1kkg - Revision history

OCA at 08:41, 22 May 2024

2024-05-22T08:41:51Z

←Older revision		Revision as of 08:41, 22 May 2024
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kkg ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kkg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribosome-binding factor A (RbfA) from Escherichia coli is a cold-shock adaptation protein. It is essential for efficient processing of 16S rRNA and is suspected to interact with the 5'-terminal helix (helix I) of 16S rRNA. RbfA is a member of a large family of small proteins found in most bacterial organisms, making it an important target for structural proteomics. Here, we describe the three-dimensional structure of RbfADelta25, a 108 residue construct with 25 residues removed from the carboxyl terminus of full-length RbfA, determined in solution at pH 5.0 by heteronuclear NMR methods. The structure determination was carried out using largely automated methods for determining resonance assignments, interpreting nuclear Overhauser effect (NOE) spectroscopy (NOESY) spectra, and structure generation. RbfADelta25 has an alpha+beta fold containing three helices and three beta-strands, alpha1-beta1-beta2-alpha2-alpha3-beta3. The structure has type-II KH-domain fold topology, related to conserved KH sequence family proteins whose betaalphaalphabeta subunits are characterized by a helix-turn-helix motif with sequence signature GxxG at the turn. In RbfA, this betaalphaalphabeta subunit is characterized by a helix-kink-helix motif in which the GxxG sequence is replaced by a conserved AxG sequence, including a strongly conserved Ala residue at position 75 forming an interhelical kink. The electrostatic field distribution about RbfADelta25 is bipolar; one side of the molecule is strongly negative and the opposite face has a strong positive electrostatic field. A "dynamic hot spot" of RbfADelta25 has been identified in the vicinity of a beta-bulge at strongly conserved residue Ser39 by 15N R(1), R(2) relaxation rate and heteronuclear 15N-1H NOE measurements. Analyses of these distributions of electrostatic field and internal dynamics, together with evolutionary implications of fold and sequence conservation, suggest that RbfA is indeed a nucleic acid-binding protein, and identify a potential RNA-binding site in or around the conserved polypeptide segment Ser76-Asp100 corresponding to the alpha3-loop-beta3 helix-loop-strand structure. While the structure of RbfADelta25 is most similar to that of the KH domain of the E.coli Era GTPase, its electrostatic field distribution is most similar to the KH1 domain of the NusA protein from Thermotoga maritima, another cold-shock associated RNA-binding protein. Both RbfA and NusA are regulated in the same E.coli operon. Structural and functional similarities between RbfA, NusA, and other bacterial type II KH domains suggest previously unsuspected evolutionary relationships between these cold-shock associated proteins.
		+
		+	Solution NMR structure of ribosome-binding factor A (RbfA), a cold-shock adaptation protein from Escherichia coli.,Huang YJ, Swapna GV, Rajan PK, Ke H, Xia B, Shukla K, Inouye M, Montelione GT J Mol Biol. 2003 Mar 21;327(2):521-36. PMID:12628255<ref>PMID:12628255</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1kkg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:01, 3 April 2024

2024-04-03T08:01:03Z

←Older revision		Revision as of 08:01, 3 April 2024
Line 1:		Line 1:

