リボヌクレアーゼ(ribonuclease, RNase)はリボ核酸を分解してオリゴヌクレオチドあるいはモノヌクレオチドにする反応を触媒する酵素。ヌクレアーゼの一種で、RNase(RNアーゼまたはRNエース)とも呼ばれる。
あらゆる生物に遍く存在する酵素で、内部からRNAを分解するエンドリボヌクレアーゼ、外側から分解していくエキソリボヌクレアーゼの2種に分類される。塩基を識別して分解を行う基質特異性の高いものもあり、種類は多様である。主なものとして塩基の種類を問わないリボヌクレアーゼT2(EC 3.1.27.1)やピリミジン塩基のある部分だけ切断するリボヌクレアーゼA(EC 3.1.27.5)、グアニンの部分のみを分解するリボヌクレアーゼT1(EC 3.1.27.4)などがあげられる。mRNAなどの必要なRNAはリボヌクレアーゼインヒビターと呼ばれるペプチドによってリボヌクレアーゼによる分解をまぬがれている。
リボヌクレアーゼは一次構造が最初に特定された酵素として歴史に残っており、これを決定した三人の化学者はノーベル化学賞を受賞している。
目次
- 1 分類
- 1.1 主要なエンドリボヌクレアーゼ
- 1.2 主要なエキソリボヌクレアーゼ
- 2 関連項目
分類
主要なエンドリボヌクレアーゼ
- EC 3.1.27.5 RNase Aは研究に広く使用されるRNaseである。RNase A （たとえばbovine pancreatic ribonuclease A: PDB 2AAS）は研究室で一般に用いられる酵素の中で最も丈夫なもののひとつであり、RNase Aを精製する方法の一つに、細胞の抽出物を煮沸しRNase A以外のすべての酵素を変性させるというものもあるほどである。RNase Aは一本鎖RNAの配列に特異的であり、一本鎖のC残基またはU残基（ピリミジン残基）の3'末端を切断して、3'末端リン酸化物を生じる。
- EC 3.1.26.4 RNase H はDNA/RNAハイブリッド二本鎖を形成しているRNAを切断し、一本鎖DNAを生じるリボヌクレアーゼである。RNase Hは非特異的なエンドヌクレアーゼであり、加水分解によってRNA切断を触媒する。酵素に結合した二価金属イオンはその活性を助ける。RNase Hは5'末端リン酸化物を生じる。
- EC number 3.1.??: RNase I は1本鎖RNAの3'末端で全てのジヌクレオチド結合を切断し5'-ヒドロキシル末端, 3'-リン酸末端を作る, このとき中間産物として2',3'環状モノリン酸が生じる.
- EC 3.1.26.3: RNase III は原核生物においてポリシストロニックに転写された rRNA (16s rRNA と 23s rRNA)を切断することで成熟させる触媒として知られる。また、2本鎖RNAを分解する double strands RNA (dsRNS)-Dicer ファミリーのRNaseでも有る。さらに、pre-miRNA (60–70bp)を消化する事でmiRNA (22–30bp)に成熟させ、この活性によってmRNAの翻訳制御やmRNAの分解による発現制御に関わる。
- EC number 3.1.26.-??: RNase Lはインターフェロン誘導性RNaseである。活性化されると細胞内のRNAを無差別に分解する。
- EC 3.1.26.5: RNase P は他のRNaseと異なり リボザイム – a ribonucleic acid の一種であり、酵素である他のRNaseと同様の活性を有する。 RNase PはtRNA前駆体の余剰配列を分解する事でtRNAを成熟させ機能を持つ。
- EC number 3.1.??: RNase PhyM は１本鎖RNAの特定領域を切断するRNaseである. 3'末端不対合塩基の A と U 残基で切断する.
- EC 3.1.27.3: RNase T1 は１本鎖RNAの特定領域を切断するRNaseである. 3'末端の不対合G残基で切断する。
- EC 3.1.27.1: RNase T2 は１本鎖RNAの特定領域を切断するRNaseである. 3'末端の4塩基全てに活性を持つが, A末端を優先的に作る.
- EC 3.1.27.4: RNase U2 iは１本鎖RNAの特定領域を切断するRNaseである. 3'末端の不対合A残基で切断する。
- EC 3.1.27.8: RNase V1は配列非特異的に2本鎖RNAを分解する.
