:159
 aligned with Q9KYU1_STRCO | Q9KYU1 from UniProtKB/TrEMBL  Length:163

    Alignment length:159
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154         
         Q9KYU1_STRCO     5 PRWLTAEEQLVWRSYIEAATLLEDHLDRQLQRDAGMPHVYYGLLVKLAESPRRRLRMTELAKYAKITRSRLSHAVARLEKNGWVRREDCPSDKRGQFAILTDEGYEVLRRTAPGHVDAVRQAVFDRLTPEQQKSLGEIMRIVAEGLQPSEAGADLPWLR 163
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.eeehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zpl B   5 PRWLTAEEQLVWRSYIEAATLLEDHLDRQLQRDAGMPHVYYGLLVKLAESPRRRLRMTELAKYAKITRSRLSHAVARLEKNGWVRREDCPSDKRGQFAILTDEGYEVLRRTAPGHVDAVRQAVFDRLTPEQQKSLGEIMRIVAEGLQPSEAGADLPWLR 163
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154         


Chain C from PDB  Type:DNA  Length:22
                                                      
                 3zpl C   1 AAAGATTGAGATCTCAATCTTT  22
                                    10        20  


Chain D from PDB  Type:DNA  Length:22
                                                      
                 3zpl D   1 AAAGATTGAGATCTCAATCTTT  22
                                    10        20  


Chain E from PDB  Type:PROTEIN  Length:160
 aligned with Q9KYU1_STRCO | Q9KYU1 from UniProtKB/TrEMBL  Length:163

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
         Q9KYU1_STRCO     2 NDEPRWLTAEEQLVWRSYIEAATLLEDHLDRQLQRDAGMPHVYYGLLVKLAESPRRRLRMTELAKYAKITRSRLSHAVARLEKNGWVRREDCPSDKRGQFAILTDEGYEVLRRTAPGHVDAVRQAVFDRLTPEQQKSLGEIMRIVAEGLQPSEAGADLPWLR 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.eeehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...--..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zpl E   2 NDEPRWLTAEEQLVWRSYIEAATLLEDHLDRQLQRDAGMPHVYYGLLVKLAESPRRRLRMTELAKYAKITRSRLSHAVARLEKNGWVRREDCPSDKRGQFAILTDEGYEVLRRTAPGHVDAVRQAVFDRLTPEQQKSLGEIMRIVAEGLQPSE--ADLPWLR 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  |  | 161  
                                                                                                                                                                                  154  |      
                                                                                                                                                                                     157      


Chain F from PDB  Type:PROTEIN  Length:154
 aligned with Q9KYU1_STRCO | Q9KYU1 from UniProtKB/TrEMBL  Length:163

    Alignment length:157
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       
         Q9KYU1_STRCO     7 WLTAEEQLVWRSYIEAATLLEDHLDRQLQRDAGMPHVYYGLLVKLAESPRRRLRMTELAKYAKITRSRLSHAVARLEKNGWVRREDCPSDKRGQFAILTDEGYEVLRRTAPGHVDAVRQAVFDRLTPEQQKSLGEIMRIVAEGLQPSEAGADLPWLR 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.eeehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...---.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zpl F   7 WLTAEEQLVWRSYIEAATLLEDHLDRQLQRDAGMPHVYYGLLVKLAESPRRRLRMTELAKYAKITRSRLSHAVARLEKNGWVRREDCPSDKRGQFAILTDEGYEVLRRTAPGHVDAVRQAVFDRLTPEQQKSLGEIMRIVAEGLQPSE---DLPWLR 163
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       | - |     
                                                                                                                                                                             154 158     


Chain G from PDB  Type:DNA  Length:22
                                                      
                 3zpl G   1 AAAGATTGAGATCTCAATCTTT  22
                                    10        20  


Chain H from PDB  Type:DNA  Length:22
                                                      
                 3zpl H   1 AAAGATTGAGATCTCAATCTTT  22
                                    10        20
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3ZPL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZPL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZPL)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,E,F   (Q9KYU1_STRCO | Q9KYU1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  3zpl
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