	==NMR Structure of Ribosome-Binding Factor A (RbfA)==		==NMR Structure of Ribosome-Binding Factor A (RbfA)==
-	<StructureSection load='1kkg' size='340' side='right'caption='[[1kkg~~]], [[NMR_Ensembles_of_Models \| 16 NMR models~~]]' scene=''>	+	<StructureSection load='1kkg' size='340' side='right'caption='[[1kkg]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KKG FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>rbfA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [https://pdbe.org/1kkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [https://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kkg ProSAT], [https://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</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=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [https://pdbe.org/1kkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [https://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kkg ProSAT], [https://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RBFA_ECOLI RBFA_ECOLI]] Essential for efficient processing of 16S rRNA. Probably part of the 30S subunit prior to or during the final step in the processing of 16S free 30S ribosomal subunits. Could be some accessory protein needed for efficient assembly of the 30S subunit. May interact with the 5'-terminal helix region of 16S rRNA. Has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Overexpression suppresses a cold-sensitive C23U 16S rRNA mutation and rimM deletion mutants. Its function probably overlaps Era.<ref>PMID:9422595</ref> <ref>PMID:16825789</ref>	+	[https://www.uniprot.org/uniprot/RBFA_ECOLI RBFA_ECOLI] Essential for efficient processing of 16S rRNA. Probably part of the 30S subunit prior to or during the final step in the processing of 16S free 30S ribosomal subunits. Could be some accessory protein needed for efficient assembly of the 30S subunit. May interact with the 5'-terminal helix region of 16S rRNA. Has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Overexpression suppresses a cold-sensitive C23U 16S rRNA mutation and rimM deletion mutants. Its function probably overlaps Era.<ref>PMID:9422595</ref> <ref>PMID:16825789</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kkg ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kkg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ribosome-binding factor A (RbfA) from Escherichia coli is a cold-shock adaptation protein. It is essential for efficient processing of 16S rRNA and is suspected to interact with the 5'-terminal helix (helix I) of 16S rRNA. RbfA is a member of a large family of small proteins found in most bacterial organisms, making it an important target for structural proteomics. Here, we describe the three-dimensional structure of RbfADelta25, a 108 residue construct with 25 residues removed from the carboxyl terminus of full-length RbfA, determined in solution at pH 5.0 by heteronuclear NMR methods. The structure determination was carried out using largely automated methods for determining resonance assignments, interpreting nuclear Overhauser effect (NOE) spectroscopy (NOESY) spectra, and structure generation. RbfADelta25 has an alpha+beta fold containing three helices and three beta-strands, alpha1-beta1-beta2-alpha2-alpha3-beta3. The structure has type-II KH-domain fold topology, related to conserved KH sequence family proteins whose betaalphaalphabeta subunits are characterized by a helix-turn-helix motif with sequence signature GxxG at the turn. In RbfA, this betaalphaalphabeta subunit is characterized by a helix-kink-helix motif in which the GxxG sequence is replaced by a conserved AxG sequence, including a strongly conserved Ala residue at position 75 forming an interhelical kink. The electrostatic field distribution about RbfADelta25 is bipolar; one side of the molecule is strongly negative and the opposite face has a strong positive electrostatic field. A "dynamic hot spot" of RbfADelta25 has been identified in the vicinity of a beta-bulge at strongly conserved residue Ser39 by 15N R(1), R(2) relaxation rate and heteronuclear 15N-1H NOE measurements. Analyses of these distributions of electrostatic field and internal dynamics, together with evolutionary implications of fold and sequence conservation, suggest that RbfA is indeed a nucleic acid-binding protein, and identify a potential RNA-binding site in or around the conserved polypeptide segment Ser76-Asp100 corresponding to the alpha3-loop-beta3 helix-loop-strand structure. While the structure of RbfADelta25 is most similar to that of the KH domain of the E.coli Era GTPase, its electrostatic field distribution is most similar to the KH1 domain of the NusA protein from Thermotoga maritima, another cold-shock associated RNA-binding protein. Both RbfA and NusA are regulated in the same E.coli operon. Structural and functional similarities between RbfA, NusA, and other bacterial type II KH domains suggest previously unsuspected evolutionary relationships between these cold-shock associated proteins.
-
-	Solution NMR structure of ribosome-binding factor A (RbfA), a cold-shock adaptation protein from Escherichia coli.,Huang YJ, Swapna GV, Rajan PK, Ke H, Xia B, Shukla K, Inouye M, Montelione GT J Mol Biol. 2003 Mar 21;327(2):521-36. PMID:12628255<ref>PMID:12628255</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kkg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Huang~~, Y J~~]]	+	[[Category: Huang YJ]]
-	[[Category: Inouye, M]]	+	[[Category: Inouye M]]
-	[[Category: Ke, H]]	+	[[Category: Ke H]]
-	[[Category: Montelione~~, G T]]~~	+	[[Category: Montelione GT]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Rajan PK]]
-	[[Category: Rajan~~, P K~~]]	+	[[Category: Shukla K]]
-	[[Category: Shukla, K]]	+	[[Category: Swapna GVT]]
-	[[Category: Swapna~~, G V.T~~]]	+	[[Category: Xia B]]
-	[[Category: Xia, B]]	+
-	~~[[Category: Cold-shock adaptation]]~~	+
-	~~[[Category: Nesg project]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Ribosome-binding factor~~]]	+

