|
|
| Line 3: |
Line 3: |
| | <StructureSection load='2z70' size='340' side='right'caption='[[2z70]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='2z70' size='340' side='right'caption='[[2z70]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2z70]] is a 2 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=2Z70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z70 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2z70]] is a 2 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=2Z70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z70 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pqx|2pqx]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rna, rnsA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Enterobacter_ribonuclease Enterobacter ribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.6 3.1.27.6] </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=2z70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z70 OCA], [https://pdbe.org/2z70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z70 RCSB], [https://www.ebi.ac.uk/pdbsum/2z70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z70 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=2z70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z70 OCA], [https://pdbe.org/2z70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z70 RCSB], [https://www.ebi.ac.uk/pdbsum/2z70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z70 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RNI_ECOLI RNI_ECOLI]] One of the few RNases that cleaves the phosphodiester bond between any two nucleotide. Shows a preference for cytidylic or guanylic acid.
| + | [https://www.uniprot.org/uniprot/RNI_ECOLI RNI_ECOLI] One of the few RNases that cleaves the phosphodiester bond between any two nucleotide. Shows a preference for cytidylic or guanylic acid. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 38: |
Line 36: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Enterobacter ribonuclease]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Loris, R]] | + | [[Category: Loris R]] |
| - | [[Category: Martinez-Rodriguez, S]] | + | [[Category: Martinez-Rodriguez S]] |
| - | [[Category: Messens, J]] | + | [[Category: Messens J]] |
| - | [[Category: Endonuclease]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Ribonuclease]]
| + | |
| Structural highlights
Function
RNI_ECOLI One of the few RNases that cleaves the phosphodiester bond between any two nucleotide. Shows a preference for cytidylic or guanylic acid.
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 crystal structure of Escherichia coli ribonuclease I (EcRNase I) reveals an RNase T2-type fold consisting of a conserved core of six beta-strands and three alpha-helices. The overall architecture of the catalytic residues is very similar to the plant and fungal RNase T2 family members, but the perimeter surrounding the active site is characterized by structural elements specific for E. coli. In the structure of EcRNase I in complex with a substrate-mimicking decadeoxynucleotide d(CGCGATCGCG), we observe a cytosine bound in the B2 base binding site and mixed binding of thymine and guanine in the B1 base binding site. The active site residues His55, His133, and Glu129 interact with the phosphodiester linkage only through a set of water molecules. Residues forming the B2 base recognition site are well conserved among bacterial homologs and may generate limited base specificity. On the other hand, the B1 binding cleft acquires true base aspecificity by combining hydrophobic van der Waals contacts at its sides with a water-mediated hydrogen-bonding network at the bottom. This B1 base recognition site is highly variable among bacterial sequences and the observed interactions are unique to EcRNaseI and a few close relatives.
Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli.,Rodriguez SM, Panjikar S, Van Belle K, Wyns L, Messens J, Loris R Protein Sci. 2008 Apr;17(4):681-90. Epub 2008 Feb 27. PMID:18305191[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Rodriguez SM, Panjikar S, Van Belle K, Wyns L, Messens J, Loris R. Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli. Protein Sci. 2008 Apr;17(4):681-90. Epub 2008 Feb 27. PMID:18305191 doi:10.1110/ps.073420708
|
