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Michal Harel

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+<StructureSection load="1rta" size="400" color=""  spin="on" Scene=  caption='Ribonuclease A (magenta) complex with thymidilic acid DNA tetramer (pink), [[1rta]]' >
+'''Ribonuclease''' (RNase) degrades RNA.  The endonucleases cleave single or double stranded RNA and include RNase III, A, T1 H and P.  Exo-RNases remove terminal nucleotide from the ends of the RNA molecule.  They include RNase II D, T, PH, Polynucleotide Phosphorylase (PNPase) and oligoribonuclease (ORNase). <br />
+*  '''RNase A''' cleaves C or U of single-stranded RNA (ssRNA).<br />
+*  '''RNase BA''' is RNase from ''Bacillus amyloliquefaciens''.<br />
+*  '''RNase D''' degrades 3'-end pre-tRNA.<br />
+*  '''RNase H''' cleaves RNA/DNA double-strand to produce ssDNA.<br />
+*  '''RNase I''' cleaves 3'-end of ssRNA.<br />
+*  '''RNase II''' degrades 3'-end ssRNA.<br />
+*  '''RNase III''' cleaves rRNA.<br />
+*  '''RNase 5''' is known as angiogenin and is a potent stimulator of new blood vessels formation.<br />
+*  '''RNase P''' is a ribozyme.<br />
+*  '''RNase S''' is RNase A cleaved by subtilisin.<br />
+*  '''RNase SA''' is RNase from ''Streptomyces auerofaciens''.<br />
+*  '''RNase T''' is involved in RNA maturation.<br />
+*  '''RNase T1''' cleaves 3'-end G from ssRNA.<br />
+*  '''RNase U2''' cleaves 3'-end A from ssRNA.<br />
+*  '''α-sarcin''' is a cytotoxic RNase which cleaves a phosphodiester bond in a conserved rRNA loop and inactivates the ribosome.<br />
+*  '''oligoribonuclease''' is an exoribonuclease which cleaves 3'-end of viral RNA-DNA hybrid.<br />
+*  '''Polynucleotide phosphorylase''' is a bifunctional enzyme which has exoribonuclease activity.<br />
+*  '''Binase''' is a microbial RNase which cleaves endonucleolyticly ssRNA.<br />
+*  '''Poly(A)-specific RNase''' cleaves exonucleolyticly the poly(A) tail.<br />
+For more details on RNase A see:<br />
+<br />
+*[[RNase A]] <br />
+*[[Ribonuclease A Catalysis]]<br />
+*[[RNase A Oligomers]]<br />
+*[[RNase A NMR]]<br />
+*[[User:R. Jeremy Johnson/RNaseA]]<br />
+*[[RNaseA Nobel Prizes]].<br />
+For RNase B and RNase S see [[RNaseS RNaseB]].
+{{Clear}}
+==Active Site of Ribonuclease A==
+Ribonuclease A cleaves RNA strands by catalyzing a transphosphorylation reaction where the 2'-OH of the ribose sugar attacks the neighboring phosphate, releasing the ribose on the the other side of the phosphate. This structure shows ribonuclease A (in blue) bound to short DNA strand composed of four thymidines (in pink). Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. <scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/2'>Three amino acids</scene> are shown that are important for catalysis. The 3' carbon on the DNA is shown in red--it is the site where the 2'-OH is connected in RNA. The two histidines perform the proton transfers that are needed in the reaction, and the lysine stabilizes the intermediate that is formed as the 2'-OH attacks the phosphate. Ribonuclease cleaves RNA strands best next to cytidine and uridine nucleotides--the reason for this may be seen in a <scene name='Goodsell_Sandbox/Ribonuclease_recognition/2'>spacefilling representation</scene>. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.<ref>PMID:1429575</ref>