OCA at 08:09, 23 February 2022

2022-02-23T08:09:27Z

←Older revision		Revision as of 08:09, 23 February 2022
Line 3:		Line 3:
	<StructureSection load='1kkg' size='340' side='right'caption='[[1kkg]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>		<StructureSection load='1kkg' size='340' side='right'caption='[[1kkg]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1KKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KKG FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([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~~://proteopedia.org/fgij/fg.htm?mol=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [~~http~~://pdbe.org/1kkg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kkg ProSAT], [~~http~~://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</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=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [https://pdbe.org/1kkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [https://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kkg ProSAT], [https://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RBFA_ECOLI RBFA_ECOLI]] Essential for efficient processing of 16S rRNA. Probably part of the 30S subunit prior to or during the final step in the processing of 16S free 30S ribosomal subunits. Could be some accessory protein needed for efficient assembly of the 30S subunit. May interact with the 5'-terminal helix region of 16S rRNA. Has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Overexpression suppresses a cold-sensitive C23U 16S rRNA mutation and rimM deletion mutants. Its function probably overlaps Era.<ref>PMID:9422595</ref> <ref>PMID:16825789</ref>	+	[[https://www.uniprot.org/uniprot/RBFA_ECOLI RBFA_ECOLI]] Essential for efficient processing of 16S rRNA. Probably part of the 30S subunit prior to or during the final step in the processing of 16S free 30S ribosomal subunits. Could be some accessory protein needed for efficient assembly of the 30S subunit. May interact with the 5'-terminal helix region of 16S rRNA. Has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Overexpression suppresses a cold-sensitive C23U 16S rRNA mutation and rimM deletion mutants. Its function probably overlaps Era.<ref>PMID:9422595</ref> <ref>PMID:16825789</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:46, 25 November 2020

2020-11-25T07:46:20Z

←Older revision		Revision as of 07:46, 25 November 2020
Line 1:		Line 1:

	==NMR Structure of Ribosome-Binding Factor A (RbfA)==		==NMR Structure of Ribosome-Binding Factor A (RbfA)==
-	<StructureSection load='1kkg' size='340' side='right' caption='[[1kkg]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>	+	<StructureSection load='1kkg' size='340' side='right'caption='[[1kkg]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1KKG FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([http://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=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [http://pdbe.org/1kkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [http://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kkg ProSAT], [http://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [http://pdbe.org/1kkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [http://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kkg ProSAT], [http://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Huang, Y J]]		[[Category: Huang, Y J]]
	[[Category: Inouye, M]]		[[Category: Inouye, M]]

OCA at 21:17, 24 January 2018

2018-01-24T21:17:54Z

←Older revision		Revision as of 21:17, 24 January 2018
Line 1:		Line 1:
		+
	==NMR Structure of Ribosome-Binding Factor A (RbfA)==		==NMR Structure of Ribosome-Binding Factor A (RbfA)==
	<StructureSection load='1kkg' size='340' side='right' caption='[[1kkg]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>		<StructureSection load='1kkg' size='340' side='right' caption='[[1kkg]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KKG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KKG FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([http://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=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [http://pdbe.org/1kkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [http://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [http://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></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=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [http://pdbe.org/1kkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [http://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kkg ProSAT], [http://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kk/1kkg_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kk/1kkg_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 07:33, 10 February 2016

2016-02-10T07:33:48Z

←Older revision		Revision as of 07:33, 10 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kkg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:44, 11 September 2015

2015-09-11T06:44:20Z

←Older revision		Revision as of 06:44, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1kkg' size='340' side='right' caption='[[1kkg]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>		<StructureSection load='1kkg' size='340' side='right' caption='[[1kkg]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KKG FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([http://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=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [http://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [http://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></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=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [http://pdbe.org/1kkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [http://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [http://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1kkg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Huang, Y J]]		[[Category: Huang, Y J]]
	[[Category: Inouye, M]]		[[Category: Inouye, M]]

OCA at 12:45, 25 December 2014

2014-12-25T12:45:20Z

←Older revision		Revision as of 12:45, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KKG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KKG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [http://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [http://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></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=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [http://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [http://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RBFA_ECOLI RBFA_ECOLI]] Essential for efficient processing of 16S rRNA. Probably part of the 30S subunit prior to or during the final step in the processing of 16S free 30S ribosomal subunits. Could be some accessory protein needed for efficient assembly of the 30S subunit. May interact with the 5'-terminal helix region of 16S rRNA. Has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Overexpression suppresses a cold-sensitive C23U 16S rRNA mutation and rimM deletion mutants. Its function probably overlaps Era.<ref>PMID:9422595</ref> <ref>PMID:16825789</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Huang, Y J.]]	+	[[Category: Huang, Y J]]
-	[[Category: Inouye, M.]]	+	[[Category: Inouye, M]]
-	[[Category: Ke, H.]]	+	[[Category: Ke, H]]
-	[[Category: Montelione, G T.]]	+	[[Category: Montelione, G T]]
-	[[Category: ~~NESG, Northeast~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Rajan, P K.]]	+	[[Category: Rajan, P K]]
-	[[Category: Shukla, K.]]	+	[[Category: Shukla, K]]
-	[[Category: Swapna, G V.T.]]	+	[[Category: Swapna, G V.T]]
-	[[Category: Xia, B.]]	+	[[Category: Xia, B]]
	[[Category: Cold-shock adaptation]]		[[Category: Cold-shock adaptation]]
	[[Category: Nesg project]]		[[Category: Nesg project]]
-	[[Category: ~~Northeast structural genomics consortium]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category:~~ Protein structure initiative]]	+
-	~~[[Category: Psi~~]]	+
	[[Category: Ribosome-binding factor]]		[[Category: Ribosome-binding factor]]
-	[[Category: Structural genomic]]

