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Crystal structure of xenotropic murine leukaemia virus-related virus (XMRV) ribonuclease H.

Kim JH, Kang S, Jung SK, Yu KR, Chung SJ, Chung BH, Erikson RL, Kim BY, Kim SJ - Biosci. Rep. (2012)

Bottom Line: RNase H (retroviral ribonuclease H) cleaves the phosphate backbone of the RNA template within an RNA/DNA hybrid to complete the synthesis of double-stranded viral DNA.In the present study we have determined the complete structure of the RNase H domain from XMRV (xenotropic murine leukaemia virus-related virus) RT (reverse transcriptase).The basic protrusion motif of the XMRV RNase H domain is folded as a short helix and an adjacent highly bent loop.

View Article: PubMed Central - PubMed

Affiliation: Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-Gu, Daejeon, Republic of Korea.

ABSTRACT
RNase H (retroviral ribonuclease H) cleaves the phosphate backbone of the RNA template within an RNA/DNA hybrid to complete the synthesis of double-stranded viral DNA. In the present study we have determined the complete structure of the RNase H domain from XMRV (xenotropic murine leukaemia virus-related virus) RT (reverse transcriptase). The basic protrusion motif of the XMRV RNase H domain is folded as a short helix and an adjacent highly bent loop. Structural superposition and subsequent mutagenesis experiments suggest that the basic protrusion motif plays a role in direct binding to the major groove in RNA/DNA hybrid, as well as in establishing the co-ordination among modules in RT necessary for proper function.

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Related in: MedlinePlus

Structure of the RNase H domain from XMRV(A) Ribbon diagram. The boundaries of secondary structural elements are β1 (519–529), β2 (534–541), β3 (547–551), α1 (558–573), β4 (577–582), α2 (585–592), α3 (595–599), α4 (614–625), β5 (629–633) and α5 (644–662). One magnesium ion (green) and four cadmium ions (pale yellow) are represented as spheres. (B) Active site. The active site of RNase H of XMRV (green) was superimposed with that of RNase H of MoMLV (cyan). The magnesium ion is represented as a sphere (orange, XMRV; magenta, MoMLV). (C) Structure-based sequence alignment. XMRV RNase H sequences are aligned with those of MoMLV, E. coli, human, HIV-1 and Bh. Sequence alignment is based on structural superposition with XMRV RNase H except for Bh; aligned sequences are shaded cyan. The secondary structural elements of XMRV RNase H are indicated above the sequences and those of the basic protrusion are shown in green. The DEDD motif, which is crucial for catalysis, is shown in red.
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Figure 1: Structure of the RNase H domain from XMRV(A) Ribbon diagram. The boundaries of secondary structural elements are β1 (519–529), β2 (534–541), β3 (547–551), α1 (558–573), β4 (577–582), α2 (585–592), α3 (595–599), α4 (614–625), β5 (629–633) and α5 (644–662). One magnesium ion (green) and four cadmium ions (pale yellow) are represented as spheres. (B) Active site. The active site of RNase H of XMRV (green) was superimposed with that of RNase H of MoMLV (cyan). The magnesium ion is represented as a sphere (orange, XMRV; magenta, MoMLV). (C) Structure-based sequence alignment. XMRV RNase H sequences are aligned with those of MoMLV, E. coli, human, HIV-1 and Bh. Sequence alignment is based on structural superposition with XMRV RNase H except for Bh; aligned sequences are shaded cyan. The secondary structural elements of XMRV RNase H are indicated above the sequences and those of the basic protrusion are shown in green. The DEDD motif, which is crucial for catalysis, is shown in red.

Mentions: XMRV RNase H has a compact structure comprising a central β-sheet of five mixed antiparallel and parallel β-strands surrounded by four helices on one face and one helix on the other (Figure 1A). The helices and strands are arranged as an αβα Rossmann-like fold. A search for homologous structures using the Dali server [32] identified several members of the RNase H family, including MoMLV RNase H ([17]; PDB code 2HB5; z-score=23.3), XMRV RNase H ([23]; PDB code 3P1G; z-score=23.1), and human RNase H1 ([19]; PDB code 2QKB; z-score=17.1). When we aligned the structure of XMRV RNase H with that of MoMLV RNase H, 134 out of 153 Cα atoms were superimposed with an rms (root-mean-square) deviation of 0.8 Å. The regions that could not be aligned were mainly found among residues 596–610 (basic protrusion; discussed below), residues 635–640 (His-containing loop) and residues near the N-terminus. Except for these regions, the XMRV-RNase H structure was nearly identical with that of MoMLV RNase H. Structural superposition showed that the location of His638 in XMRV RNase H was distinct from that of HIV-1 or E. coli [14,16]. This conserved His residue within the His-containing loop is necessary for proper binding to the nucleic acid template [33]. Since the side chain of His638 directly interacts with cadmium ion in our model, it is possible that this difference in conformation reflects a crystallization artefact.


