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(-) Description

Title :  CRYSTAL STRUCTURE OF EFFECTOR BINDING DOMAIN OF CENTRAL GLYCOLYTIC GENE REGULATOR (CGGR) FROM BACILLUS SUBTILIS IN COMPLEX WITH FRUCTOSE-6-PHOSPHATE
 
Authors :  P. Rezacova, Z. Otwinowski
Date :  13 Jan 08  (Deposition) - 01 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Effector Binding Domain, Catabolic Repressor, Transcriptional Regulator, Deor Family, Dna-Binding, Transcription Regulation, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Rezacova, M. Kozisek, S. F. Moy, I. Sieglova, A. Joachimiak, M. Machius, Z. Otwinowski
Crystal Structures Of The Effector-Binding Domain Of Repressor Central Glycolytic Gene Regulator From Bacillus Subtilis Reveal Ligand-Induced Structural Changes Upon Binding Of Several Glycolytic Intermediates.
Mol. Microbiol. V. 69 895 2008
PubMed-ID: 18554327  |  Reference-DOI: 10.1111/J.1365-2958.2008.06318.X

(-) Compounds

Molecule 1 - CENTRAL GLYCOLYTIC GENE REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CGGR, YVBQ, BSU33950
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1F6P2Ligand/IonFRUCTOSE-6-PHOSPHATE
2SCN2Ligand/IonTHIOCYANATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:148 , GLY A:149 , GLY A:150 , THR A:151 , THR A:152 , GLU A:180 , ILE A:241 , GLY A:242 , MET A:247 , ARG A:250 , ARG A:251 , GLU A:269 , PHE A:271 , LYS A:310BINDING SITE FOR RESIDUE F6P A 401
2AC2SOFTWARETHR B:148 , GLY B:149 , GLY B:150 , THR B:151 , THR B:152 , GLU B:180 , GLY B:242 , MET B:247 , ARG B:250 , ARG B:251 , GLU B:269 , PHE B:271 , LYS B:310BINDING SITE FOR RESIDUE F6P B 401
3AC3SOFTWARETHR A:148 , GLY A:149 , ARG A:175 , LEU A:178 , ALA A:186BINDING SITE FOR RESIDUE SCN A 1
4AC4SOFTWARETHR B:148 , GLY B:149 , ALA B:174 , ARG B:175 , LEU B:178 , ALA B:186BINDING SITE FOR RESIDUE SCN B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BXH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BXH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BXH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BXH)

(-) Exons   (0, 0)

(no "Exon" information available for 3BXH)

(-) 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:248
 aligned with CGGR_BACSU | O32253 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:248
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
           CGGR_BACSU    93 GLTLLEKTLKERLNLKDAIIVSGDSDQSPWVKKEMGRAAVACMKKRFSGKNIVAVTGGTTIEAVAEMMTPDSKNRELLFVPARGGLGEDVKNQANTICAHMAEKASGTYRLLFVPGQLSQGAYSSIIEEPSVKEVLNTIKSASMLVHGIGEAKTMAQRRNTPLEDLKKIDDNDAVTEAFGYYFNADGEVVHKVHSVGMQLDDIDAIPDIIAVAGGSSKAEAIEAYFKKPRNTVLVTDEGAAKKLLRDE 340
               SCOP domains d3bxha_ A: Central glycolytic gene regulator CggR                                                                                                                                                                                                        SCOP domains
               CATH domains 3bxhA00 A:93-340  [code=3.40.50.1360, no name defined]                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh.......eeeeee.......hhhhhhhhhhhhhhhhhh.ee.........hhhhhhhhhhhhhhhhhhhhhhh..eeee..eehhhhhhhh..hhhhhhhhhhh...eee..eee.....eeee......hhhhhhhh.eeeee..hhhhhhhhhhhh......eeeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxh A  93 GLTLLEKTLKERLNLKDAIIVSGDSDQSPWVKKEMGRAAVACMKKRFSGKNIVAVTGGTTIEAVAEMMTPDSKNRELLFVPARGGLGEDVKNQANTICAHMAEKASGTYRLLFVPGQLSQGAYSSIIEEPSVKEVLNTIKSASMLVHGIGEAKTMAQRRNTPLEDLKKIDDNDAVTEAFGYYFNADGEVVHKVHSVGMQLDDIDAIPDIIAVAGGSSKAEAIEAYFKKPRNTVLVTDEGAAKKLLRDE 340
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        


Chain B from PDB  Type:PROTEIN  Length:253
 aligned with CGGR_BACSU | O32253 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:253
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335   
           CGGR_BACSU    86 DTMKDVLGLTLLEKTLKERLNLKDAIIVSGDSDQSPWVKKEMGRAAVACMKKRFSGKNIVAVTGGTTIEAVAEMMTPDSKNRELLFVPARGGLGEDVKNQANTICAHMAEKASGTYRLLFVPGQLSQGAYSSIIEEPSVKEVLNTIKSASMLVHGIGEAKTMAQRRNTPLEDLKKIDDNDAVTEAFGYYFNADGEVVHKVHSVGMQLDDIDAIPDIIAVAGGSSKAEAIEAYFKKPRNTVLVTDEGAAKKLLR 338
               SCOP domains d3bxhb_ B: Central glycolytic gene regulator CggR                                                                                                                                                                                                             SCOP domains
               CATH domains 3bxhB00 B:86-338  [code=3.40.50.1360, no name defined]                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh.......eeeeee.......hhhhhhhhhhhhhhhhhh.ee.........hhhhhhhhh.hhhhhhhhhhhhh..eeee..eehhhhhhhh..hhhhhhhhhhh...eee..eee.....eeee......hhhhhhhh.eeeee..hhhhhhhhhhhh.....eeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxh B  86 SNAKDVLGLTLLEKTLKERLNLKDAIIVSGDSDQSPWVKKEMGRAAVACMKKRFSGKNIVAVTGGTTIEAVAEMMTPDSKNRELLFVPARGGLGEDVKNQANTICAHMAEKASGTYRLLFVPGQLSQGAYSSIIEEPSVKEVLNTIKSASMLVHGIGEAKTMAQRRNTPLEDLKKIDDNDAVTEAFGYYFNADGEVVHKVHSVGMQLDDIDAIPDIIAVAGGSSKAEAIEAYFKKPRNTVLVTDEGAAKKLLR 338
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BXH)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CGGR_BACSU | O32253)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        CGGR_BACSU | O32253: 2okg 3bxe 3bxf 3bxg

(-) Related Entries Specified in the PDB File

2okg CRYSTAL STRUCTURE OF EFFECTOR BINDING DOMAIN OF CENTRAL GLYCOLYTIC GENE REGULATOR (CGGR) FROM BACILLUS SUBTILIS
3bxe CRYSTAL STRUCTURE OF EFFECTOR BINDING DOMAIN OF CENTRAL GLYCOLYTIC GENE REGULATOR (CGGR) FROM BACILLUS SUBTILIS IN COMPLEX WITH DIHYDROXYACETONE PHOSPHATE
3bxf CRYSTAL STRUCTURE OF EFFECTOR BINDING DOMAIN OF CENTRAL GLYCOLYTIC GENE REGULATOR (CGGR) FROM BACILLUS SUBTILIS IN COMPLEX WITH EFFECTOR FRUCTOSE-1,6-BISPHOSPHATE
3bxg CRYSTAL STRUCTURE OF EFFECTOR BINDING DOMAIN OF CENTRAL GLYCOLYTIC GENE REGULATOR (CGGR) FROM BACILLUS SUBTILIS IN COMPLEX WITH GLUCOSE-6-PHOSPHATE