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| | <StructureSection load='2cbn' size='340' side='right'caption='[[2cbn]], [[Resolution|resolution]] 2.90Å' scene=''> | | <StructureSection load='2cbn' size='340' side='right'caption='[[2cbn]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2cbn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CBN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2cbn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CBN FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_Z Ribonuclease Z], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.11 3.1.26.11] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cbn OCA], [https://pdbe.org/2cbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cbn RCSB], [https://www.ebi.ac.uk/pdbsum/2cbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cbn ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cbn OCA], [https://pdbe.org/2cbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cbn RCSB], [https://www.ebi.ac.uk/pdbsum/2cbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cbn ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RBN_ECOLI RBN_ECOLI] Zinc phosphodiesterase, which has both exoribonuclease and endoribonuclease activities, depending on the nature of the substrate and of the added divalent cation, and on its 3'-terminal structure. Can process the 3' termini of both CCA-less and CCA-containing tRNA precursors. CCA-less tRNAs are cleaved endonucleolytically after the discriminator base, whereas residues following the CCA sequence can be removed exonucleolytically or endonucleolytically in CCA-containing molecules. Does not remove the CCA sequence. May also be involved in the degradation of mRNAs. In vitro, hydrolyzes bis(p-nitrophenyl)phosphate and thymidine-5'-p-nitrophenyl phosphate.<ref>PMID:12029081</ref> <ref>PMID:15764599</ref> <ref>PMID:16629673</ref> <ref>PMID:19366704</ref> <ref>PMID:20489203</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ribonuclease Z]]
| + | [[Category: Kostelecky B]] |
| - | [[Category: Kostelecky, B]] | + | [[Category: Meyer-Klaucke W]] |
| - | [[Category: Meyer-Klaucke, W]] | + | [[Category: Pohl E]] |
| - | [[Category: Pohl, E]] | + | |
| - | [[Category: Endonuclease]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metal- binding]]
| + | |
| - | [[Category: Phosphodiesterase beta lactamase trnase z]]
| + | |
| - | [[Category: Trna processing]]
| + | |
| - | [[Category: Zinc]]
| + | |
| Structural highlights
Function
RBN_ECOLI Zinc phosphodiesterase, which has both exoribonuclease and endoribonuclease activities, depending on the nature of the substrate and of the added divalent cation, and on its 3'-terminal structure. Can process the 3' termini of both CCA-less and CCA-containing tRNA precursors. CCA-less tRNAs are cleaved endonucleolytically after the discriminator base, whereas residues following the CCA sequence can be removed exonucleolytically or endonucleolytically in CCA-containing molecules. Does not remove the CCA sequence. May also be involved in the degradation of mRNAs. In vitro, hydrolyzes bis(p-nitrophenyl)phosphate and thymidine-5'-p-nitrophenyl phosphate.[1] [2] [3] [4] [5]
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
The elaC gene product from Escherichia coli, ZiPD, is a 3' tRNA-processing endonuclease belonging to the tRNase Z family of enzymes that have been identified in a wide variety of organisms. In contrast to the elaC homologue from Bacillus subtilis, E. coli elaC is not essential for viability, and although both enzymes process only precursor tRNA (pre-tRNA) lacking a CCA triplet at the 3' end in vitro, the physiological role of ZiPD remains enigmatic because all pre-tRNA species in E. coli are transcribed with the CCA triplet. We present the first crystal structure of ZiPD determined by multiple anomalous diffraction at a resolution of 2.9 A. This structure shares many features with the tRNase Z enzymes from B. subtilis and Thermotoga maritima, but there are distinct differences in metal binding and overall domain organization. Unlike the previously described homologous structures, ZiPD dimers display crystallographic symmetry and fully loaded metal sites. The ZiPD exosite is similar to that of the B. subtilis enzyme structurally, but its position with respect to the protein core differs substantially, illustrating its ability to act as a clamp in binding tRNA. Furthermore, the ZiPD crystal structure presented here provides insight into the enzyme's cooperativity and assists the ongoing attempt to elucidate the physiological function of this protein.
The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins.,Kostelecky B, Pohl E, Vogel A, Schilling O, Meyer-Klaucke W J Bacteriol. 2006 Feb;188(4):1607-14. PMID:16452444[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Vogel A, Schilling O, Niecke M, Bettmer J, Meyer-Klaucke W. ElaC encodes a novel binuclear zinc phosphodiesterase. J Biol Chem. 2002 Aug 9;277(32):29078-85. PMID:12029081 doi:10.1074/jbc.M112047200
- ↑ Ezraty B, Dahlgren B, Deutscher MP. The RNase Z homologue encoded by Escherichia coli elaC gene is RNase BN. J Biol Chem. 2005 Apr 29;280(17):16542-5. PMID:15764599 doi:10.1074/jbc.C500098200
- ↑ Perwez T, Kushner SR. RNase Z in Escherichia coli plays a significant role in mRNA decay. Mol Microbiol. 2006 May;60(3):723-37. PMID:16629673 doi:10.1111/j.1365-2958.2006.05124.x
- ↑ Dutta T, Deutscher MP. Catalytic properties of RNase BN/RNase Z from Escherichia coli: RNase BN is both J Biol Chem. 2009 Jun 5;284(23):15425-31. PMID:19366704 doi:10.1074/jbc.M109.005462
- ↑ Dutta T, Deutscher MP. Mode of action of RNase BN/RNase Z on tRNA precursors: RNase BN does not remove the CCA sequence from tRNA. J Biol Chem. 2010 Jul 23;285(30):22874-81. PMID:20489203 doi:10.1074/jbc.M110.141101
- ↑ Kostelecky B, Pohl E, Vogel A, Schilling O, Meyer-Klaucke W. The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins. J Bacteriol. 2006 Feb;188(4):1607-14. PMID:16452444 doi:188/4/1607
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