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(-) Description

Title :  CRYSTAL STRUCTURE OF EFFECTOR BINDING DOMAIN OF CENTRAL GLYCOLYTIC GENE REGULATOR (CGGR) FROM BACILLUS SUBTILIS IN COMPLEX WITH EFFECTOR FRUCTOSE-1,6-BISPHOSPHATE
 
Authors :  P. Rezacova, Z. Otwinowski
Date :  13 Jan 08  (Deposition) - 01 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
113P1Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CL4Ligand/IonCHLORIDE ION
3FBP1Ligand/IonBETA-FRUCTOSE-1,6-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:148 , GLY A:149 , GLY A:150 , THR A:151 , THR A:152 , ARG A:175 , GLN A:185 , GLY A:242 , MET A:247 , ARG A:250 , ARG A:251 , GLU A:269 , PHE A:271 , LYS A:310BINDING SITE FOR RESIDUE FBP A 401
2AC2SOFTWAREARG A:202 , LEU A:203 , LYS B:183BINDING SITE FOR RESIDUE CL B 501
3AC3SOFTWAREGLY A:115 , ASP A:116 , SER A:120 , ARG B:129BINDING SITE FOR RESIDUE CL B 502
4AC4SOFTWAREARG A:129 , GLY B:115 , ASP B:116 , SER B:120BINDING SITE FOR RESIDUE CL B 503
5AC5SOFTWARELEU B:178 , GLY B:179 , GLU B:180 , GLN B:185BINDING SITE FOR RESIDUE CL B 504
6AC6SOFTWAREGLY B:150 , THR B:151 , THR B:152 , MET B:247 , ARG B:250 , ARG B:251 , GLU B:269 , LYS B:310BINDING SITE FOR RESIDUE 13P B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BXF)

(-) 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: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 d3bxfa_ A: Central glycolytic gene regulator CggR                                                                                                                                                                                                             SCOP domains
               CATH domains 3bxfA00 A:86-338  [code=3.40.50.1360, no name defined]                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh.......eeeeee.eee......hhhhhhhhhhhhhhh.ee.........hhhhhhhhhhhhhhhhhhhhhhh..eeee..eehhhhhhhh..hhhhhhhhhhh.eeeee..eeee....eeee..eee.hhhhhhhh.eeeee..hhhhhhhhhhhh......eeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxf A  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   


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with CGGR_BACSU | O32253 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:245
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333     
           CGGR_BACSU    94 LTLLEKTLKERLNLKDAIIVSGDSDQSPWVKKEMGRAAVACMKKRFSGKNIVAVTGGTTIEAVAEMMTPDSKNRELLFVPARGGLGEDVKNQANTICAHMAEKASGTYRLLFVPGQLSQGAYSSIIEEPSVKEVLNTIKSASMLVHGIGEAKTMAQRRNTPLEDLKKIDDNDAVTEAFGYYFNADGEVVHKVHSVGMQLDDIDAIPDIIAVAGGSSKAEAIEAYFKKPRNTVLVTDEGAAKKLLR 338
               SCOP domains d3bxfb_ B: Central glycolytic gene regulator CggR                                                                                                                                                                                                     SCOP domains
               CATH domains 3bxfB00 B:94-338  [code=3.40.50.1360, no name defined]                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh.......eeeeee.......hhhhhhhhhhhhhhhhhh.ee.........hhhhhhhhh.hhhhhhhhhhhhh..eeee..eehhhhhhhh..hhhhhhhhhhh...eee..eee.....eeee......hhhhhhhh.eeeee..hhhhhhhhhhhh.....eeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxf B  94 LTLLEKTLKERLNLKDAIIVSGDSDQSPWVKKEMGRAAVACMKKRFSGKNIVAVTGGTTIEAVAEMMTPDSKNRELLFVPARGGLGEDVKNQANTICAHMAEKASGTYRLLFVPGQLSQGAYSSIIEEPSVKEVLNTIKSASMLVHGIGEAKTMAQRRNTPLEDLKKIDDNDAVTEAFGYYFNADGEVVHKVHSVGMQLDDIDAIPDIIAVAGGSSKAEAIEAYFKKPRNTVLVTDEGAAKKLLR 338
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333
   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  (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 3BXF)

(-) 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 3bxg 3bxh

(-) 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
3bxg CRYSTAL STRUCTURE OF EFFECTOR BINDING DOMAIN OF CENTRAL GLYCOLYTIC GENE REGULATOR (CGGR) FROM BACILLUS SUBTILIS IN COMPLEX WITH GLUCOSE-6-PHOSPHATE
3bxh CRYSTAL STRUCTURE OF EFFECTOR BINDING DOMAIN OF CENTRAL GLYCOLYTIC GENE REGULATOR (CGGR) FROM BACILLUS SUBTILIS IN COMPLEX WITH FRUCTOSE-6-PHOSPHATE