1v77

Crystal structure of the PH1877 proteinCrystal structure of the PH1877 protein

Structural highlights

1v77 is a 1 chain structure with sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNP3_PYRHO Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Not absolutely essential for activity in vitro, however it strongly stimulates activity. Binds RNase P RNA.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the processing of pre-tRNA. Protein Ph1877p is one of essential components of the hyperthermophilic archaeon Pyrococcus horikoshii OT3 RNase P [Biochem. Biophys. Res. Commun. 306 (2003) 666]. The crystal structure of Ph1877p was determined at 1.8A by X-ray crystallography and refined to a crystallographic R factor of 22.96% (Rfree of 26.77%). Ph1877p forms a TIM barrel structure, consisting of ten alpha-helices and seven beta-strands, and has the closest similarity to the TIM barrel domain of Escherichia coli cytosine deaminase with a root-mean square deviation of 3.0A. The protein Ph1877p forms an oblate ellipsoid, approximate dimensions being 45Ax43Ax39A, and the electrostatic representation indicated the presence of several clusters of positively charged amino acids present on the molecular surface. We made use of site-directed mutagenesis to assess the role of twelve charged amino acids, Lys42, Arg68, Arg87, Arg90, Asp98, Arg107, His114, Lys123, Lys158, Arg176, Asp180, and Lys196 related to the RNase P activity. Individual mutations of Arg90, Arg107, Lys123, Arg176, and Lys196 by Ala resulted in reconstituted particles with reduced enzymatic activities (32-48%) as compared with that reconstituted RNase P by wild-type Ph1877p. The results presented here provide an initial step for definite understanding of how archaeal and eukaryotic RNase Ps mediate substrate recognition and process 5'-leader sequence of pre-tRNA.

Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3.,Takagi H, Watanabe M, Kakuta Y, Kamachi R, Numata T, Tanaka I, Kimura M Biochem Biophys Res Commun. 2004 Jul 2;319(3):787-94. PMID:15184052^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kouzuma Y, Mizoguchi M, Takagi H, Fukuhara H, Tsukamoto M, Numata T, Kimura M. Reconstitution of archaeal ribonuclease P from RNA and four protein components. Biochem Biophys Res Commun. 2003 Jul 4;306(3):666-73. PMID:12810070
↑ Fukuhara H, Kifusa M, Watanabe M, Terada A, Honda T, Numata T, Kakuta Y, Kimura M. A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3. Biochem Biophys Res Commun. 2006 May 12;343(3):956-64. Epub 2006 Mar 15. PMID:16574071 doi:10.1016/j.bbrc.2006.02.192
↑ Terada A, Honda T, Fukuhara H, Hada K, Kimura M. Characterization of the archaeal ribonuclease P proteins from Pyrococcus horikoshii OT3. J Biochem. 2006 Aug;140(2):293-8. Epub 2006 Jul 7. PMID:16829535 doi:http://dx.doi.org/10.1093/jb/mvj144
↑ Takagi H, Watanabe M, Kakuta Y, Kamachi R, Numata T, Tanaka I, Kimura M. Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3. Biochem Biophys Res Commun. 2004 Jul 2;319(3):787-94. PMID:15184052 doi:10.1016/j.bbrc.2004.05.055

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OCA

[1] Kouzuma Y, Mizoguchi M, Takagi H, Fukuhara H, Tsukamoto M, Numata T, Kimura M. Reconstitution of archaeal ribonuclease P from RNA and four protein components. Biochem Biophys Res Commun. 2003 Jul 4;306(3):666-73. PMID:12810070

[2] Fukuhara H, Kifusa M, Watanabe M, Terada A, Honda T, Numata T, Kakuta Y, Kimura M. A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3. Biochem Biophys Res Commun. 2006 May 12;343(3):956-64. Epub 2006 Mar 15. PMID:16574071 doi:10.1016/j.bbrc.2006.02.192

[3] Terada A, Honda T, Fukuhara H, Hada K, Kimura M. Characterization of the archaeal ribonuclease P proteins from Pyrococcus horikoshii OT3. J Biochem. 2006 Aug;140(2):293-8. Epub 2006 Jul 7. PMID:16829535 doi:http://dx.doi.org/10.1093/jb/mvj144

[4] Takagi H, Watanabe M, Kakuta Y, Kamachi R, Numata T, Tanaka I, Kimura M. Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3. Biochem Biophys Res Commun. 2004 Jul 2;319(3):787-94. PMID:15184052 doi:10.1016/j.bbrc.2004.05.055

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