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(-) Description

Title :  STRUCTURE OF B. SUBTILIS TREHALOSE REPRESSOR (TRER) EFFECTOR BINDING DOMAIN
 
Authors :  P. Rezacova, V. Krejcirikova, D. Borek, S. F. Moy, A. Joachimiak, Z. Otw Midwest Center For Structural Genomics (Mcsg)
Date :  05 Jan 07  (Deposition) - 06 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Gene Repressor, Sugar Binding, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Rezacova, V. Krejcirikova, D. Borek, S. F. Moy, A. Joachimiak, Z. Otwinowski
The Crystal Structure Of The Effector-Binding Domain Of The Trehalose Repressor Trer From Bacillus Subtilis 168 Reveals A Unique Quarternary Assembly.
Proteins V. 69 679 2007
PubMed-ID: 17705272  |  Reference-DOI: 10.1002/PROT.21516

(-) Compounds

Molecule 1 - TREHALOSE OPERON TRANSCRIPTIONAL REPRESSOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EFFECTOR BINDING DOMAIN, RESIDUES 90-238
    Gene: TRER
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE1Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
4SO48Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:34 , HOH A:35 , HIS A:200BINDING SITE FOR RESIDUE NA A 301
2AC2SOFTWAREHOH A:19 , ARG A:128 , ARG A:130 , SER A:160 , ILE A:161 , TYR A:162 , LYS A:238BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREHOH A:14 , ASP A:120 , ASP A:121 , ASP A:122 , ARG A:146 , LYS A:147BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREHOH A:6 , GLU A:105 , PRO A:106 , PRO A:107 , SER A:108 , ILE A:111 , ILE A:123 , GLU A:125BINDING SITE FOR RESIDUE GOL A 304
5AC5SOFTWARELEU A:115 , ARG A:116 , PHE A:145 , SER A:214 , LEU A:215BINDING SITE FOR RESIDUE GOL A 305
6AC6SOFTWAREARG A:116BINDING SITE FOR RESIDUE GOL A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OGG)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:133 -Gly A:134
2Phe A:233 -Ala A:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OGG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OGG)

(-) Exons   (0, 0)

(no "Exon" information available for 2OGG)

(-) 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:144
 aligned with TRER_BACSU | P39796 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:144
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234    
           TRER_BACSU    95 TKTTVHKFGLEPPSELIQKQLRANLDDDIWEVIRSRKIDGEHVILDKDYFFRKHVPHLTKEICENSIYEYIEGELGLSISYAQKEIVAEPCTDEDRELLDLRGYDHMVVVRNYVFLEDTSLFQYTESRHRLDKFRFVDFARRGK 238
               SCOP domains d2ogga1 A:95-238 Trehalose operon transcriptional repressor TreR                                                                                 SCOP domains
               CATH domains 2oggA01 A:95-228 Chorismate lyase                                                                                                     ---------- CATH domains
               Pfam domains UTRA-2oggA01 A:95-229                                                                                                                  --------- Pfam domains
         Sec.struct. author ..eeeeeeeee..hhhhhhhhh......eeeeeeeeee..eeeeeeeeeee.......hhhhhh.hhhhhhhhhhh..eeeeeeeeeeee.hhhhhhhh......eeeeeeeeeee....eeeeeeeeee.hhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ogg A  95 TKTTVHKFGLEPPSELIQKQLRANLDDDIWEVIRSRKIDGEHVILDKDYFFRKHVPHLTKEICENSIYEYIEGELGLSISYAQKEIVAEPCTDEDRELLDLRGYDHmVVVRNYVFLEDTSLFQYTESRHRLDKFRFVDFARRGK 238
                                   104       114       124       134       144       154       164       174       184       194      |204       214       224       234    
                                                                                                                                    201-MSE
   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Chor_lyase (11)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRER_BACSU | P39796)
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.
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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