来自嗜热栖热菌的PIN结构域蛋白PH0500的结构
Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.
作者信息
Jeyakanthan Jeyaraman, Inagaki Eiji, Kuroishi Chizu, Tahirov Tahir H
机构信息
Advanced Protein Crystallography Research Group, RIKEN Harima Institute, 1-1-1 Kouto, Sayo-gun, Hyogo 679-5148, Japan.
出版信息
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 May 1;61(Pt 5):463-8. doi: 10.1107/S1744309105012406. Epub 2005 Apr 26.
Abstract
The Pyrococcus horikoshii OT3 protein PH0500 is highly conserved within the Pyrococcus genus of hyperthermophilic archaea and shows low amino-acid sequence similarity with a family of PIN-domain proteins. The protein has been expressed, purified and crystallized in two crystal forms: PH0500-I and PH0500-II. The structure was determined at 2.0 A by the multiple anomalous dispersion method using a selenomethionyl derivative of crystal form PH0500-I (PH0500-I-Se). The structure of PH0500-I has been refined at 1.75 A resolution to an R factor of 20.9% and the structure of PH0500-II has been refined at 2.0 A resolution to an R factor of 23.4%. In both crystal forms as well as in solution the molecule appears to be a dimer. Searches of the databases for protein-fold similarities confirmed that the PH0500 protein is a PIN-domain protein with possible exonuclease activity and involvement in DNA or RNA editing.
摘要
嗜热栖热菌OT3蛋白PH0500在嗜热古菌的栖热菌属中高度保守，并且与PIN结构域蛋白家族的氨基酸序列相似性较低。该蛋白已被表达、纯化，并以两种晶体形式结晶：PH0500-I和PH0500-II。使用晶体形式PH0500-I（PH0500-I-Se）的硒代甲硫氨酸衍生物，通过多波长反常散射法在2.0 Å分辨率下确定了其结构。PH0500-I的结构已在1.75 Å分辨率下精修至R因子为20.9%，PH0500-II的结构已在2.0 Å分辨率下精修至R因子为23.4%。在两种晶体形式以及溶液中，该分子似乎都是二聚体。在数据库中搜索蛋白质折叠相似性证实，PH0500蛋白是一种具有可能的核酸外切酶活性并参与DNA或RNA编辑的PIN结构域蛋白。
相似文献
1
Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.来自嗜热栖热菌的PIN结构域蛋白PH0500的结构
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 May 1;61(Pt 5):463-8. doi: 10.1107/S1744309105012406. Epub 2005 Apr 26.
2
Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 A resolution.嗜热栖热菌OT3丙氨酰-tRNA合成酶编辑结构域同源物（PH0574）的晶体结构，分辨率为1.45埃
Proteins. 2006 Mar 1;62(4):1133-7. doi: 10.1002/prot.20760.
3
Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P protein Rpp21.嗜热栖热菌OT3核糖核酸酶P蛋白Ph1601p的晶体结构：人类核糖核酸酶P蛋白Rpp21的古菌同源物
Biochemistry. 2005 Sep 13;44(36):12086-93. doi: 10.1021/bi050738z.
4
Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3.嗜热古菌火球菌OT3来源的核糖核酸酶P蛋白Ph1877p的晶体结构
Biochem Biophys Res Commun. 2004 Jul 2;319(3):787-94. doi: 10.1016/j.bbrc.2004.05.055.
5
Crystal structure of the regulatory subunit of archaeal initiation factor 2B (aIF2B) from hyperthermophilic archaeon Pyrococcus horikoshii OT3: a proposed structure of the regulatory subcomplex of eukaryotic IF2B.嗜热古菌火球菌OT3的古菌起始因子2B（aIF2B）调节亚基的晶体结构：真核生物IF2B调节亚复合物的推测结构
Biochem Biophys Res Commun. 2004 Jul 2;319(3):725-32. doi: 10.1016/j.bbrc.2004.05.045.
6
Crystal structure of the DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3.嗜热古菌火球菌OT3中DUF54家族蛋白PH1010的晶体结构
Proteins. 2009 Jan;74(1):256-60. doi: 10.1002/prot.22255.
7
Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29.嗜热栖热菌OT3中古菌核糖核酸酶P蛋白Ph1771p的晶体结构：真核核糖核酸酶P蛋白Rpp29的古菌同源物
RNA. 2004 Sep;10(9):1423-32. doi: 10.1261/rna.7560904.
8
Structural analysis of the transcriptional regulator homolog protein from Pyrococcus horikoshii OT3.嗜热栖热菌OT3转录调节同源蛋白的结构分析
Proteins. 2006 Jun 1;63(4):1084-6. doi: 10.1002/prot.20913.
9
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.来自嗜热栖热菌OT3的古菌核糖核酸酶P的蛋白质Ph1481p与蛋白质Ph1877p形成复合物的晶体结构：全酶二聚体形成的意义
J Mol Biol. 2006 Mar 24;357(2):583-91. doi: 10.1016/j.jmb.2005.12.086. Epub 2006 Jan 11.
10
Crystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3.嗜热古菌火球菌OT3中类KaiC蛋白PH0186的晶体结构
Proteins. 2009 Jun;75(4):1035-9. doi: 10.1002/prot.22367.
