7VSE

E. coli Ribonuclease HI in complex one Zn2+ (His124 N-epsilon binding)

Summary for 7VSE

• Entry DOI: 10.2210/pdb7vse/pdb
• Related: 7VSA 7VSB 7VSC 7VSD
• Descriptor: Ribonuclease HI, SULFATE ION, ZINC ION, ... (5 entities in total)
• Functional Keywords: endonuclease, metalloenzyme, hydrolase
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 2
• Total formula weight: 35853.16

Authors

Liao, Z.,Oyama, T. (deposition date: 2021-10-26, release date: 2022-03-02, Last modification date: 2023-11-29)

Primary citation

Liao, Z.,Oyama, T.,Kitagawa, Y.,Katayanagi, K.,Morikawa, K.,Oda, M.
Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography.
Acta Crystallogr D Struct Biol, 78:390-398, 2022

PubMed Abstract: The ribonuclease (RNase) H family of enzymes catalyze the specific cleavage of RNA strands of RNA/DNA hybrid duplexes and play an important role in DNA replication and repair. Since the first report of the crystal structure of RNase HI, its catalytic mechanisms, which require metal ions, have been discussed based on numerous structural and functional analyses, including X-ray crystallography. In contrast, the function of the conserved histidine residue (His124 in Escherichia coli) in the flexible loop around the active site remains poorly understood, although an important role was suggested by NMR analyses. Here, novel high-resolution X-ray crystal structures of E. coli RNase HI are described, with a particular focus on the interactions of divalent cations with His124 oriented towards the active site. The enzyme-Mg complex contains two metal ions in the active site, one of which has previously been observed. The second ion lies alongside the first and binds to His124 in an octahedral coordination scheme. In the enzyme-Zn complex a single metal ion was found to bind to the active site, showing a tetrahedral coordination geometry with the surrounding atoms, including His124. These results provide structural evidence that His124 plays a crucial role in the catalytic activity of RNase HI by interacting weakly and transiently with metal ions in the catalytic center.

PubMed: 35234152
DOI: 10.1107/S2059798322000870

Experimental method

X-RAY DIFFRACTION (2.08 Å)