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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL LENGTH YVOA IN COMPLEX WITH PALINDROMIC OPERATOR DNA
 
Authors :  F. C. Grau, S. B. Fillenberg, Y. A. Muller
Date :  10 Nov 14  (Deposition) - 14 Jan 15  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,E,F
Keywords :  Transcription, Repressor, Bacterial Transcription Regulation, Transcription Factor, Gntr/Hutc Family, Winged Helix-Turn-Helix Motif, N-Acetylglucosamine Utilization, Dna-Binding, Operator- Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Fillenberg, F. C. Grau, G. Seidel, Y. A. Muller
Structural Insight Into Operator Dre-Sites Recognition And Effector Binding In The Gntr/Hutc Transcription Regulator Nagr.
Nucleic Acids Res. V. 43 1283 2015
PubMed-ID: 25564531  |  Reference-DOI: 10.1093/NAR/GKU1374

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REPRESSOR YVOA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YVOA, BSU35030
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 224308
    Other Details: FULL LENGTH YVOA
    Strain: 168
 
Molecule 2 - DNA (5'- D(P*CP*AP*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*TP*GP*G)-3')
    Chains: E, F
    Engineered: YES
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
    Organism Taxid: 224308
    Other Details: 19 MER PALINDROMIC CONSTRUCT;
DERIVED FROM THE CONSENSUS SEQUENCE OF THE TWO NATIVE NON-PALINDROMIC DRE-SITE SEQUENCES UPSTREAM OF NAGAB-YVOA AND NAGP
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:49 , MET B:49binding site for residue EDO A 301
2AC2SOFTWARETHR B:87 , SER B:88 , ASP B:92 , GLN B:183 , ARG B:211 , TYR B:228 , TYR B:233binding site for residue EDO B 301
3AC3SOFTWAREGLN A:53 , MET B:49 , ARG B:52 , DT E:7 , DC E:8binding site for residue EDO B 302
4AC4SOFTWARETHR B:132binding site for residue EDO B 303
5AC5SOFTWARETYR B:167 , THR B:213 , PHE B:221 , GLU B:222binding site for residue EDO B 304
6AC6SOFTWAREDC E:13 , DT F:7binding site for residue EDO E 101
7AC7SOFTWAREDG E:5 , DG E:6 , DC F:14 , DA F:15binding site for residue EDO E 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WWC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WWC)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhh...eeee...eeee.........hhhhhhhh....eeeeeee..ee..hhhhhhh.......eeeeeeeeee..eeeeeeeeee......eeeeeeeee.hhhhhhhhh.....eeeeeeeeee.....eeeeeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wwc A   0 HMNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVSKPKMQGLTSFTEDMKSRGMTPGSRLIDYQLIDSTEELAAILGCGHSSIHKITRVRLANDIPMAIESSHIPFEISRAKQELEPSAATTEEANILGIQKGAPVLLIKRTTYLQNGTAFEHAKSVYRGDRYTFVHYMDRL 242
                                     9        19        29        39        49        59        69        79|       93       103       113       123||     134       144       179       189       199       209       219       229       239   
                                                                                                          79|                                     124|                       152|                                                                
                                                                                                           84                                      126                        178                                                                


Chain B from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee..........hhhhhhhh....eeeeeeeeeee...hhhhh.......eeeeeeeeee..eeeeeeeeeee............hhhhhhh......eeeeeeeee.hhhhhhhhh.....eeeeeeeeee.....eeeeeeeeee.....ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wwc B   0 HMNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVSKPKMEQGLTSFTEDMKSRGMTPGSRLIDYQLIDSEELAAILGCGPSSIHKITRVRLANDIPMAIESSHIPFELAGELNESIYDHIERYNSIPISRAKQELEPSAATTEEANILGIQKGAPVLLIKRTTYLQNGTAFEHAKSVYRGDRYTFVHYMD 240
                                     9        19        29        39        49        59        69        79 ||     92       102       112|      123|      134       144       154     ||169       179       189       199       209       219       229       239 
                                                                                                            81|                        112|      123|                                160|                                                                          
                                                                                                             85                         114       125                                 166                                                                          


Chain E from PDB  Type:DNA  Length:19
                                                   
                 4wwc E   1 CAGTGGTCTAGACCACTGG  19
                                    10         


Chain F from PDB  Type:DNA  Length:19
                                                   
                 4wwc F   1 CAGTGGTCTAGACCACTGG  19
                                    10
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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 4WWC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  4wwc
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  YVOA_BACSU | O34817
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 Related Entries

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

UniProtKB/Swiss-Prot
        YVOA_BACSU | O34817: 2wv0 4u0v 4u0w 4u0y

(-) Related Entries Specified in the PDB File

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