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1i82

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms. Biochemistry 40 6248-6256 2001
    Site OTHER
    PDB Id 1i82
    Molecular Characteristics
    Source Thermotoga maritima
    Alias Ids TPS18730, Molecular Weight 21306.79 Da.
    Residues 189 Isoelectric Point 4.84
    Sequence mvatakygtpvidgeideiwntteeietkavamgsldknatakvrvlwdenylyvlaivkdpvlnkdnsn pweqdsveifidennhktgyyedddaqfrvnymneqtfgtggsparfktavklieggyiveaaikwkti kptpntvigfniqvndanekgqrvgiiswsdptnnswrdpskfgnlrlik
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.235
    Matthews' coefficent 2.31 Rfactor 0.215
    Waters 156 Solvent Content 46.83

    Ligand Information
    Ligands BGC-GLC (BETA-D-GLUCOSE) x 1
    Metals CA (CALCIUM) x 3

    Jmol

     

    Protein Summary

    The TM0061 gene of Thermotoga maritima encodes xylanase 10A, and this PDB entry contains a second of the two C-terminal type 9 carbohydrate-binding modules (CBM9-2) that can bind to all cellulose allomorphs and a range of small soluble sugars up to four sugar moieties in length. The first of the two CBM9 modules (CMB9-1) is very divergent and its exact function is not clear. TM0061 contains also two unrelated, type 4  carbohydrate-binding modules (CBM4) modules on the N-terminus and a central catalytic hydrolase domain.

    CBM9 folds into an immunoglobulin-like ?-sandwich with three calcium ions, thought to contribute to the thermostability of the protein, coordinated at loop regions (Fig. 1). Two tryptophan residues, Trp71 and Trp175, arranged parallel to each other, stack against the apolar surfaces of the carbohydrate ligand (Fig. 1). The reducing end of the sugar points inside the pocket formed by the tryptophans and provides the remaining interactions in an intricate hydrogen network involving mainly charged residues (1).




    Figure 1. Ribbon diagram of CBM9-2 bound to ?-D-glucose. CBM9-2 is spectrally colored from N-terminus (blue) to C-terminus (red). Calcium ions are shown in gray. Residues interacting with the ligand are indicated.

    Glucose binding in the pocket occurs in a different orientation to the one observed with cellobiose (1), which is surprising, given the similarity between the two substrates. The reasons for this difference are not clear. Analysis of CBM9-2  homologs shows conservation of secondary structure elements, metal binding sites and residues involved in substrate binding, suggesting that carbohydrate-binding function is also conserved.

    Ligand Summary

     

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