主要なエキソリボヌクレアーゼ
- EC number EC 2.7.7.8: Polynucleotide Phosphorylase (PNPase)エキソヌクレアーゼ と同様にnucleotidyltransferase活性を有する。
- EC number EC 2.7.7.56: RNase PH エキソヌクレアーゼ と同様にnucleotidyltransferase活性を有する。
- EC number 3.1.??: RNase II 3'から5'方向のエキソリボヌクレアーゼ活性を有し、 1本鎖RNAを分解する事で成熟させる.
- EC number 3.1.??: RNase R RNase IIと非常に近縁のホモログであるがRNase IIと異なり, RNAの2次構造をアクセサリーファクター無しに分解可能である。
- EC number EC 3.1.13.5: RNase DｔRNA前駆体を3'-5'方向に消化する事でtRNAの成熟に関わる。
- EC number 3.1.??: RNase T ｒRNAやｔRNAの成熟において中心的な役割を担うリボヌクレアーゼである。
- EC 3.1.13.3: Oligoribonuclease 短いRNA断片をモノヌクレオチドまで分解する。
- EC 3.1.11.1: Exoribonuclease I 1本鎖RNAを分解する。原核生物にのみ存在する。
- EC 3.1.13.1: Exoribonuclease II Exoribonuclease Iの非常に近縁のホモログとして知られる.
関連項目
| ribonuclease |
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Ustilago sphaerogena Ribonuclease U2 with AMP PDB entry 3agn[1]
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| Identifiers |
| Symbol |
Ribonuclease |
| Pfam |
PF00545 |
| InterPro |
IPR000026 |
| SCOP |
1brn |
| SUPERFAMILY |
1brn |
| Available protein structures: |
| Pfam |
structures |
| PDB |
RCSB PDB; PDBe; PDBj |
| PDBsum |
structure summary |
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Ribonuclease (commonly abbreviated RNase) is a type of nuclease that catalyzes the degradation of RNA into smaller components. Ribonucleases can be divided into endoribonucleases and exoribonucleases, and comprise several sub-classes within the EC 2.7 (for the phosphorolytic enzymes) and 3.1 (for the hydrolytic enzymes) classes of enzymes.
Contents
- 1 Function
- 2 Classification
- 2.1 Major types of endoribonucleases
- 2.2 Major types of exoribonucleases
- 3 RNase specificity
- 4 RNase contamination during RNA extraction
- 5 References
- 6 Sources
- 7 External links
Function
All organisms studied contain many RNases of many different classes, showing that RNA degradation is a very ancient and important process. As well as cleaning of cellular RNA that is no longer required, RNases play key roles in the maturation of all RNA molecules, both messenger RNAs that carry genetic material for making proteins, and non-coding RNAs that function in varied cellular processes. In addition, active RNA degradation systems are a first defense against RNA viruses, and provide the underlying machinery for more advanced cellular immune strategies such as RNAi.
Some cells also secrete copious quantities of non-specific RNases such as A and T1. RNases are, therefore, extremely common, resulting in very short lifespans for any RNA that is not in a protected environment. It is worth noting that all intracellular RNAs are protected from RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding within an RNA protein complex (ribonucleoprotein particle or RNP).
Another mechanism of protection is ribonuclease inhibitor (RI), which comprises a relatively large fraction of cellular protein (~0.1%) in some cell types, and which binds to certain ribonucleases with the highest affinity of any protein-protein interaction; the dissociation constant for the RI-RNase A complex is ~20 fM under physiological conditions. RI is used in most laboratories that study RNA to protect their samples against degradation from environmental RNases.
Similar to restriction enzymes, which cleave highly specific sequences of double-stranded DNA, a variety of endoribonucleases that recognize and cleave specific sequences of single-stranded RNA have been recently classified.
