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(-) Description

Title :  GLUCOSE/GALACTOSE BINDING PROTEIN BOUND TO 3-O-METHYL D-GLUCOSE
 
Authors :  M. J. Borrok, L. L. Kiessling, K. T. Forest
Date :  09 Aug 07  (Deposition) - 05 Aug 08  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Periplasmic Binding Protein, Antagonist, Chemotaxis, Transport, Ggbp, 3-O-Methyl Glucose, Sugar Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Borrok, Y. Zhu, K. T. Forest, L. L. Kiessling
Structure-Based Design Of A Periplasmic Binding Protein Antagonist That Prevents Domain Closure.
Acs Chem. Biol. V. 4 447 2009
PubMed-ID: 19348466  |  Reference-DOI: 10.1021/CB900021Q

(-) Compounds

Molecule 1 - D-GALACTOSE-BINDING PERIPLASMIC PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVB2
    Expression System Strain: HB929
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MGLB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: K12
    Synonym: GBP, D-GALACTOSE/ D-GLUCOSE-BINDING PROTEIN, GGBP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
13MG1Ligand/Ion3-O-METHYL-BETA-D-GLUCOPYRANOSE
2CA1Ligand/IonCALCIUM ION
3NA2Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:152 , ASP A:154 , TRP A:183 , ASN A:211 , ASP A:236 , HOH A:600BINDING SITE FOR RESIDUE 3MG A 310
2AC2SOFTWAREASP A:134 , ASN A:136 , ASP A:138 , GLN A:140 , GLN A:142 , GLU A:205BINDING SITE FOR RESIDUE CA A 311
3AC3SOFTWARETHR A:110 , TYR A:295 , HOH A:339 , HOH A:428 , HOH A:429 , HOH A:603BINDING SITE FOR RESIDUE NA A 312
4AC4SOFTWARESER A:228 , ILE A:230 , HOH A:412 , HOH A:413 , HOH A:414 , HOH A:415BINDING SITE FOR RESIDUE NA A 313

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QW1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QW1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QW1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QW1)

(-) Exons   (0, 0)

(no "Exon" information available for 2QW1)

(-) 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:305
 aligned with DGAL_ECOLI | P0AEE5 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:305
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     
           DGAL_ECOLI    25 DTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLADGKGAADGTNWKIDNKVVRVPYVGVDKDNLAEF 329
               SCOP domains d2qw1a_ A: Galactose/glucose-binding protein                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2qw1A01 A:2-110,A:257-294  [code=3.40.50.2300, no name defined]                                              2qw1A02 A:111-256,A:295-306  [code=3.40.50.2300, no name defined]                                                                                 2qw1A01 A:2-110,A:257-294             2qw1A02      CATH domains
               Pfam domains ---Peripla_BP_4-2qw1A01 A:5-277                                                                                                                                                                                                                                                     ----------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh....eeee....hhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhhhh......ee....hhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhh...............ee....eee...hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qw1 A   2 DTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLADGKGAADGTNWKIDNKVVRVPYVGVDKDNLAEF 306
                                    11        21        31        41        51        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
   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, 1)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Periplas_BP (97)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DGAL_ECOLI | P0AEE5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0008643    carbohydrate transport    The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        DGAL_ECOLI | P0AEE5: 1glg 2fvy 2fw0 2gbp 2hph 2ipl 2ipm 2ipn

(-) Related Entries Specified in the PDB File

2fvy 2fw0 2gbp