Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: Implication of dimer formation of the holoenzyme

Shin Kawano, Takashi Nakashima, Yoshimitsu Kakuta, Isao Tanaka, Makoto Kimura

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Abstract

Ribonuclease P (RNase P) in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNA and five protein subunits. We previously determined crystal structures of four protein subunits. Ph1481p, an archaeal homologue for human hPop5, is the protein component of the P. horikoshii RNase P for which no structural information is available. Here we report the crystal structure of Ph1481p in complex with another protein subunit, Ph1877p, determined at 2.0 Å resolution. Ph1481p consists of a five-stranded antiparallel β-sheet and five helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. Ph1481p is, however, distinct from the typical RNP domain in that it has additional helices at the C terminus, which pack against one face of the β-sheet. The presence of two complexes in the asymmetric unit, together with gel filtration chromatography indicates that the heterotetramer is stable in solution and represents a fundamental building block in the crystals. In the heterotetrameric structure (Ph1877p-(Ph1481p)2-Ph1877p), a homodimer of Ph1481p sits between two Ph1877p monomers. Ph1481p dimerizes through hydrogen bonding interaction from the loop between α1 and α2 helices, and each Ph1481p interacts with two Ph1877p molecules, where α2 and α3 in Ph1481p interact with α7 in one Ph1877p and α8 in the other Ph1877p molecule, respectively. Deletion of the α1-α2 loop in Ph1481p caused heterodimerization with Ph1877p, and abolished ability to homodimerize itself and heterotetramerize with Ph1877p. Furthermore, the reconstituted particle containing the deletion mutant Ph1481p (mPh1481p) exhibited significantly reduced nuclease activity. These results suggest the presence of the heterotetramer of Ph1481p and Ph1877p in P. horikoshii RNase P.

Original languageEnglish
Pages (from-to)583-591
Number of pages9
JournalJournal of Molecular Biology
Volume357
Issue number2
DOIs
Publication statusPublished - Mar 24 2006

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Pyrococcus horikoshii
Archaeal Proteins
Ribonuclease P
Holoenzymes
Protein Subunits
Catalytic RNA
Proteins
Archaea
Hydrogen Bonding
Gel Chromatography
RNA Recognition Motif

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

@article{247004f638034da1b55528a283ddf559,
title = "Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: Implication of dimer formation of the holoenzyme",
abstract = "Ribonuclease P (RNase P) in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNA and five protein subunits. We previously determined crystal structures of four protein subunits. Ph1481p, an archaeal homologue for human hPop5, is the protein component of the P. horikoshii RNase P for which no structural information is available. Here we report the crystal structure of Ph1481p in complex with another protein subunit, Ph1877p, determined at 2.0 {\AA} resolution. Ph1481p consists of a five-stranded antiparallel β-sheet and five helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. Ph1481p is, however, distinct from the typical RNP domain in that it has additional helices at the C terminus, which pack against one face of the β-sheet. The presence of two complexes in the asymmetric unit, together with gel filtration chromatography indicates that the heterotetramer is stable in solution and represents a fundamental building block in the crystals. In the heterotetrameric structure (Ph1877p-(Ph1481p)2-Ph1877p), a homodimer of Ph1481p sits between two Ph1877p monomers. Ph1481p dimerizes through hydrogen bonding interaction from the loop between α1 and α2 helices, and each Ph1481p interacts with two Ph1877p molecules, where α2 and α3 in Ph1481p interact with α7 in one Ph1877p and α8 in the other Ph1877p molecule, respectively. Deletion of the α1-α2 loop in Ph1481p caused heterodimerization with Ph1877p, and abolished ability to homodimerize itself and heterotetramerize with Ph1877p. Furthermore, the reconstituted particle containing the deletion mutant Ph1481p (mPh1481p) exhibited significantly reduced nuclease activity. These results suggest the presence of the heterotetramer of Ph1481p and Ph1877p in P. horikoshii RNase P.",
author = "Shin Kawano and Takashi Nakashima and Yoshimitsu Kakuta and Isao Tanaka and Makoto Kimura",
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T1 - Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3

T2 - Implication of dimer formation of the holoenzyme

AU - Kawano, Shin

AU - Nakashima, Takashi

AU - Kakuta, Yoshimitsu

AU - Tanaka, Isao

AU - Kimura, Makoto

PY - 2006/3/24

Y1 - 2006/3/24

N2 - Ribonuclease P (RNase P) in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNA and five protein subunits. We previously determined crystal structures of four protein subunits. Ph1481p, an archaeal homologue for human hPop5, is the protein component of the P. horikoshii RNase P for which no structural information is available. Here we report the crystal structure of Ph1481p in complex with another protein subunit, Ph1877p, determined at 2.0 Å resolution. Ph1481p consists of a five-stranded antiparallel β-sheet and five helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. Ph1481p is, however, distinct from the typical RNP domain in that it has additional helices at the C terminus, which pack against one face of the β-sheet. The presence of two complexes in the asymmetric unit, together with gel filtration chromatography indicates that the heterotetramer is stable in solution and represents a fundamental building block in the crystals. In the heterotetrameric structure (Ph1877p-(Ph1481p)2-Ph1877p), a homodimer of Ph1481p sits between two Ph1877p monomers. Ph1481p dimerizes through hydrogen bonding interaction from the loop between α1 and α2 helices, and each Ph1481p interacts with two Ph1877p molecules, where α2 and α3 in Ph1481p interact with α7 in one Ph1877p and α8 in the other Ph1877p molecule, respectively. Deletion of the α1-α2 loop in Ph1481p caused heterodimerization with Ph1877p, and abolished ability to homodimerize itself and heterotetramerize with Ph1877p. Furthermore, the reconstituted particle containing the deletion mutant Ph1481p (mPh1481p) exhibited significantly reduced nuclease activity. These results suggest the presence of the heterotetramer of Ph1481p and Ph1877p in P. horikoshii RNase P.

AB - Ribonuclease P (RNase P) in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNA and five protein subunits. We previously determined crystal structures of four protein subunits. Ph1481p, an archaeal homologue for human hPop5, is the protein component of the P. horikoshii RNase P for which no structural information is available. Here we report the crystal structure of Ph1481p in complex with another protein subunit, Ph1877p, determined at 2.0 Å resolution. Ph1481p consists of a five-stranded antiparallel β-sheet and five helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. Ph1481p is, however, distinct from the typical RNP domain in that it has additional helices at the C terminus, which pack against one face of the β-sheet. The presence of two complexes in the asymmetric unit, together with gel filtration chromatography indicates that the heterotetramer is stable in solution and represents a fundamental building block in the crystals. In the heterotetrameric structure (Ph1877p-(Ph1481p)2-Ph1877p), a homodimer of Ph1481p sits between two Ph1877p monomers. Ph1481p dimerizes through hydrogen bonding interaction from the loop between α1 and α2 helices, and each Ph1481p interacts with two Ph1877p molecules, where α2 and α3 in Ph1481p interact with α7 in one Ph1877p and α8 in the other Ph1877p molecule, respectively. Deletion of the α1-α2 loop in Ph1481p caused heterodimerization with Ph1877p, and abolished ability to homodimerize itself and heterotetramerize with Ph1877p. Furthermore, the reconstituted particle containing the deletion mutant Ph1481p (mPh1481p) exhibited significantly reduced nuclease activity. These results suggest the presence of the heterotetramer of Ph1481p and Ph1877p in P. horikoshii RNase P.

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