RNases play a critical role in many biological processes, including angiogenesis and self-incompatibility in flowering plants (angiosperms).[2][3] Many stress-response toxins of prokaryotic toxin-antitoxin systems have been shown to have RNase activity and homology.[4]
Classification
Major types of endoribonucleases
- EC 3.1.27.5: RNase A is an RNase that is commonly used in research. RNase A (e.g., bovine pancreatic ribonuclease A: PDB: 2AAS) is one of the hardiest enzymes in common laboratory usage; one method of isolating it is to boil a crude cellular extract until all enzymes other than RNase A are denatured. It is specific for single-stranded RNAs. It cleaves the 3'-end of unpaired C and U residues, ultimately forming a 3'-phosphorylated product via a 2',3'-cyclic monophosphate intermediate.[5] It does not require any cofactors for its activity [6]
- EC 3.1.26.4: RNase H is a ribonuclease that cleaves the RNA in a DNA/RNA duplex to produce ssDNA. RNase H is a non-specific endonuclease and catalyzes the cleavage of RNA via a hydrolytic mechanism, aided by an enzyme-bound divalent metal ion. RNase H leaves a 5'-phosphorylated product.[7]
- EC 3.1.26.3: RNase III is a type of ribonuclease that cleaves rRNA (16s rRNA and 23s rRNA) from transcribed polycistronic RNA operon in prokaryotes. It also digests double strands RNA (dsRNA)-Dicer family of RNAse, cutting pre-miRNA (60–70bp long) at a specific site and transforming it in miRNA (22–30bp), that is actively involved in the regulation of transcription and mRNA life-time.
- EC number 3.1.26.-??: RNase L is an interferon-induced nuclease that, upon activation, destroys all RNA within the cell
- EC 3.1.26.5: RNase P is a type of ribonuclease that is unique in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way as an enzyme. Its function is to cleave off an extra, or precursor, sequence on tRNA molecules. RNase P is one of two known multiple turnover ribozymes in nature (the other being the ribosome). A form of RNase P that is a protein and does not contain RNA has recently been discovered.[8]
- EC number 3.1.??: RNase PhyM is sequence specific for single-stranded RNAs. It cleaves 3'-end of unpaired A and U residues.
- EC 3.1.27.3: RNase T1 is sequence specific for single-stranded RNAs. It cleaves 3'-end of unpaired G residues.
- EC 3.1.27.1: RNase T2 is sequence specific for single-stranded RNAs. It cleaves 3'-end of all 4 residues, but preferentially 3'-end of As.
- EC 3.1.27.4: RNase U2 is sequence specific for single-stranded RNAs. It cleaves 3'-end of unpaired A residues.
- EC 3.1.27.8: RNase V is specific for polyadenine and polyuridine RNA.
Major types of exoribonucleases
- EC number EC 2.7.7.8: Polynucleotide Phosphorylase (PNPase) functions as an exonuclease as well as a nucleotidyltransferase.
- EC number EC 2.7.7.56: RNase PH functions as an exonuclease as well as a nucleotidyltransferase.
- EC number 3.1.??: RNase R is a close homolog of RNase II, but it can, unlike RNase II, degrade RNA with secondary structures without help of accessory factors.
- EC number EC 3.1.13.5: RNase D is involved in the 3'-to-5' processing of pre-tRNAs.
- EC number 3.1.??: RNase T is the major contributor for the 3'-to-5' maturation of many stable RNAs.
- EC 3.1.13.3: Oligoribonuclease degrades short oligonucleotides to mononucleotides.
- EC 3.1.11.1: Exoribonuclease I degrades single-stranded RNA from 5'-to-3', exists only in eukaryotes.
- EC 3.1.13.1: Exoribonuclease II is a close homolog of Exoribonuclease I.
RNase specificity
The active site looks like a rift valley where all the active side residues create the wall and bottom of the valley. the rift is very thin and the small substrate fits perfectly in the middle of the active site, which allows for perfect interaction with the residues. It actually has a little curvature to the site which the substrate also has. Although, usually most of exo- and endoribonucleases are not sequence specific, recently CRISPR/Cas system natively recognizing and cutting DNA was engineered to cleave ssRNA in sequence specific manner.[9]
The extraction of RNA in molecular biology experiments is greatly complicated by the presence of ubiquitous and hardy ribonucleases that degrade RNA samples. Certain RNases can be extremely hardy and inactivating them is difficult compared to neutralizing DNases. In addition to the cellular RNases that are released, there are several RNases that are present in the environment. RNases have evolved to have many extracellular functions in various organisms.[10][11][12] For example, RNase 7, a member of the RNase A superfamily, is secreted by human skin and serves as a potent antipathogen defence.[13][14] In these secreted RNases, the enzymatic RNase activity may not even be necessary for its new, exapted function. For example, immune RNases act by destabilizing the cell membranes of bacteria.[15][16]
References
- ^ Noguchi, Shuji (2010). "Isomerization mechanism of aspartate to isoaspartate implied by structures ofUstilago sphaerogenaribonuclease U2 complexed with adenosine 3′-monophosphate". Acta Crystallographica Section D Biological Crystallography 66 (7): 843–849. doi:10.1107/S0907444910019621. ISSN 0907-4449.