+{{Clear}}
 ==Your Heading Here (maybe something like 'Structure')==
 <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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 **[[1tto]], [[1rn1]], [[1rn4]], [[1rnt]], [[2aad]], [[2aae]] - AoRNase T1 - ''Aspergillus oryzae'' <br />
-[[1q9e]], [[1iyy]], [[1i2e]], [[1i2f]],  [[1i2g]],  [[1i3f]], [[1i3i]], [[1hz1]], [[1fys]], [[1fzu]], [[1ch0]], [[4bir]], [[3bir]], [[5bir]], [[1g02]], [[1hyf]], [[1trp]], [[1trq]], [[2bir]], [[4rnt]], [[5rnt]], [[6rnt]], [[7rnt]], [[8rnt]], [[9rnt]] - AoRNase T1 (mutant)<br />
+**[[1q9e]], [[1iyy]], [[1i2e]], [[1i2f]],  [[1i2g]],  [[1i3f]], [[1i3i]], [[1hz1]], [[1fys]], [[1fzu]], [[1ch0]], [[4bir]], [[3bir]], [[5bir]], [[1g02]], [[1hyf]], [[1trp]], [[1trq]], [[2bir]], [[4rnt]], [[5rnt]], [[6rnt]], [[7rnt]], [[8rnt]], [[9rnt]] - AoRNase T1 (mutant)<br />
 **[[1lov]], [[1low]], [[1loy]], [[1i0v]],  [[1i0x]],  [[1b2m]], [[1rhl]], [[1bir]], [[1rgk]], [[1rgl]] - AoRNase T1 (mutant) + nucleotide<br />
 **[[1bvi]], [[2bu4]], [[2hoh]], [[3hoh]], [[4hoh]], [[5hoh]], [[1gsp]], [[2gsp]]. [[3gsp]], [[4gsp]], [[5gsp]]. [[6gsp]], [[7gsp]], [[1det]], [[1rls]], [[1lra]], [[1rga]], [[1bu4]], [[1rgc]], [[3bu4]], [[4bu4]], [[5bu4]], [[3syu]], [[3urp]] - AoRNase T1 + nucleotide<br />
@@ Line 299: / Line 336: @@
 **[[3agn]], [[3ago]], [[3ahw]] - UsRNase U2 + AMP - ''Ustilago sphaerogena''<br />
+**[[1rtu]] - UsRNase U2<br />
+**[[3ahs]] - UsRNase U2B<br />
+*RNase Z
+**[[2e7y]] - TmRNase Z<br />
+**[[2fk6]], [[4gcw]] - BsRNase Z (mutant) + tRNA Thr<br />
+**[[1y44]] - BsRNase Z (mutant) <br />
+**[[2cbn]] - EcRNase Z<br />
+**[[3v32]], [[3v33]], [[3v34]] - hRNase Z<br />
+*RNase α-sarcin
+**[[1de3]] - AgRNase αs - ''Aspergillus giganteus''<br />
+**[[1r4y]] - AgRNase αs (mutant)<br />
+*Oligoribonuclease
+**[[2igi]], [[1yta]] - EcORNase<br />
+**[[2gbz]] - ORNase - ''Xanthomonas campestris''<br />
+**[[1j9a]] - ORNase - ''Haemophilus influenza''<br />
+**[[3tr8]] - ORNase - ''Coxiella burnetii''<br />
+*Polynucleotide phosphorylase
+**[[3cdi]] - EcPNPase<br />
+**[[3gll]] - EcPNPase core<br />
+**[[3cdj]] - EcPNPase C terminal truncated<br />
+**[[1e3h]], [[1e3p]] - PNPase - ''Streptomyces antibioticus''<br />
+**[[3gcm]], [[3gme]], [[3h1c]] - EcPNPase + RNase E recognition domain<br />
+**[[3h36]] - PNPase fragment - ''Streptomyces mutans''<br />
+*Binase
+**[[1gou]], [[1gov]], [[1goy]] - BiBinase - ''Bacillus intermedius''<br />
+**[[2rbi]], [[4haa]] - BiBinase (mutant)<br />
+**[[1buj]] - BiBinase - NMR<br />
+*Poly(A)-specific RNase
+**[[1ug8]] - mParn R3H domain - NMR<br />
+**[[1whv]] - mParn RNA-binding domain - NMR<br />
+**[[2rok]] - mParn CAP-binding domain - NMR<br />
+**[[3d45]] - mParn + nucleotide<br />
+**[[2a1s]] - hParn <br />
+**[[2a1r]], [[3ctr]] - hParn + nucleotide<br />
+*RNase pop2
+**[[4b8a]] - yRNase pop2 + cell division cycle protein 39<br />
+**[[4b8c]] - yRNase pop2 + cell division cycle protein 39 + CCR4<br />
+*Other RNases
+**[[2zpo]] - RNase - ''Chelonia mydas''<br />
+**[[3a4y]], [[3idz]], [[3ie0]], [[3ie2]] - TtRNase  (mutant) - ''Thermus thermophilus''<br />
+**[[3iek]] - TtRNase<br />
+**[[3ie1]], [[3iem]] - TtRNase (mutant)<br />
+**[[3iel]] - TtRNase + nucleotide<br />
 }}