Crystal structure of xenotropic murine leukaemia virus-related virus (XMRV) ribonuclease H.

Kim JH, Kang S, Jung SK, Yu KR, Chung SJ, Chung BH, Erikson RL, Kim BY, Kim SJ - Biosci. Rep. (2012)

Structure of the RNase H domain from XMRV(A) Ribbon diagram. The boundaries of secondary structural elements are β1 (519–529), β2 (534–541), β3 (547–551), α1 (558–573), β4 (577–582), α2 (585–592), α3 (595–599), α4 (614–625), β5 (629–633) and α5 (644–662). One magnesium ion (green) and four cadmium ions (pale yellow) are represented as spheres. (B) Active site. The active site of RNase H of XMRV (green) was superimposed with that of RNase H of MoMLV (cyan). The magnesium ion is represented as a sphere (orange, XMRV; magenta, MoMLV). (C) Structure-based sequence alignment. XMRV RNase H sequences are aligned with those of MoMLV, E. coli, human, HIV-1 and Bh. Sequence alignment is based on structural superposition with XMRV RNase H except for Bh; aligned sequences are shaded cyan. The secondary structural elements of XMRV RNase H are indicated above the sequences and those of the basic protrusion are shown in green. The DEDD motif, which is crucial for catalysis, is shown in red.
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Related In: Results  -  Collection

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Figure 1: Structure of the RNase H domain from XMRV(A) Ribbon diagram. The boundaries of secondary structural elements are β1 (519–529), β2 (534–541), β3 (547–551), α1 (558–573), β4 (577–582), α2 (585–592), α3 (595–599), α4 (614–625), β5 (629–633) and α5 (644–662). One magnesium ion (green) and four cadmium ions (pale yellow) are represented as spheres. (B) Active site. The active site of RNase H of XMRV (green) was superimposed with that of RNase H of MoMLV (cyan). The magnesium ion is represented as a sphere (orange, XMRV; magenta, MoMLV). (C) Structure-based sequence alignment. XMRV RNase H sequences are aligned with those of MoMLV, E. coli, human, HIV-1 and Bh. Sequence alignment is based on structural superposition with XMRV RNase H except for Bh; aligned sequences are shaded cyan. The secondary structural elements of XMRV RNase H are indicated above the sequences and those of the basic protrusion are shown in green. The DEDD motif, which is crucial for catalysis, is shown in red.
Mentions: XMRV RNase H has a compact structure comprising a central β-sheet of five mixed antiparallel and parallel β-strands surrounded by four helices on one face and one helix on the other (Figure 1A). The helices and strands are arranged as an αβα Rossmann-like fold. A search for homologous structures using the Dali server [32] identified several members of the RNase H family, including MoMLV RNase H ([17]; PDB code 2HB5; z-score=23.3), XMRV RNase H ([23]; PDB code 3P1G; z-score=23.1), and human RNase H1 ([19]; PDB code 2QKB; z-score=17.1). When we aligned the structure of XMRV RNase H with that of MoMLV RNase H, 134 out of 153 Cα atoms were superimposed with an rms (root-mean-square) deviation of 0.8 Å. The regions that could not be aligned were mainly found among residues 596–610 (basic protrusion; discussed below), residues 635–640 (His-containing loop) and residues near the N-terminus. Except for these regions, the XMRV-RNase H structure was nearly identical with that of MoMLV RNase H. Structural superposition showed that the location of His638 in XMRV RNase H was distinct from that of HIV-1 or E. coli [14,16]. This conserved His residue within the His-containing loop is necessary for proper binding to the nucleic acid template [33]. Since the side chain of His638 directly interacts with cadmium ion in our model, it is possible that this difference in conformation reflects a crystallization artefact.

Bottom Line: RNase H (retroviral ribonuclease H) cleaves the phosphate backbone of the RNA template within an RNA/DNA hybrid to complete the synthesis of double-stranded viral DNA.In the present study we have determined the complete structure of the RNase H domain from XMRV (xenotropic murine leukaemia virus-related virus) RT (reverse transcriptase).The basic protrusion motif of the XMRV RNase H domain is folded as a short helix and an adjacent highly bent loop.

View Article: PubMed Central - PubMed

Affiliation: Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-Gu, Daejeon, Republic of Korea.

ABSTRACT
RNase H (retroviral ribonuclease H) cleaves the phosphate backbone of the RNA template within an RNA/DNA hybrid to complete the synthesis of double-stranded viral DNA. In the present study we have determined the complete structure of the RNase H domain from XMRV (xenotropic murine leukaemia virus-related virus) RT (reverse transcriptase). The basic protrusion motif of the XMRV RNase H domain is folded as a short helix and an adjacent highly bent loop. Structural superposition and subsequent mutagenesis experiments suggest that the basic protrusion motif plays a role in direct binding to the major groove in RNA/DNA hybrid, as well as in establishing the co-ordination among modules in RT necessary for proper function.

Show MeSH
Related in: MedlinePlus