5FCH

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Zn bound

5FCH の概要

• エントリーDOI: 10.2210/pdb5fch/pdb
• 関連するPDBエントリー: 4R60 5FCF
• 分子名称: Proline dipeptidase, GLY-GLY-GLY, ZINC ION, ... (7 entities in total)
• 機能のキーワード: xaa-pro dipeptidase, prolidase, m24 family, phosphate, hydrolase
• 由来する生物種: Xanthomonas campestris pv. campestris str. ATCC 33913; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 86630.26

構造登録者

Kumar, A.,Are, V.,Ghosh, B.,Jamdar, S.,Makde, R.D. (登録日: 2015-12-15, 公開日: 2016-12-07, 最終更新日: 2024-03-20)

主引用文献

Are, V.N.,Kumar, A.,Kumar, S.,Goyal, V.D.,Ghosh, B.,Bhatnagar, D.,Jamdar, S.N.,Makde, R.D.
Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro dipeptidases
Biochim. Biophys. Acta, 1865:153-164, 2017

PubMed Abstract: Xaa-Pro dipeptidase (XPD) catalyzes hydrolysis of iminopeptide bond in dipeptides containing trans-proline as a second residue. XPDs are found in all living organisms and are believed to play an essential role in proline metabolism. Here, we report crystal structures and extensive enzymatic studies of XPD from Xanthomonas campestris (XPDxc), the first such comprehensive study of a bacterial XPD. We also report enzymatic activities of its ortholog from Mycobacterium tuberculosis (XPDmt). These enzymes are strictly dipeptidases with broad substrate specificities. They exhibit substrate inhibition and allostericity, as described earlier for XPD from Lactococcus lactis (XPDll). The structural, mutational and comparative data have revealed a novel mechanism of dipeptide selectivity and substrate binding in these enzymes. Moreover, we have identified conserved sequence motifs that distinguish these enzymes from other prolidases, thus defining a new subfamily. This study provides a suitable structural template for explaining unique properties of this XPDxc subfamily. In addition, we report unique structural features of XPDxc protein like an extended N-terminal tail region and absence of a conserved Tyr residue near the active site.

PubMed: 27816563
DOI: 10.1016/j.bbapap.2016.10.016

実験手法

X-RAY DIFFRACTION (1.95 Å)