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![[Figure 10]](dz5341fig10mag.jpg)
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Figure 10
A comparison of the current structure of Abp with the structure of SaArap27A (PDB entries 3a21, 3a22 and 3a23), a related arabinopyranosidase from the GH27 family. (a) A superposition of the monomers of Abp (chain A, yellow) and SaArap27A (chain B, other colours). The four domains of SaArap27A, the TIM-barrel domain, the β-sheet domain, the CBM13 domain and the jelly-roll domain, are shown in red, pink, purple and blue, respectively. The comparison demonstrates the relatively high structural similarities between the two Abp domains and the corresponding TIM-barrel and β-sheet domains of SaArap27A. Small differences are observed in the Abp monomer parts that interact with neighbouring monomers forming the Abp tetramer. The residues participating in these contacts are shown in dark blue (ball-and-stick representation). The captured arabinose molecules are also shown (blue for Abp; green for SaArap27A). (b) Electrostatic surface potential of the SaArap27A monomer (calculated with the APBS plug-in as implemented in PyMOL). The potential is calculated according to the linearized Poisson–Boltzmann equation using the PARSE force field at pH 7. The potential gradient is in the range 3kT/e to −3kT/e, where dark blue represents the most positive potential and dark red represents the most negative potential. Lower potential levels are shown in lighter shades of the corresponding colour. A local concentration of negative potential is noticed between the catalytic TIM-barrel domain and the CBM13 domain. Bound arabinose molecules are shown in green. (c) A superposition of the active sites of Abp-D197A–ARB (in yellow) and SaArap27A (in red). Most of the residues involved in binding the sugar product molecules are shown, demonstrating relatively high similarities in the product-binding modes of the two enzymes. A pronounced difference, however, is caused by the replacement of Ile67 in Abp (blue) by the corresponding Glu99 in SaArap27A (green). Bound sugar products are shown in blue (Abp) and green (SaArap27A). |
![[Figure 10]](dz5341fig10.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