- ^ Michael B. Sporn; Anita B. Roberts (6 December 2012). Peptide Growth Factors and Their Receptors II. Springer Science & Business Media. p. 556. ISBN 978-3-642-74781-6.
- ^ V. Raghavan (6 December 2012). Developmental Biology of Flowering Plants. Springer Science & Business Media. p. 237. ISBN 978-1-4612-1234-8.
- ^ Rosenberg, Susan M.; Ramage, Holly R.; Connolly, Lynn E.; Cox, Jeffery S. (2009). "Comprehensive Functional Analysis of Mycobacterium tuberculosis Toxin-Antitoxin Systems: Implications for Pathogenesis, Stress Responses, and Evolution". PLoS Genetics 5 (12): e1000767. doi:10.1371/journal.pgen.1000767. ISSN 1553-7404.
- ^ Cuchillo, C. M.; Nogués, M. V.; Raines, R. T. (2011). "Bovine pancreatic ribonuclease: Fifty years of the first enzymatic reaction mechanism". Biochemistry 50: 7835–7841. doi:10.1021/bi201075b. PMC 3172371. PMID 21838247.
- ^ [1]
- ^ Nowotny, Marcin (2009). "Retroviral integrase superfamily: the structural perspective". EMBO Reports 10 (2): 144–151. doi:10.1038/embor.2008.256. ISSN 1469-221X.
- ^ J. Holzmann, P. Frank, E. Löffler, K. Bennett, C. Gerner & W. Rossmanith (2008). "RNase P without RNA: Identification and functional reconstitution of the human mitochondrial tRNA processing enzyme". Cell 135 (3): 462–474. doi:10.1016/j.cell.2008.09.013. PMID 18984158.
- ^ Tamulaitis, Gintautas; Kazlauskiene, Migle; Manakova, Elena; Venclovas, Česlovas; Nwokeoji, Alison O.; Dickman, Mark J.; Horvath, Philippe; Siksnys, Virginijus (2014). "Programmable RNA Shredding by the Type III-A CRISPR-Cas System of Streptococcus thermophilus". Molecular Cell 56 (4): 506–517. doi:10.1016/j.molcel.2014.09.027. ISSN 1097-2765.
- ^ Rossier, O.; Dao, J.; Cianciotto, N. P. (2009). "A type II secreted RNase of Legionella pneumophila facilitates optimal intracellular infection of Hartmannella vermiformis". Microbiology 155 (3): 882–890. doi:10.1099/mic.0.023218-0.
- ^ Luhtala, N.; Parker, R. (2010). "T2 Family ribonucleases: Ancient enzymes with diverse roles". Trends in Biochemical Sciences 35 (5): 253–259. doi:10.1016/j.tibs.2010.02.002.
- ^ Dyer, K. D.; Rosenberg, H. F. (2006). "The RNase a superfamily: Generation of diversity and innate host defense". Molecular Diversity 10 (4): 585–597. doi:10.1007/s11030-006-9028-2.
- ^ Harder, J. (2002). "RNase 7, a Novel Innate Immune Defense Antimicrobial Protein of Healthy Human Skin". Journal of Biological Chemistry 277 (48): 46779–46784. doi:10.1074/jbc.M207587200.
- ^ Köten, B.; Simanski, M.; Gläser, R.; Podschun, R.; Schröder, J. M.; Harder, J. R. (2009). "RNase 7 Contributes to the Cutaneous Defense against Enterococcus faecium". PLoS ONE 4 (7): e6424. doi:10.1371/journal.pone.0006424.
- ^ Huang, Y. -C.; Lin, Y. -M.; Chang, T. -W.; Wu, S. -J.; Lee, Y. -S.; Chang, M. D. -T.; Chen, C.; Wu, S. -H.; Liao, Y. -D. (2006). "The Flexible and Clustered Lysine Residues of Human Ribonuclease 7 Are Critical for Membrane Permeability and Antimicrobial Activity". Journal of Biological Chemistry 282 (7): 4626–4633. doi:10.1074/jbc.M607321200.
