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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAINS OF YVOA IN COMPLEX WITH PALINDROMIC OPERATOR DNA
 
Authors :  S. B. Fillenberg, Y. A. Muller
Date :  14 Jul 14  (Deposition) - 14 Jan 15  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B,C,D,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, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-75
    Gene: YVOA, BSU35030
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
    Organism Taxid: 224308
    Other Details: TRUNCATED FORM OF YVOA;
COMPRISES ONLY THE DNA-BINDING DOMAIN (RESIDUES 1-75)
 
Molecule 2 - DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)- 3')
    Chains: E, F
    Engineered: YES
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
    Organism Taxid: 224308
    Other Details: 15MER PALINDROMIC DSDNA 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

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:48 , ARG B:38 , DC E:11 , HOH E:117binding site for residue CL B 101
2AC2SOFTWAREARG C:48 , ARG D:38 , DC F:11 , HOH F:113binding site for residue CL C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U0Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U0Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U0Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U0Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4U0Y)

(-) 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:75
                                                                                                          
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  4u0y A  1 MNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVS 75
                                    10        20        30        40        50        60        70     


Chain B from PDB  Type:PROTEIN  Length:75
                                                                                                          
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  4u0y B  1 MNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVS 75
                                    10        20        30        40        50        60        70     


Chain C from PDB  Type:PROTEIN  Length:75
                                                                                                          
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  4u0y C  1 MNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVS 75
                                    10        20        30        40        50        60        70     


Chain D from PDB  Type:PROTEIN  Length:74
                                                                                                         
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  4u0y D  2 NINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVS 75
                                    11        21        31        41        51        61        71    


Chain E from PDB  Type:DNA  Length:15
                                              
                  4u0y E  1 GTGGTCTAGACCACT 15
                                    10     


Chain F from PDB  Type:DNA  Length:15
                                              
                  4u0y F  1 GTGGTCTAGACCACT 15
                                    10
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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 4U0Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U0Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U0Y)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

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