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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

Basic protrusion motif(A) Electron density map. The 2Fo–Fc map of XMRV RNase H was contoured at the 1σ level around the basic protrusion (residues 594–611) and was superposed with the refined model. (B) Comparison of our model of the basic protrusion of RNase H (right panel) with that in E. coli, MoMLV and XMRV. All ribbon diagrams are shown from the same point of view. Our model (basic protrusion in green and the remainder in magenta) was superposed with that of XMRV with a truncated basic protrusion (pink; PDB code 3P1G).
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Figure 2: Basic protrusion motif(A) Electron density map. The 2Fo–Fc map of XMRV RNase H was contoured at the 1σ level around the basic protrusion (residues 594–611) and was superposed with the refined model. (B) Comparison of our model of the basic protrusion of RNase H (right panel) with that in E. coli, MoMLV and XMRV. All ribbon diagrams are shown from the same point of view. Our model (basic protrusion in green and the remainder in magenta) was superposed with that of XMRV with a truncated basic protrusion (pink; PDB code 3P1G).

Mentions: Previous models of RNase H from MoMLV (Lim et al. [17]; PDB code 2HB5) and XMRV ([23]; PDB code 3P1G) were obtained only after deleting the loop containing helix α3 (residues 593–603 for MoMLV; residues 595–605 for XMRV). Helix α3 (residues 595–599) occurs immediately after helix α2, and the following residues adopt a highly bent loop structure formed by several stabilizing hydrogen-bonding contacts (O in Gly602–NZ in Lys614, 3.1 Å; N in Thr605–O in Arg609, 2.9 Å; OG1 in Thr605–N in R609, 3.0 Å) (Figures 2A and 2B). Except for the contact between Gly602 and Lys604, helix α3 and the following loop have no contact with the remaining part of the RNase H domain. Bound cadmium ions are not found in this region, implying that this region is in a native conformation.


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)

Basic protrusion motif(A) Electron density map. The 2Fo–Fc map of XMRV RNase H was contoured at the 1σ level around the basic protrusion (residues 594–611) and was superposed with the refined model. (B) Comparison of our model of the basic protrusion of RNase H (right panel) with that in E. coli, MoMLV and XMRV. All ribbon diagrams are shown from the same point of view. Our model (basic protrusion in green and the remainder in magenta) was superposed with that of XMRV with a truncated basic protrusion (pink; PDB code 3P1G).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3475449&req=5

Figure 2: Basic protrusion motif(A) Electron density map. The 2Fo–Fc map of XMRV RNase H was contoured at the 1σ level around the basic protrusion (residues 594–611) and was superposed with the refined model. (B) Comparison of our model of the basic protrusion of RNase H (right panel) with that in E. coli, MoMLV and XMRV. All ribbon diagrams are shown from the same point of view. Our model (basic protrusion in green and the remainder in magenta) was superposed with that of XMRV with a truncated basic protrusion (pink; PDB code 3P1G).
Mentions: Previous models of RNase H from MoMLV (Lim et al. [17]; PDB code 2HB5) and XMRV ([23]; PDB code 3P1G) were obtained only after deleting the loop containing helix α3 (residues 593–603 for MoMLV; residues 595–605 for XMRV). Helix α3 (residues 595–599) occurs immediately after helix α2, and the following residues adopt a highly bent loop structure formed by several stabilizing hydrogen-bonding contacts (O in Gly602–NZ in Lys614, 3.1 Å; N in Thr605–O in Arg609, 2.9 Å; OG1 in Thr605–N in R609, 3.0 Å) (Figures 2A and 2B). Except for the contact between Gly602 and Lys604, helix α3 and the following loop have no contact with the remaining part of the RNase H domain. Bound cadmium ions are not found in this region, implying that this region is in a native conformation.

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