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(-) Description

Title :  PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS
 
Authors :  S. L. Mowbray, L. B. Cole
Date :  23 Sep 94  (Deposition) - 26 Jan 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Sugar Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Bjorkman, R. A. Binnie, H. Zhang, L. B. Cole, M. A. Hermodson, S. L. Mowbray
Probing Protein-Protein Interactions. The Ribose-Binding Protein In Bacterial Transport And Chemotaxis.
J. Biol. Chem. V. 269 30206 1994
PubMed-ID: 7982928
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-RIBOSE-BINDING PROTEIN
    ChainsA
    EngineeredYES
    Expression System Vector TypeBACTERIAL
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 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
1RIP1Ligand/IonRIBOSE(PYRANOSE FORM)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:13 , PHE A:15 , PHE A:16 , ASP A:89 , ARG A:90 , ALA A:137 , ARG A:141 , PHE A:164 , ASN A:190 , ASP A:215 , GLN A:235BINDING SITE FOR RESIDUE RIP A 272
2RIBUNKNOWNASN A:13 , PHE A:15 , PHE A:16 , ASP A:89 , ARG A:90 , ARG A:141 , PHE A:164 , ASN A:190 , ASP A:215 , GLN A:235NULL

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DRI)

(-) 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:271
 aligned with RBSB_ECOLI | P02925 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:271
                                    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 
           RBSB_ECOLI    26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 296
               SCOP domains d2dria_ A: D-ribose-binding protein                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2driA01 A:1-101,A:238-261  [code=3.40.50.2300, no name defined]                                      2driA02 A:102-237,A:262-271  [code=3.40.50.2300, no name defined]                                                                       2driA01                 2driA02    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh......eeee...hhhhhhhhhhhhhh....eeee..........eeeee.hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh.....eeeeee..hhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh.......eeee..eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dri A   1 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DRI)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RBSB_ECOLI | P02925)
molecular function
    GO:0015145    monosaccharide transmembrane transporter activity    Enables the transfer of a monosaccharide from one side of a membrane to the other.
    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: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.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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).
    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
        RBSB_ECOLI | P029251ba2 1dbp 1drj 1drk 1urp 2gx6

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