1RDD

CRYSTAL STRUCTURE OF ESCHERICHIA COLI RNASE HI IN COMPLEX WITH MG2+ AT 2.8 ANGSTROMS RESOLUTION: PROOF FOR A SINGLE MG2+ SITE

1RDD の概要

• エントリーDOI: 10.2210/pdb1rdd/pdb
• 分子名称: RIBONUCLEASE H, MAGNESIUM ION (3 entities in total)
• 機能のキーワード: hydrolase(endoribonuclease)
• 由来する生物種: Escherichia coli
• 細胞内の位置: Cytoplasm : P0A7Y4
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 17647.30

構造登録者

Katayanagi, K.,Morikawa, K. (登録日: 1993-06-23, 公開日: 1993-10-31, 最終更新日: 2024-02-14)

主引用文献

Katayanagi, K.,Okumura, M.,Morikawa, K.
Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site.
Proteins, 17:337-346, 1993

PubMed Abstract: To obtain more precise insight into the Mg(2+)-binding site essential for RNase HI catalytic activity, we have determined the crystal structure of E. coli RNase HI in complex with Mg2+. The analyzed cocrystal, which is not isomorphous with the Mg(2+)-free crystal previously refined at 1.48 A resolution, was grown at a high MgSO4 concentration more than 100 mM so that even weakly bound Mg2+ sites could be identified. The structure was solved by the molecular replacement method, using the Mg(2+)-free crystal structure as a search model, and was refined to give a final R-value of 0.190 for intensity data from 10 to 2.8 A, using the XPLOR and PROLSQ programs. The backbone structures are in their entirety very similar to each other between the Mg(2+)-bound and the metal-free crystals, except for minor regions in the enzyme interface with the DNA/RNA hybrid. The active center clearly revealed a single Mg2+ atom located at a position almost identical to that previously found by the soaking method. Although the two metal-ion mechanism had been suggested by another group (Yang, W., Hendrickson, W.A., Crouch, R.J., Satow, Y. Science 249:1398-1405, 1990) and partially supported by the crystallographic study of inactive HIV-1 RT RNase H fragment (Davies, J.F., II, Hostomska, Z., Hostomsky, Z., Jordan, S.R., Matthews, D. Science 252:88-95, 1991), the present result excludes the possibility that RNase HI requires two metal-binding sites for activity. In contrast to the features in the metal-free enzyme, the side chains of Asn-44 and Glu-48 are found to form coordinate bonds with Mg2+ in the metal-bound crystal.

PubMed: 8108376
DOI: 10.1002/prot.340170402

実験手法

X-RAY DIFFRACTION (2.8 Å)