7OI1

Crystal structure of Synechocystis sp PCC6803 guanidinium hydrolase

7OI1 の概要

• エントリーDOI: 10.2210/pdb7oi1/pdb
• 分子名称: Probable agmatinase 2, CHLORIDE ION, NICKEL (II) ION, ... (7 entities in total)
• 機能のキーワード: ureohydrolase family protein, arginase/agmatinase family protein, ni2+ enzyme, 2-metal ion cluster, metal binding protein
• 由来する生物種: Synechocystis sp. (strain PCC 6803 / Kazusa)
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 130663.91

構造登録者

Fleming, J.R.,Mayans, O.M. (登録日: 2021-05-11, 公開日: 2021-12-15, 最終更新日: 2024-01-31)

主引用文献

Funck, D.,Sinn, M.,Fleming, J.R.,Stanoppi, M.,Dietrich, J.,Lopez-Igual, R.,Mayans, O.,Hartig, J.S.
Discovery of a Ni 2+ -dependent guanidine hydrolase in bacteria.
Nature, 603:515-521, 2022

PubMed Abstract: Nitrogen availability is a growth-limiting factor in many habitats, and the global nitrogen cycle involves prokaryotes and eukaryotes competing for this precious resource. Only some bacteria and archaea can fix elementary nitrogen; all other organisms depend on the assimilation of mineral or organic nitrogen. The nitrogen-rich compound guanidine occurs widely in nature, but its utilization is impeded by pronounced resonance stabilization, and enzymes catalysing hydrolysis of free guanidine have not been identified. Here we describe the arginase family protein GdmH (Sll1077) from Synechocystis sp. PCC 6803 as a Ni-dependent guanidine hydrolase. GdmH is highly specific for free guanidine. Its activity depends on two accessory proteins that load Ni instead of the typical Mn ions into the active site. Crystal structures of GdmH show coordination of the dinuclear metal cluster in a geometry typical for arginase family enzymes and allow modelling of the bound substrate. A unique amino-terminal extension and a tryptophan residue narrow the substrate-binding pocket and identify homologous proteins in further cyanobacteria, several other bacterial taxa and heterokont algae as probable guanidine hydrolases. This broad distribution suggests notable ecological relevance of guanidine hydrolysis in aquatic habitats.

PubMed: 35264792
DOI: 10.1038/s41586-022-04490-x

実験手法

X-RAY DIFFRACTION (1.9 Å)