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(-) Description

Title :  CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM AI-2 RECEPTOR LSRB IN COMPLEX WITH R-THMF
 
Authors :  S. T. Miller, K. B. Xavier, S. R. Campagna, M. E. Taga, M. F. Semmelhack, B. L. Bassler, F. M. Hughson
Date :  07 Jun 04  (Deposition) - 28 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Ligand Complex, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. T. Miller, K. B. Xavier, S. R. Campagna, M. E. Taga, M. F. Semmelhack, B. L. Bassler, F. M. Hughson
Salmonella Typhimurium Recognizes A Chemically Distinct For Of The Bacterial Quorum-Sensing Signal Ai-2
Mol. Cell V. 15 677 2004
PubMed-ID: 15350213  |  Reference-DOI: 10.1016/J.MOLCEL.2004.07.020

(-) Compounds

Molecule 1 - SUGAR TRANSPORT PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX4-T1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: LSRB
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PAV1Ligand/Ion(2R,4S)-2-METHYL-2,3,3,4-TETRAHYDROXYTETRAHYDROFURAN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:35 , PHE A:41 , PHE A:42 , ASP A:116 , GLN A:130 , ASP A:166 , GLN A:167 , TRP A:170 , PRO A:220 , ASP A:221 , ALA A:222 , TRP A:266BINDING SITE FOR RESIDUE PAV A 400

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:99 -A:123

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TJY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TJY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TJY)

(-) Exons   (0, 0)

(no "Exon" information available for 1TJY)

(-) 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:316
 aligned with LSRB_SALTI | Q8Z2X8 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:316
                                    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       334      
           LSRB_SALTI    25 QAAERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTYDGPTEPSVSGQVQLVNNFVNQGYDAIIVSAVSPDGLCPALKRAMQRGVKILTWDSDTKPECRSYYINQGTPKQLGSMLVEMAAHQVDKEKAKVAFFYSSPTVTDQNQWVKEAKAKISQEHPGWEIVTTQFGYNDATKSLQTAEGIIKAYPDLDAIIAPDANALPAAAQAAENLKRNNLAIVGFSTPNVMRPYVQRGTVKEFGLWDVVQQGKISVYVANALLKNMPMNVGDSLDIPGIGKVTVSPNSEQGYHYEAKGNGIVLLPERVIFNKDNIDKYDF 340
               SCOP domains d1tjya_ A: AI-2 receptor LsrB                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Peripla_BP_4-1tjyA01 A:30-287                                                                                                                                                                                                                                     ----------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhh..eeeee....hhhhh.eeee..hhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh.....eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh........eeee...eeeeeehhhhhh........eeee....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tjy A  25 GSAERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTYDGPTEPSVSGQVQLVNNFVNQGYDAIIVSAVSPDGLCPALKRAMQRGVKILTWDSDTKPECRSYYINQGTPKQLGSMLVEMAAHQVDKEKAKVAFFYSSPTVTDQNQWVKEAKAKISQEHPGWEIVTTQFGYNDATKSLQTAEGIIKAYPDLDAIIAPDANALPAAAQAAENLKRNNLAIVGFSTPNVMRPYVQRGTVKEFGLWDVVQQGKISVYVANALLKNMPMNVGDSLDIPGIGKVTVSPNSEQGYHYEAKGNGIVLLPERVIFNKDNIDKYDF 340
                                    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       334      


Chain A from PDB  Type:PROTEIN  Length:316
 aligned with LSRB_SALTY | Q8ZKQ1 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:316
                                    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       334      
           LSRB_SALTY    25 QAAERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTYDGPTEPSVSGQVQLVNNFVNQGYDAIIVSAVSPDGLCPALKRAMQRGVKILTWDSDTKPECRSYYINQGTPKQLGSMLVEMAAHQVDKEKAKVAFFYSSPTVTDQNQWVKEAKAKISQEHPGWEIVTTQFGYNDATKSLQTAEGIIKAYPDLDAIIAPDANALPAAAQAAENLKRNNLAIVGFSTPNVMRPYVQRGTVKEFGLWDVVQQGKISVYVANALLKNMPMNVGDSLDIPGIGKVTVSPNSEQGYHYEAKGNGIVLLPERVIFNKDNIDKYDF 340
               SCOP domains d1tjya_ A: AI-2 receptor LsrB                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Peripla_BP_4-1tjyA01 A:30-287                                                                                                                                                                                                                                     ----------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhh..eeeee....hhhhh.eeee..hhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh.....eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh........eeee...eeeeeehhhhhh........eeee....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tjy A  25 GSAERIAFIPKLVGVGFFTSGGNGAQEAGKALGIDVTYDGPTEPSVSGQVQLVNNFVNQGYDAIIVSAVSPDGLCPALKRAMQRGVKILTWDSDTKPECRSYYINQGTPKQLGSMLVEMAAHQVDKEKAKVAFFYSSPTVTDQNQWVKEAKAKISQEHPGWEIVTTQFGYNDATKSLQTAEGIIKAYPDLDAIIAPDANALPAAAQAAENLKRNNLAIVGFSTPNVMRPYVQRGTVKEFGLWDVVQQGKISVYVANALLKNMPMNVGDSLDIPGIGKVTVSPNSEQGYHYEAKGNGIVLLPERVIFNKDNIDKYDF 340
                                    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       334
   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  (0, 0)

(no "CATH Domain" information available for 1TJY)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (6, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LSRB_SALTI | Q8Z2X8)
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    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).

Chain A   (LSRB_SALTY | Q8ZKQ1)
molecular function
    GO:0015145    monosaccharide transmembrane transporter activity    Enables the transfer of a monosaccharide from one side of a membrane to the other.
biological process
    GO:0015749    monosaccharide transport    The directed movement of monosaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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).
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LSRB_SALTI | Q8Z2X8: 1tm2
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(-) Related Entries Specified in the PDB File

1jx6 VIBRIO HARVEYI AI-2 RECEPTOR LUXP IN COMPLEX WITH S-THMF- BORATE
1tm2 CRYSTAL STRUCTURE OF THE APO FORM OF THE SALMONELLA TYPHIMURIUM AI-2 RECEPTOR LSRB