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| | ==Crystal structure of a new RNA polymerase interacting protein== | | ==Crystal structure of a new RNA polymerase interacting protein== |
| - | <StructureSection load='3bmb' size='340' side='right' caption='[[3bmb]], [[Resolution|resolution]] 1.91Å' scene=''> | + | <StructureSection load='3bmb' size='340' side='right'caption='[[3bmb]], [[Resolution|resolution]] 1.91Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3bmb]] is a 2 chain structure with sequence from [http://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=3BMB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BMB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3bmb]] 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=3BMB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BMB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnk ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bmb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bmb OCA], [http://pdbe.org/3bmb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bmb RCSB], [http://www.ebi.ac.uk/pdbsum/3bmb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bmb 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=3bmb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bmb OCA], [https://pdbe.org/3bmb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bmb RCSB], [https://www.ebi.ac.uk/pdbsum/3bmb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bmb ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RNK_ECOLI RNK_ECOLI]] May act as an anti-Gre factor. Regulates the level of the nucleoside diphosphate kinase Ndk.<ref>PMID:8596442</ref> <ref>PMID:18760284</ref> | + | [[https://www.uniprot.org/uniprot/RNK_ECOLI RNK_ECOLI]] May act as an anti-Gre factor. Regulates the level of the nucleoside diphosphate kinase Ndk.<ref>PMID:8596442</ref> <ref>PMID:18760284</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Bacillus coli migula 1895]] | | [[Category: Bacillus coli migula 1895]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Darst, S A]] | | [[Category: Darst, S A]] |
| | [[Category: Lamour, V]] | | [[Category: Lamour, V]] |
| Structural highlights
Function
[RNK_ECOLI] May act as an anti-Gre factor. Regulates the level of the nucleoside diphosphate kinase Ndk.[1] [2]
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
Sequence-based searches identified a new family of genes in proteobacteria, named rnk, which shares high sequence similarity with the C-terminal domains of the Gre factors (GreA and GreB) and the Thermus/Deinococcus anti-Gre factor Gfh1. We solved the X-ray crystal structure of Escherichia coli regulator of nucleoside kinase (Rnk) at 1.9 A resolution using the anomalous signal from the native protein. The Rnk structure strikingly resembles those of E. coli GreA and GreB and Thermus Gfh1, all of which are RNA polymerase (RNAP) secondary channel effectors and have a C-terminal domain belonging to the FKBP fold. Rnk, however, has a much shorter N-terminal coiled coil. Rnk does not stimulate transcript cleavage in vitro, nor does it reduce the lifetime of the complex formed by RNAP on promoters. We show that Rnk competes with the Gre factors and DksA (another RNAP secondary channel effector) for binding to RNAP in vitro, and although we found that the concentration of Rnk in vivo was much lower than that of DksA, it was similar to that of GreB, consistent with a potential regulatory role for Rnk as an anti-Gre factor.
Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein.,Lamour V, Rutherford ST, Kuznedelov K, Ramagopal UA, Gourse RL, Severinov K, Darst SA J Mol Biol. 2008 Nov 7;383(2):367-79. Epub 2008 Aug 12. PMID:18760284[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shankar S, Schlictman D, Chakrabarty AM. Regulation of nucleoside diphosphate kinase and an alternative kinase in Escherichia coli: role of the sspA and rnk genes in nucleoside triphosphate formation. Mol Microbiol. 1995 Sep;17(5):935-43. PMID:8596442
- ↑ Lamour V, Rutherford ST, Kuznedelov K, Ramagopal UA, Gourse RL, Severinov K, Darst SA. Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein. J Mol Biol. 2008 Nov 7;383(2):367-79. Epub 2008 Aug 12. PMID:18760284 doi:10.1016/j.jmb.2008.08.011
- ↑ Lamour V, Rutherford ST, Kuznedelov K, Ramagopal UA, Gourse RL, Severinov K, Darst SA. Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein. J Mol Biol. 2008 Nov 7;383(2):367-79. Epub 2008 Aug 12. PMID:18760284 doi:10.1016/j.jmb.2008.08.011
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