- ^ Rosenberg, H. F. (2008). "RNase a ribonucleases and host defense: An evolving story". Journal of Leukocyte Biology 83 (5): 1079–87. doi:10.1189/jlb.1107725. PMC 2692241. PMID 18211964.
Sources
- D'Alessio G and Riordan JF, eds. (1997) Ribonucleases: Structures and Functions, Academic Press.
- Gerdes K, Christensen SK and Lobner-Olesen A (2005). "Prokaryotic toxin-antitoxin stress response loci". Nat. Rev. Microbiol. (3) 371–382.
External links
- IUBMB Enzyme Database for EC 3.1
- Integrated Enzyme Database for EC 3.1
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Hydrolase: esterases (EC 3.1)
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3.1.1: Carboxylic
ester hydrolases |
- Cholinesterase
- Acetylcholinesterase
- Butyrylcholinesterase
- Pectinesterase
- 6-phosphogluconolactonase
- PAF acetylhydrolase
- Lipase
- Bile salt-dependent
- Gastric/Lingual
- Pancreatic
- Lysosomal
- Hormone-sensitive
- Endothelial
- Hepatic
- Lipoprotein
- Monoacylglycerol
- Diacylglycerol
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| 3.1.2: Thioesterase |
- Palmitoyl protein thioesterase
- Ubiquitin carboxy-terminal hydrolase L1
- 4-hydroxybenzoyl-CoA thioesterase
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| 3.1.3: Phosphatase |
- Alkaline phosphatase
- Acid phosphatase (Prostatic)/Tartrate-resistant acid phosphatase/Purple acid phosphatases
- Nucleotidase
- Glucose 6-phosphatase
- Fructose 1,6-bisphosphatase
- Protein phosphatase
- OCRL
- Pyruvate dehydrogenase phosphatase
- Fructose 6-P,2-kinase:fructose 2,6-bisphosphatase
- PTEN
- Phytase
- Inositol-phosphate phosphatase
- Protein phosphatase: Protein tyrosine phosphatase
- Protein serine/threonine phosphatase
- Dual-specificity phosphatase
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| 3.1.4: Phosphodiesterase |
- Autotaxin
- Phospholipase
- Sphingomyelin phosphodiesterase
- PDE1
- PDE2
- PDE3
- PDE4A/PDE4B
- PDE5
- Lecithinase (Clostridium perfringens alpha toxin)
- Cyclic nucleotide phosphodiesterase
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| 3.1.6: Sulfatase |
- arylsulfatase
- Arylsulfatase A
- Arylsulfatase B
- Arylsulfatase E
- Steroid sulfatase
- Galactosamine-6 sulfatase
- Iduronate-2-sulfatase
- N-acetylglucosamine-6-sulfatase
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Nuclease (includes
deoxyribonuclease and
ribonuclease) |
| 3.1.11-16: Exonuclease |
| Exodeoxyribonuclease |
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| Exoribonuclease |
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| 3.1.21-31: Endonuclease |
| Endodeoxyribonuclease |
- Deoxyribonuclease I
- Deoxyribonuclease II
- Deoxyribonuclease IV
- Restriction enzyme
- UvrABC endonuclease
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| Endoribonuclease |
- RNase III
- RNase H
- RNase P
- RNase A
- RNase T1
- RNA-induced silencing complex
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| either deoxy- or ribo- |
- Aspergillus nuclease S1
- Micrococcal nuclease
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Enzymes
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| Activity |
- Active site
- Binding site
- Catalytic triad
- Oxyanion hole
- Enzyme promiscuity
- Catalytically perfect enzyme
- Coenzyme
- Cofactor
- Enzyme catalysis
- Enzyme kinetics
- Lineweaver–Burk plot
- Michaelis–Menten kinetics
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| Regulation |
- Allosteric regulation
- Cooperativity
- Enzyme inhibitor
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| Classification |
- EC number
- Enzyme superfamily
- Enzyme family
- List of enzymes
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| Types |
- EC1 Oxidoreductases(list)
- EC2 Transferases(list)
- EC3 Hydrolases(list)
- EC4 Lyases(list)
- EC5 Isomerases(list)
- EC6 Ligases(list)
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