OCA at 10:54, 28 September 2014

2014-09-28T10:54:02Z

←Older revision		Revision as of 10:54, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1kkg.~~png\|left~~\|200px]]	+	==NMR Structure of Ribosome-Binding Factor A (RbfA)==
		+	<StructureSection load='1kkg' size='340' side='right' caption='[[1kkg]], [[NMR_Ensembles_of_Models \| 16 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kkg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KKG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rbfA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kkg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kkg RCSB], [http://www.ebi.ac.uk/pdbsum/1kkg PDBsum], [http://www.topsan.org/Proteins/NESGC/1kkg TOPSAN]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kk/1kkg_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribosome-binding factor A (RbfA) from Escherichia coli is a cold-shock adaptation protein. It is essential for efficient processing of 16S rRNA and is suspected to interact with the 5'-terminal helix (helix I) of 16S rRNA. RbfA is a member of a large family of small proteins found in most bacterial organisms, making it an important target for structural proteomics. Here, we describe the three-dimensional structure of RbfADelta25, a 108 residue construct with 25 residues removed from the carboxyl terminus of full-length RbfA, determined in solution at pH 5.0 by heteronuclear NMR methods. The structure determination was carried out using largely automated methods for determining resonance assignments, interpreting nuclear Overhauser effect (NOE) spectroscopy (NOESY) spectra, and structure generation. RbfADelta25 has an alpha+beta fold containing three helices and three beta-strands, alpha1-beta1-beta2-alpha2-alpha3-beta3. The structure has type-II KH-domain fold topology, related to conserved KH sequence family proteins whose betaalphaalphabeta subunits are characterized by a helix-turn-helix motif with sequence signature GxxG at the turn. In RbfA, this betaalphaalphabeta subunit is characterized by a helix-kink-helix motif in which the GxxG sequence is replaced by a conserved AxG sequence, including a strongly conserved Ala residue at position 75 forming an interhelical kink. The electrostatic field distribution about RbfADelta25 is bipolar; one side of the molecule is strongly negative and the opposite face has a strong positive electrostatic field. A "dynamic hot spot" of RbfADelta25 has been identified in the vicinity of a beta-bulge at strongly conserved residue Ser39 by 15N R(1), R(2) relaxation rate and heteronuclear 15N-1H NOE measurements. Analyses of these distributions of electrostatic field and internal dynamics, together with evolutionary implications of fold and sequence conservation, suggest that RbfA is indeed a nucleic acid-binding protein, and identify a potential RNA-binding site in or around the conserved polypeptide segment Ser76-Asp100 corresponding to the alpha3-loop-beta3 helix-loop-strand structure. While the structure of RbfADelta25 is most similar to that of the KH domain of the E.coli Era GTPase, its electrostatic field distribution is most similar to the KH1 domain of the NusA protein from Thermotoga maritima, another cold-shock associated RNA-binding protein. Both RbfA and NusA are regulated in the same E.coli operon. Structural and functional similarities between RbfA, NusA, and other bacterial type II KH domains suggest previously unsuspected evolutionary relationships between these cold-shock associated proteins.

-	~~{{STRUCTURE_1kkg\| PDB=1kkg \| SCENE= }}~~	+	Solution NMR structure of ribosome-binding factor A (RbfA), a cold-shock adaptation protein from Escherichia coli.,Huang YJ, Swapna GV, Rajan PK, Ke H, Xia B, Shukla K, Inouye M, Montelione GT J Mol Biol. 2003 Mar 21;327(2):521-36. PMID:12628255<ref>PMID:12628255</ref>

-	~~===NMR Structure~~ of ~~Ribosome-Binding Factor A (RbfA)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12628255}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1kkg]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1KKG OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012628255<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Huang, Y J.]]		[[Category: Huang, Y J.]]

OCA: Protected "1kkg" [edit=sysop:move=sysop]

2012-12-05T20:41:24Z

Protected "1kkg" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:41, 5 December 2012