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Title: Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain

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 ({Delta}C). The 1.6-{angstrom} 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 {beta}1-{beta}2, {alpha}A, and {alpha}B and residues from {alpha}B to {alpha}D 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 ofmore » 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.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
930113
Report Number(s):
BNL-80757-2008-JA
Journal ID: ISSN 0022-538X; JOVIAM; TRN: US200822%%1326
DOE Contract Number:
DE-AC02-98CH10886
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Virology; Journal Volume: 80
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; AMINO ACIDS; BACILLUS; BASIC; CHARGES; CRYSTAL STRUCTURE; CRYSTALLIZATION; DENSITY; ESCHERICHIA COLI; HUMAN POPULATIONS; HYBRIDIZATION; JOINTS; LEUKEMIA; MAGNESIUM IONS; MAPPING; MUTANTS; NUCLEOTIDES; RESIDUES; RESOLUTION; SUBSTRATES; SURFACES; national synchrotron light source

Citation Formats

Lim,D., Gregorio, G., Bingman, C., Martinez-Hackert, E., Hendrickson, W., and Goff, S. Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain. United States: N. p., 2006. Web. doi:10.1128/JVI.00750-06.
Lim,D., Gregorio, G., Bingman, C., Martinez-Hackert, E., Hendrickson, W., & Goff, S. Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain. United States. doi:10.1128/JVI.00750-06.
Lim,D., Gregorio, G., Bingman, C., Martinez-Hackert, E., Hendrickson, W., and Goff, S. Sun . "Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain". United States. doi:10.1128/JVI.00750-06.
@article{osti_930113,
title = {Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain},
author = {Lim,D. and Gregorio, G. and Bingman, C. and Martinez-Hackert, E. and Hendrickson, W. and Goff, S.},
abstractNote = {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 ({Delta}C). The 1.6-{angstrom} 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 {beta}1-{beta}2, {alpha}A, and {alpha}B and residues from {alpha}B to {alpha}D 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.},
doi = {10.1128/JVI.00750-06},
journal = {Journal of Virology},
number = ,
volume = 80,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}