引用本文的文献
1
Domain definition and preliminary functional exploration of the endonuclease NOBP-1 in Strongyloides stercoralis.在粪类圆线虫中内切核酸酶 NOBP-1 的结构定义和初步功能探索。
Parasit Vectors. 2023 Nov 3;16(1):399. doi: 10.1186/s13071-023-05940-9.
2
Functional Characterization, Mechanism, and Mode of Action of Putative Streptomycin Adenylyltransferase from .来自……的假定链霉素腺苷酸转移酶的功能表征、作用机制及作用方式
Antibiotics (Basel). 2022 Nov 30;11(12):1722. doi: 10.3390/antibiotics11121722.
3
Structural conservation of the PIN domain active site across all domains of life.PIN结构域活性位点在所有生命域中的结构保守性。
Protein Sci. 2017 Aug;26(8):1474-1492. doi: 10.1002/pro.3193. Epub 2017 May 24.
4
Growth and translation inhibition through sequence-specific RNA binding by Mycobacterium tuberculosis VapC toxin.结核分枝杆菌 VapC 毒素通过序列特异性 RNA 结合抑制生长和翻译。
J Biol Chem. 2012 Apr 13;287(16):12835-47. doi: 10.1074/jbc.M112.340109. Epub 2012 Feb 21.
5
Structural components and architectures of RNA exosomes.RNA 外切体的结构组成和架构。
Adv Exp Med Biol. 2010;702:9-28.
6
Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain.Nob1通过其PIN结构域与18S rRNA 3'端的单链切割位点D结合。
Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14259-64. doi: 10.1073/pnas.0905403106. Epub 2009 Aug 14.
7
An endoribonuclease functionally linked to perinuclear mRNP quality control associates with the nuclear pore complexes.一种与核周mRNA核糖核蛋白体质量控制功能相关的核糖核酸内切酶与核孔复合体相关联。
PLoS Biol. 2009 Jan 6;7(1):e8. doi: 10.1371/journal.pbio.1000008.
8
Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing.酵母Rrp44外切体复合物的结构揭示了用于3'末端加工的RNA招募途径。
Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16844-9. doi: 10.1073/pnas.0705526104. Epub 2007 Oct 17.
9
Crystal structures of the pilus retraction motor PilT suggest large domain movements and subunit cooperation drive motility.菌毛回缩马达PilT的晶体结构表明，大结构域运动和亚基协作驱动运动性。
Structure. 2007 Mar;15(3):363-76. doi: 10.1016/j.str.2007.01.018.
10
Crystallization and preliminary X-ray analysis of the PIN domain of human EST1A.人类EST1A的PIN结构域的结晶及初步X射线分析。
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Jul 1;62(Pt 7):656-8. doi: 10.1107/S1744309106020057. Epub 2006 Jun 10.
本文引用的文献
1
Processing of X-ray diffraction data collected in oscillation mode.振荡模式下收集的X射线衍射数据的处理。
Methods Enzymol. 1997;276:307-26. doi: 10.1016/S0076-6879(97)76066-X.
2
Crystallographic R factor refinement by molecular dynamics.利用分子动力学进行晶体学 R 因子精修。
Science. 1987 Jan 23;235(4787):458-60. doi: 10.1126/science.235.4787.458.
3
Raster3D Version 2.0. A program for photorealistic molecular graphics.光栅3D版本2.0。一个用于逼真分子图形的程序。
Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):869-73. doi: 10.1107/S0907444994006396.
4
Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution.嗜热栖热菌PIN（PilT N端）结构域（AF0591）在1.90埃分辨率下的晶体结构。
Proteins. 2004 Aug 1;56(2):404-8. doi: 10.1002/prot.20090.
5
Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease.远距离结构同源性导致古菌PIN结构域被鉴定为一种核酸外切酶。
J Biol Chem. 2004 Apr 16;279(16):16471-8. doi: 10.1074/jbc.M313833200. Epub 2004 Jan 20.
6
TOPS: an enhanced database of protein structural topology.TOPS：一个蛋白质结构拓扑增强数据库。
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D251-4. doi: 10.1093/nar/gkh060.
7
An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi.嗜热古菌深渊热球菌基因组的综合分析。
Mol Microbiol. 2003 Mar;47(6):1495-512. doi: 10.1046/j.1365-2958.2003.03381.x.
8
Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology.嗜热菌激烈火球菌的基因组序列：对生理学和酶学的启示
Methods Enzymol. 2001;330:134-57. doi: 10.1016/s0076-6879(01)30372-5.
9
PIN domains in nonsense-mediated mRNA decay and RNAi.无义介导的mRNA衰变和RNA干扰中的PIN结构域。
Curr Biol. 2000;10(24):R888-90. doi: 10.1016/s0960-9822(00)00858-7.
10
2.9 A crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site.2.9 无配体色氨酰 - tRNA合成酶的晶体结构：结构域运动使腺嘌呤核苷酸结合位点碎片化
Protein Sci. 2000 Feb;9(2):218-31. doi: 10.1110/ps.9.2.218.
Zotero 插件