HypR - Revision history

134.76.70.252 at 11:26, 17 April 2014

2014-04-17T11:26:25Z

134.76.38.147 at 15:17, 2 April 2014

2014-04-02T15:17:24Z

134.76.70.252 at 15:02, 16 May 2013

2013-05-16T15:02:24Z

134.76.70.252 at 11:45, 14 May 2013

2013-05-14T11:45:04Z

134.76.70.252 at 14:19, 13 May 2013

2013-05-13T14:19:57Z

134.76.70.252 at 17:51, 7 August 2012

2012-08-07T17:51:05Z

Jstuelk: /* Database entries */

2012-05-04T17:52:08Z

‎Database entries

134.76.70.252 at 13:06, 23 April 2012

2012-04-23T13:06:39Z

134.76.70.252 at 10:30, 17 April 2012

2012-04-17T10:30:54Z

Jstuelk at 09:04, 17 January 2012

2012-01-17T09:04:00Z

← Older revision		Revision as of 11:26, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' [[MarR/DUF24 family]] transcription regulator, positively controls the nitroreductase gene ''[[hypO]]'' in response to disulfide stress <br/><br/>~~	+	{{#bank: HypR}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\| ''hypR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yybR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[MarR/DUF24 family]] transcription regulator HypR~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of the nitroreductase gene ''[[hypO]]'' in response to disulfide stress (diamide, NaOCl)~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40540 hypR]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 14 kDa, 8.415~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 375 bp, 125 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[cotF]]'', ''[[ppaC]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40540 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40540 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40540 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yybR_context.gif]]~~
−	~~<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>~~
−	\|-
−	\|colspan="2" \|'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yybR_4167622_4167999_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:hypR_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40540]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−
−
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[resistance against oxidative and electrophile stress]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[HypR regulon]]}}~~
−
−	~~= The [[HypR regulon]]:=~~
−	* ''[[hypR]]'', ''[[hypO]]''
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU40540
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40540&redirect=T BSU40540]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]
−
−	~~=== Additional information===~~
−	* ''hypR'' is autoregulated by disulfide stress
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' [[MarR/DUF24 family]]
−
−	* '''Paralogous protein(s):''' [[YdeP]],[[YkvN]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed\|22238377}}
−
−	* '''Domains:'''
−	** 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed\|22238377}}
−
−	* '''Modification:'''
−	** oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed\|22238377}}
−	** Cys14 and Cys49' are about 8-9 Angström apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed\|22238377}}
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** cytoplasmic
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40540&redirect=T BSU40540]
−
−	* '''Structure:'''
−	** [http://www.pdb.org/pdb/explore.do?structureId=4A5N 4A5N] (reduced HypRC14S dimer) {{PubMed\|22238377}}
−	** [http://www.pdb.org/pdb/explore.do?structureId=4A5M 4A5M] (oxidized HypR C14-C49' intersubunit disulfide-linked dimer ) {{PubMed\|22238377}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''hypR'' {{PubMed\|22238377}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yybR_4167622_4167999_-1 hypR] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−	** activated by disulfide stress conditions (diamide, NaOCl) ''in vivo'' and ''in vitro '' (autoregulation) {{PubMed\|22238377}}
−
−	* '''Regulatory mechanism:'''
−	** [[HypR]]: transcription activation (autoregulation){{PubMed\|22238377}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	* [[Haike Antelmann]],University of Greifswald, Germany
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~==Reviews==~~
−
−	~~Antelmann H, Helmann JD.~~
−	~~Thiol-based redox switches and gene regulation.~~
−	~~Antioxid Redox Signal. 2011,14:1049-63.~~
−	~~{{PubMed\|20626317}}~~
−
−	~~==Original articles==~~
−
−	~~Palm GJ, Khanh Chi B, Waack P, Gronau K, Becher D, Albrecht D, Hinrichs W, Read RJ, Antelmann H.~~
−	~~Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR.~~
−	~~Nucleic Acids Res. 2012, Jan 11. [Epub ahead of print]~~
−	~~{{PubMed\|22238377}}~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 60: / Line 60: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]
@@ Line 100: / Line 101: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 27: / Line 27: @@
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
-|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yybR_4167622_4167999_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:hypR_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yybR_4167622_4167999_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:hypR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40540]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40540 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40540 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40540 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40540 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40540 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40540 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || control of the nitroreductase gene ''[[hypO]]'' in response to disulfide stress (diamide, NaOCl)
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40540 hypR]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40540 hypR]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40540 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40540 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40540 Advanced_DNA]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]

@@ Line 100: / Line 100: @@
 * '''Structure:'''
-** reduced HypRC14S dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5N] {{PubMed|22238377}}
+** [http://www.pdb.org/pdb/explore.do?structureId=4A5N 4A5N] (reduced HypRC14S dimer) {{PubMed|22238377}}
-** oxidized HypR C14-C49' intersubunit disulfide-linked dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5M] {{PubMed|22238377}}
+** [http://www.pdb.org/pdb/explore.do?structureId=4A5M 4A5M] (oxidized HypR C14-C49' intersubunit disulfide-linked dimer ) {{PubMed|22238377}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]

@@ Line 107: / Line 107: @@
 * '''Operon:''' ''hypR'' {{PubMed|22238377}}
-* '''[[Sigma factor]]:'''
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yybR_4167622_4167999_-1 hypR] {{PubMed|22383849}}
 * '''Regulation:'''
@@ Line 115: / Line 117: @@
 ** [[HypR]]: transcription activation (autoregulation){{PubMed|22238377}}
 * '''Additional information:'''
 =Biological materials =

@@ Line 1: / Line 1: @@
-* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[hypO]]'' in response to disulfide stress <br/><br/>
+* '''Description:''' [[MarR/DUF24 family]] transcription regulator, positively controls the nitroreductase gene ''[[hypO]]'' in response to disulfide stress <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR
+|style="background:#ABCDEF;" align="center"| '''Product''' || [[MarR/DUF24 family]] transcription regulator HypR
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || control of the nitroreductase gene ''[[hypO]]'' in response to disulfide stress (diamide, NaOCl)
@@ Line 56: / Line 56: @@
 === Additional information===
-''hypR'' is autoregulated by disulfide stress
+* ''hypR'' is autoregulated by disulfide stress
@@ Line 65: / Line 65: @@
 * '''Catalyzed reaction/ biological activity:'''
-* '''Protein family:''' MarR/DUF24-family regulator
+* '''Protein family:''' [[MarR/DUF24 family]]
 * '''Paralogous protein(s):''' [[YdeP]],[[YkvN]]