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(-) Description

Title :  X-RAY STRUCTURE OF GLUCOSE/GALACTOSE RECEPTOR FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH (2R)-GLYCERYL-BETA-D-GALACTOPYRANOSIDE
 
Authors :  S. Sooriyaarachchi, W. Ubhayasekera, S. L. Mowbray
Date :  16 Feb 09  (Deposition) - 14 Apr 09  (Release) - 14 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glucose/Galactose Binding Protein, Glyceryl Galactoside, Salmonella Enterica Serovar Typhimurium, Calcium, Chemotaxis, Periplasm, Sugar Transport, Transport, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sooriyaarachchi, W. Ubhayasekera, W. Boos, S. L. Mowbray
X-Ray Structure Of Glucose/Galactose Receptor From Salmonella Typhimurium In Complex With The Physiological Ligand, (2R)-Glyceryl-Beta-D-Galactopyranoside
Febs J. V. 276 2116 2009
PubMed-ID: 19292879  |  Reference-DOI: 10.1111/J.1742-4658.2009.06945.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-GALACTOSE-BINDING PERIPLASMIC PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBD10
    Expression System Strain: LA5709
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MGLB
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Strain: LT2
    Synonym: GBP, D-GALACTOSE/ D-GLUCOSE-BINDING PROTEIN, GGBP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2NA2Ligand/IonSODIUM ION
3RGG2Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL BETA-D-GALACTOPYRANOSIDE
4SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3RGG1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL BETA-D-GALACTOPYRANOSIDE
4SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3RGG1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL BETA-D-GALACTOPYRANOSIDE
4SCN-1Ligand/IonTHIOCYANATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:14 , PHE A:16 , ASN A:91 , LYS A:92 , THR A:110 , HIS A:152 , ASP A:154 , ARG A:158 , ASN A:211 , ASP A:236 , ASN A:256 , GLN A:261 , TYR A:295 , HOH A:310 , HOH A:345BINDING SITE FOR RESIDUE RGG A 400
2AC2SOFTWAREASP A:134 , ASN A:136 , ASP A:138 , LYS A:140 , GLN A:142 , GLU A:205BINDING SITE FOR RESIDUE CA A 500
3AC3SOFTWAREASN A:288 , LYS A:289 , TYR B:106 , ASN B:288 , LYS B:289BINDING SITE FOR RESIDUE SCN A 600
4AC4SOFTWAREGLY A:28 , ALA A:31 , VAL A:34 , HOH A:566BINDING SITE FOR RESIDUE NA A 700
5AC5SOFTWAREASP B:14 , PHE B:16 , ASN B:91 , LYS B:92 , THR B:110 , HIS B:152 , ASP B:154 , ARG B:158 , ASN B:211 , ASP B:236 , ASN B:256 , GLN B:261 , TYR B:295 , HOH B:311 , HOH B:324BINDING SITE FOR RESIDUE RGG B 401
6AC6SOFTWAREASP B:134 , ASN B:136 , ASP B:138 , LYS B:140 , GLN B:142 , GLU B:205BINDING SITE FOR RESIDUE CA B 501
7AC7SOFTWAREGLY B:28 , ALA B:31 , VAL B:34 , HOH B:318 , HOH B:353 , HOH B:359BINDING SITE FOR RESIDUE NA B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GA5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GA5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GA5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GA5)

(-) Exons   (0, 0)

(no "Exon" information available for 3GA5)

(-) 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:305
 aligned with DGAL_SALTY | P23905 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:305
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325     
           DGAL_SALTY    26 TRIGVTIYKYDDNFMSVVRKAIEKDGKSAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGVIQGDLIAKHWQANQGWDLNKDGKIQYVLLKGEPGHPDAEARTTYVVKELNDKGIQTEQLALDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKSSIPVFGVDALPEALALVKSGAMAGTVLNDANNQAKATFDLAKNLAEGKGAADGTSWKIENKIVRVPYVGVDKDNLSEFT 330
               SCOP domains d3ga5a_ A: Galactose/glucose-binding protein                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3ga5A01 A:3-110,A:257-294  [code=3.40.50.2300, no name defined]                                             3ga5A02 A:111-256,A:295-307  [code=3.40.50.2300, no name defined]                                                                                 3ga5A01 A:3-110,A:257-294             3ga5A02       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh....eeee....hhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhh.hhhhh.eeee.hhhhhhhhhhhhhhh......ee....hhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhh...............eee...eee...hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ga5 A   3 TRIGVTIYKYDDNFMSVVRKAIEKDGKSAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGVIQGDLIAKHWQANQGWDLNKDGKIQYVLLKGEPGHPDAEARTTYVVKELNDKGIQTEQLALDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKSSIPVFGVDALPEALALVKSGAMAGTVLNDANNQAKATFDLAKNLAEGKGAADGTSWKIENKIVRVPYVGVDKDNLSEFT 307
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302     


Chain B from PDB  Type:PROTEIN  Length:305
 aligned with DGAL_SALTY | P23905 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:305
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325     
           DGAL_SALTY    26 TRIGVTIYKYDDNFMSVVRKAIEKDGKSAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGVIQGDLIAKHWQANQGWDLNKDGKIQYVLLKGEPGHPDAEARTTYVVKELNDKGIQTEQLALDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKSSIPVFGVDALPEALALVKSGAMAGTVLNDANNQAKATFDLAKNLAEGKGAADGTSWKIENKIVRVPYVGVDKDNLSEFT 330
               SCOP domains d3ga5b_ B: Galactose/glucose-binding protein                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3ga5B01 B:3-110,B:257-294  [code=3.40.50.2300, no name defined]                                             3ga5B02 B:111-256,B:295-307  [code=3.40.50.2300, no name defined]                                                                                 3ga5B01 B:3-110,B:257-294             3ga5B02       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh...eeee....hhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhh.hhhhh.eeee.hhhhhhhhhhhhhhh......ee....hhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhh...............eee...eee...hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ga5 B   3 TRIGVTIYKYDDNFMSVVRKAIEKDGKSAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGVIQGDLIAKHWQANQGWDLNKDGKIQYVLLKGEPGHPDAEARTTYVVKELNDKGIQTEQLALDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKSSIPVFGVDALPEALALVKSGAMAGTVLNDANNQAKATFDLAKNLAEGKGAADGTSWKIENKIVRVPYVGVDKDNLSEFT 307
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GA5)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DGAL_SALTY | P23905)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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_SALTY | P23905: 1gca 1gcg 3gbp

(-) Related Entries Specified in the PDB File

1gca THE 1.7 ANGSTROMS REFINED X-RAY STRUCTURE OF THE PERIPLASMIC GLUCOSE(SLASH)GALACTOSE RECEPTOR FROM SALMONELLA TYPHIMURIUM
1gcg THE 1.9 ANGSTROMS X-RAY STRUCTURE OF A CLOSED UNLIGANDED FORM OF THE PERIPLASMIC GLUCOSE(SLASH)GALACTOSE RECEPTOR FROM SALMONELLA TYPHIMURIUM
3gbp STRUCTURE OF THE PERIPLASMIC GLUCOSE/GALACTOSE RECEPTOR OF SALMONELLA TYPHIMURIUM