2HB5

Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain

Summary for 2HB5

• Entry DOI: 10.2210/pdb2hb5/pdb
• Descriptor: Reverse transcriptase/ribonuclease H, MAGNESIUM ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: rnase h, hydrolase
• Biological source: Moloney murine leukemia virus
• Cellular location: Gag-Pol polyprotein: Host cell membrane ; Lipid-anchor . Matrix protein p15: Virion . Capsid protein p30: Virion . Nucleocapsid protein p10: Virion : P03355
• Total number of polymer chains: 1
• Total formula weight: 17908.18

Authors

Lim, D.,Gregorio, G.G.,Bingman, C.A.,Martinez-Hackert, E.,Hendrickson, W.A.,Goff, S.P. (deposition date: 2006-06-13, release date: 2006-08-29, Last modification date: 2024-10-16)

Primary citation

Lim, D.,Gregorio, G.G.,Bingman, C.A.,Martinez-Hackert, E.,Hendrickson, W.A.,Goff, S.P.
Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain.
J.Virol., 80:8379-8389, 2006

PubMed Abstract: A crystallographic study of the Moloney murine leukemia virus (Mo-MLV) RNase H domain was performed to provide information about its structure and mechanism of action. These efforts resulted in the crystallization of a mutant Mo-MLV RNase H lacking the putative helix C (DeltaC). The 1.6-Angstroms resolution structure resembles the known structures of the human immunodeficiency virus type 1 (HIV-1) and Escherichia coli RNase H. The structure revealed the coordination of a magnesium ion within the catalytic core comprised of the highly conserved acidic residues D524, E562, and D583. Surface charge mapping of the Mo-MLV structure revealed a high density of basic charges on one side of the enzyme. Using a model of the Mo-MLV structure superimposed upon a structure of HIV-1 reverse transcriptase bound to an RNA/DNA hybrid substrate, Mo-MLV RNase H secondary structures and individual amino acids were examined for their potential roles in binding substrate. Identified regions included Mo-MLV RNase H beta1-beta2, alphaA, and alphaB and residues from alphaB to alphaD and its following loop. Most of the identified substrate-binding residues corresponded with residues directly binding nucleotides in an RNase H from Bacillus halodurans as observed in a cocrystal structure with RNA/DNA. Finally, superimposition of RNases H of Mo-MLV, E. coli, and HIV-1 revealed that a loop of the HIV-1 connection domain resides within the same region of the Mo-MLV and E. coli C-helix. The HIV-1 connection domain may serve to recognize and bind the RNA/DNA substrate major groove.

PubMed: 16912289
DOI: 10.1128/JVI.00750-06

Experimental method

X-RAY DIFFRACTION (1.59 Å)