A novel glycosyl hydrolase family 10 (GH 10) xylanase (XynAGN16), consisting of five domains, was revealed from the genome sequence of Arthrobacter sp. GN16 isolated from the feces of Grus nigricollis. XynAGN16 and its truncated derivatives XynAGN16L (GH 10 domain at N-terminus) and XynAGN16Lpd (GH 10 domain at N-terminus and polysaccharide deacetylases domain) were expressed in Escherichia coli and characterized. Biochemical characterizations and hydrolysis products analyses of recombinant XynAGN16L and XynAGN16Lpd showed similar features, including showing catalytic activities at 0 °C, thermolabilities at temperatures of more than 50 °C, and similar substrate specificity. However, the polysaccharide deacetylases domain improved the affinity and catalytic efficiency towards xylans of the recombinant XynAGN16Lpd. The K m and k cat/K m values of recombinant XynAGN16L towards birchwood xylan were 2.6 mg/mL and 19.5 mL/mg/s, respectively, while the two values of recombinant XynAGN16Lpd were 1.2 mg/mL and 42.7 mL/mg/s, respectively. Towards beechwood xylan, the K m and k cat/K m values of recombinant XynAGN16L were 1.8 mg/mL and 27.1 mL/mg/s, respectively, while the two values of recombinant XynAGN16Lpd were 1.0 mg/mL and 35.3 mL/mg/s, respectively. Compared with three thermophilic endoxylanases, XynAGN16L has a surface loop from A57 to Y77 and a decreased number of salt bridges.