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(-) Description

Title :  OPEN LIGANDED CRYSTAL STRUCTURE OF XYLOSE BINDING PROTEIN FROM ESCHERICHIA COLI
 
Authors :  S. Sooriyaarachchi, W. Ubhayasekera, S. L. Mowbray
Date :  22 Mar 10  (Deposition) - 18 Aug 10  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Xylose Binding Protein, Xylose, Conformational Changes, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sooriyaarachchi, W. Ubhayasekera, C. Park, S. L. Mowbray
Conformational Changes And Ligand Recognition Of Escherichi Coli D-Xylose Binding Protein Revealed
J. Mol. Biol. V. 402 657 2010
PubMed-ID: 20678502  |  Reference-DOI: 10.1016/J.JMB.2010.07.038

(-) Compounds

Molecule 1 - D-XYLOSE-BINDING PERIPLASMIC PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEXP-5-CT/TOPO
    Expression System Strain: BL21(AI)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 511145
    Strain: K-12 SUBSTR. MG1655
    Synonym: XYLOSE BINDING PROTEIN

 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
1XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:135 , ASN A:137 , PHE A:141 , TRP A:169 , ASN A:196 , ASP A:222 , LYS A:242 , HOH A:339 , HOH A:340BINDING SITE FOR RESIDUE XYP A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M9X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M9X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M9X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M9X)

(-) Exons   (0, 0)

(no "Exon" information available for 3M9X)

(-) 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 XYLF_ECOLI | P37387 from UniProtKB/Swiss-Prot  Length:330

    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     
           XYLF_ECOLI    26 VKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL 330
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Peripla_BP_4-3m9xA01 A:5-263                                                                                                                                                                                                                                       -------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhh..eeeee..........eeeeehhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.......ee.....hhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhh.......eeee....eeeeeee..eee...............hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m9x A   3 VKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL 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  (0, 0)

(no "SCOP Domain" information available for 3M9X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M9X)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYLF_ECOLI | P37387)
molecular function
    GO:0048029    monosaccharide binding    Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
biological process
    GO:0015753    D-xylose transport    The directed movement of D-xylose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. D-xylose (the naturally occurring enantiomer is always D-) is a constituent of plant polysaccharides.
    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: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
        XYLF_ECOLI | P37387: 3m9w 3ma0

(-) Related Entries Specified in the PDB File

3m9w OPEN LIGAND-FREE CRYSTAL STRUCTURE OF XYLOSE BINDING PROTEIN FROM ESCHERICHIA COLI
3ma0 CLOSE LIGANDED XYLOSE BINDING PROTEIN STRUCTURE FROM ESCHERICHIA COLI