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(-) Description

Title :  STRUCTURES OF INACTIVE AND ACTIVATED DNTR PROVIDE CONCLUSIVE EVIDENCE FOR THE MECHANISM OF ACTION OF LYSR TRANSCRIPTION FACTORS
 
Authors :  M. Lerche, C. Dian, A. Round, R. Lonneborg, P. Brzezinski, G. A. Leonard
Date :  25 Aug 15  (Deposition) - 13 Jan 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Transcription, Lysr-Type Transcription Regulators, Lttr, Transcription Factor, Helix-Turn-Helix, Dna Binding Protein, Rossmann-Like Fold, Apo-Dntr (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lerche, C. Dian, A. Round, R. Lonneborg, P. Brzezinski, G. A. Leonar
The Solution Configurations Of Inactive And Activated Dntr Have Implications For The Sliding Dimer Mechanism Of Lysr Transcription Factors.
Sci. Rep. V. 6 19988 2016
PubMed-ID: 26817994  |  Reference-DOI: 10.1038/SREP19988

(-) Compounds

Molecule 1 - LYSR-TYPE REGULATORY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M15
    Expression System Taxid: 1007065
    Expression System Variant: PREP4
    Expression System Vector: PQE-60
    Expression System Vector Type: PLASMID
    Organism Scientific: BURKHOLDERIA CEPACIA
    Organism Taxid: 292
    Strain: DNT
    Synonym: DNTR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1GOL18Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:159 , PHE A:161 , PHE A:162 , ARG B:164 , GLN B:292 , VAL B:295 , GOL B:1303BINDING SITE FOR RESIDUE GOL A1304
2AC2SOFTWAREALA A:279 , ASN A:282 , ARG A:283 , SER B:299BINDING SITE FOR RESIDUE GOL A1305
3AC3SOFTWAREASP A:105 , ARG A:132 , HIS A:228 , HOH A:2055 , ASP B:105 , ARG B:132 , HIS B:228BINDING SITE FOR RESIDUE GOL A1306
4AC4SOFTWAREVAL A:199 , ASP A:210 , ARG A:220 , THR A:244BINDING SITE FOR RESIDUE GOL A1307
5AC5SOFTWAREARG A:252BINDING SITE FOR RESIDUE GOL A1308
6AC6SOFTWAREMET A:116 , ALA A:120 , GLU B:195 , ARG B:223 , THR B:239 , ASP B:240 , LEU B:241 , HOH B:2022BINDING SITE FOR RESIDUE GOL B1301
7AC7SOFTWAREMET A:109 , ILE A:230 , PHE A:257 , MET B:109 , PHE B:229 , ILE B:230 , GLY B:233 , PHE B:249 , PHE B:257BINDING SITE FOR RESIDUE GOL B1302
8AC8SOFTWAREGOL A:1304 , TRP B:277 , ASN B:282 , ARG B:291BINDING SITE FOR RESIDUE GOL B1303
9AC9SOFTWARESER B:89 , PHE B:90BINDING SITE FOR RESIDUE GOL B1304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AE5)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser A:184 -Pro A:185
2Ser B:24 -Thr B:25
3Asn B:134 -Ala B:135
4Gly B:136 -Asn B:137
5Ser B:184 -Pro B:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AE5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AE5)

(-) Exons   (0, 0)

(no "Exon" information available for 5AE5)

(-) 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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhh.....eeeeee....hhhhhhhhh...eeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ae5 A   1 MDLRDIDLNLLVVFNQLLLDRSVSTAGEKTQPAVSNSLKRLRTALNDDLEPTPYALHLAEPVIYALNTLQTALTTRDSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSEARH 303
                                    10        20        33        43        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301  
                                                       29|                 52|                                                                                                                                                                                                                                                  
                                                        33                  61                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee....hhhhhhhhhhhhh....eeeeee....hhhhhhhhh..eeeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ae5 B   5 DIDLNLLVVFNQLLLDRSVSTAGEKLGLTQPAVSNSLKRLRTALNDDLEPTPYALHLAEPVIYALNTLQTALTTRDSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFSELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSE 300
                                    14        24        34        44       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292        
                                                                          52|                                                                                                                                                                                                                                               
                                                                           61
   Legend:   → Mismatch (orange background)
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    → 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 5AE5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AE5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AE5)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn B:134 - Ala B:135   [ RasMol ]  
    Gly B:136 - Asn B:137   [ RasMol ]  
    Ser A:184 - Pro A:185   [ RasMol ]  
    Ser B:184 - Pro B:185   [ RasMol ]  
    Ser B:24 - Thr B:25   [ RasMol ]  
 
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        Q7WT50_9BURK | Q7WT50: 1utb 1uth 2y7k 2y7p 2y7r 2y7w 2y84 5ae4

(-) Related Entries Specified in the PDB File

5ae4 STRUCTURES OF INACTIVE AND ACTIVATED DNTR PROVIDE CONCLUSIVE EVIDENCE FOR THE MECHANISM OF ACTION OF LYSR TRANSCRIPTION FACTORS