The consensus sequence logo of the loop T3 regions of 1,000 GH28 endo-PGs generated using the WEBLOGO.

<p>The consensus sequence logo of the loop T3 regions of 1,000 GH28 endo-PGs generated using the WEBLOGO.</p

Kinetic values of wild type PG8fn and its mutants ^a.

<p>^<i>a</i> The kinetic values are shown as means ± standard deviations (n = 3).</p><p>^<i>b</i> The <i>k</i>_<i>cat</i> values were calculated by considering the enzyme to be a monomeric form.</p><p>^<i>c</i> △(△G) = −RT·ln[(<i>k</i>_<i>cat</i>/<i>K</i>_<i>m</i>)_mut/(<i>k</i>_<i>cat</i>/<i>K</i>_<i>m</i>)_wt], where (<i>k</i>_<i>cat</i>/<i>K</i>_<i>m</i>)_mut and (<i>k</i>_<i>cat</i>/<i>K</i>_<i>m</i>)_wt are the <i>k</i>_<i>cat</i>/<i>K</i>_<i>m</i> ratios of the mutant and wild type enzyme, respectively, R is the ideal gas constant, and T is the temperature in Kelvin.</p><p>Kinetic values of wild type PG8fn and its mutants <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135413#t002fn001" target="_blank">^a</a>.</p

Illustration of the substrate pentagalacturonic acid docked to the wild type PG8fn catalytic pocket.

<p>The system was constructed using PyMOL. The protein surface is shown in transparent gray. The catalytic region forms a tunnel through which the substrate passes. Hydrogen bond is depicted as blue dashed lines. Asn94 is marked in green. Catalytic triads in the active center are marked in cyan. The key amino acids interacted with GalpA at –1/+1 subsites are marked in orange.</p

Structure analysis of wild type PG8fn.

<p>(A) Schematic structure of PG8fn with the N-terminus on the left and the C-terminus on the right viewed onto β-sheet PB1 (yellow). PB2a, PB2b, and PB3 are shown in orange, pink, and blue, respectively. The key residues, Asn94, Asp155, Asp176, and Asp177, are shown in stick models. The structure viewed from the N-terminal side shows the cleft that is formed by the loops T1 (right side) and T3 (left side). (B) Ribbon diagram of the cross section of PG8fn on the right panel; the color code indicates the secondary structure elements in a representative coil.</p

Hydrogen bonds^a existing in T3 loop (residues from 88 to 101) of wild type PG8fn and two mutants (N94Q, N94A), and their occupancies during the last 20 ns of MD simulations.

<p>^<i>a</i> Only H-bonds with occupancies >50% are shown.</p><p>^<i>b</i> Not observed.</p><p>Hydrogen bonds<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135413#t001fn001" target="_blank">^a</a> existing in T3 loop (residues from 88 to 101) of wild type PG8fn and two mutants (N94Q, N94A), and their occupancies during the last 20 ns of MD simulations.</p

Conformation analysis of the last 20 ns MD trajectory of the enzymes.

<p>(A) The RMSF value of each residue C_α atom of the wild type PG8fn (black) and mutants N94Q (red) and N94A (green) measured against the corresponding starting structures. (B) Superimpositions of the average structure of the wild type PG8fn and two mutants viewed from the C-terminal side.</p

Root mean square deviation (RMSD) analysis of the wild type PG8fn (black), N94Q (red) and N94A (green) during a 50-ns MD simulation.

<p>(A) The enzyme backbones. (B) The pentagalacturonic acid. Each simulation was repeated three times with the same initial configurations.</p