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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FULL-LENGTH RESPONSE REGULATOR DESR IN THE ACTIVE STATE
 
Authors :  F. Trajtenberg, N. Larrieux, A. Buschiazzo
Date :  25 Jun 13  (Deposition) - 16 Jul 14  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Response Regulator, Two-Component System, Transcription Factor, Receiver Domain, Dna Binding Domain, Phosphorylation, Active State, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Trajtenberg, D. Albanesi, N. Ruetalo, H. Botti, A. E. Mechaly, M. Nieves, P. S. Aguilar, L. Cybulski, N. Larrieux, D. De Mendoza, A. Buschiazzo
Allosteric Activation Of Bacterial Response Regulators: The Role Of The Cognate Histidine Kinase Beyond Phosphorylation
Mbio V. 5 02105 2014
PubMed-ID: 25406381  |  Reference-DOI: 10.1128/MBIO.02105-14

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATORY PROTEIN DESR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE80L
    Expression System Strain: TOP10F'
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DESR, YOCG, BSU19200
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1BEF2Ligand/IonBERYLLIUM TRIFLUORIDE ION
2GOL2Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , ASP A:54 , GLU A:56 , BEF A:202 , HOH A:302 , HOH A:303BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREASP A:54 , ILE A:55 , GLU A:56 , THR A:80 , THR A:81 , PHE A:82 , LYS A:102 , MG A:201 , GOL A:203 , HOH A:302BINDING SITE FOR RESIDUE BEF A 202
3AC3SOFTWAREGLN A:10 , THR A:81 , PHE A:82 , LYS A:102 , BEF A:202 , HOH A:303 , GLN B:10BINDING SITE FOR RESIDUE GOL A 203
4AC4SOFTWARESER A:19 , ASN A:22BINDING SITE FOR RESIDUE GOL A 204
5AC5SOFTWAREASN A:22 , GLU A:24 , MET A:27 , HOH A:313BINDING SITE FOR RESIDUE NA A 205
6AC6SOFTWAREASP B:9 , ASP B:54 , GLU B:56 , BEF B:202 , HOH B:301 , HOH B:302BINDING SITE FOR RESIDUE MG B 201
7AC7SOFTWAREASP B:54 , ILE B:55 , GLU B:56 , THR B:80 , THR B:81 , PHE B:82 , LYS B:102 , MG B:201 , HOH B:301 , HOH B:302BINDING SITE FOR RESIDUE BEF B 202
8AC8SOFTWAREASN B:22 , GLU B:24 , MET B:27BINDING SITE FOR RESIDUE NA B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LDZ)

(-) 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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeee.......hhhhhhhhh.....eeeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh...eehhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ldz A  -1 GSMISIFIAEDQQMLLGALGSLLNLEDDMEVVGKGTTGQDAVDFVKKRQPDVCIMDIEMPGKTGLEAAEELKDTGCKIIILTTFARPGYFQRAIKAGVKGYLLKDSPSEELANAIRSVMNGKRIYAPELMEDLYSEANPLTDREKEVLELVADGKNTKEIAQELSIKSGTVRNYISMILEKLEVKNRIEAITRSKE 194
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      


Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeee.......hhhhhhhhh.....eeeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh...ee.hhhhhh........hhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ldz B   0 SMISIFIAEDQQMLLGALGSLLNLEDDMEVVGKGTTGQDAVDFVKKRQPDVCIMDIEMPGKTGLEAAEELKDTGCKIIILTTFARPGYFQRAIKAGVKGYLLKDSPSEELANAIRSVMNGKRIYAPELMEDLYSEANPLTDREKEVLELVADGKNTKEIAQELSIKSGTVRNYISMILEKLEVKNRIE 187
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   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 4LDZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DESR_BACSU | O34723: 4le0 4le1 4le2 5iuj 5iuk 5iul 5iun

(-) Related Entries Specified in the PDB File

4le0 4le1 4le2