Pyk - Revision history

Jstuelk at 17:13, 16 May 2014

2014-05-16T17:13:43Z

134.76.70.252 at 09:48, 17 April 2014

2014-04-17T09:48:21Z

134.76.38.147 at 14:29, 2 April 2014

2014-04-02T14:29:56Z

Jstuelk at 14:43, 5 March 2014

2014-03-05T14:43:36Z

Jstuelk at 16:32, 28 February 2014

2014-02-28T16:32:41Z

134.76.70.252 at 11:26, 7 January 2014

2014-01-07T11:26:36Z

Jstuelk: /* References */

2013-11-28T11:22:23Z

‎References

Jstuelk at 16:02, 13 July 2013

2013-07-13T16:02:14Z

134.76.70.252 at 14:16, 16 May 2013

2013-05-16T14:16:04Z

134.76.70.252 at 10:59, 14 May 2013

2013-05-14T10:59:25Z

← Older revision		Revision as of 17:13, 16 May 2014
Line 1:		Line 1:
−	* '''Description:~~''' pyruvate kinase, glycolytic enzyme <br/><br/>~~	+	{{#bank: Pyk}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pyk''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''pykA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| pyruvate kinase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| catabolic enzyme in glycolysis~~
−	\|-
−	\|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=BSU29180 pyk]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=pyk pyk]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 61,9 kDa, 4.88~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1755 bp, 585 amino acids~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ytzA]]'', ''[[pfkA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29180 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29180 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29180 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:pyk_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=pyk_2984788_2986545_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:pyk_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29180]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[ATP synthesis]]}},~~
−	~~{{SubtiWiki category\|[[carbon core metabolism]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU29180
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~Unable to grow with non-[[PTS]] carbohydrates (such as glucitol or glycerol) as single carbon source.~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29180&redirect=T BSU29180]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12661]
−
−	~~=== Additional information===~~
−	* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed\|21821766}}
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' ADP + phosphoenolpyruvate --> ATP + pyruvate
−	** The reaction is irreversible under physiological conditions
−
−	* '''Protein family:''' PEP-utilizing enzyme family (according to Swiss-Prot) pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−	** allosteric Regulation [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
−	** specific activity: 0.231 µmol min<sup>-1</sup> (mg protein)<sup>-1</sup> {{PubMed\|24571712}}
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' phosphorylation on Ser36 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], phosphorylation on Ser536 or Ser546 [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], please note that the Ser is not on position 536 but rather at 538
−
−	* '''[[Cofactors]]:''' Mg2+, K+
−
−	* '''Effectors of protein activity:'''
−	** Activated by PEP (Hill Coefficient 1,8) [http://www.ncbi.nlm.nih.gov/sites/entrez/4623707 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
−	** Allosterically activated by AMP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
−	** Activation by r5p and ADP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
−	** Inhibition by ADP and f16bp in high concentrations; and ATP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29180&redirect=T BSU29180]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2E28 2E28] (Geobacillus stearothermophilus)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P80885 P80885]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29180]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.40 2.7.1.40]
−
−	~~=== Additional information===~~
−	~~The enzyme is a tetramer with four active sites [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[pfkA]]-[[pyk]]-[[ytzA]]'' {{PubMed\|11489127}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pyk_2984788_2986545_-1 pyk] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** twofold induced by glucose {{PubMed\|11489127}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2986 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 11657 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	* GP589 (''pyk''::''cat''), available in [[Jörg Stülke]]'s lab, {{PubMed\|23420519}}
−	* GP600 (''pyk''::''erm''), available in [[Jörg Stülke]]'s lab, {{PubMed\|23420519}}
−
−	* '''Expression vector:'''
−	** expression in ''E. coli'', N-terminal His-tag: pGP1100 (in [[pWH844]]), available in [[Jörg Stülke]]'s lab
−	** expression in ''B. subtilis'', native protein: pGP1411 (in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
−	** expression in ''B. subtilis'', N-terminal Strep-tag: pGP1409 (in [[pGP380]]), available in [[Jörg Stülke]]'s lab
−	** expression in ''B. subtilis'', C-terminal Strep-tag: pGP1410 (in [[pGP382]]), available in [[Jörg Stülke]]'s lab
−
−	* '''lacZ fusion:''' see ''[[pfkA]]''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Stülke\|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>17726680 16493705 11489127 17505547 10966427 17218307 3711058 4623707 21821766 22846916 23420519 24158146 24571712 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 130: / Line 130: @@
 * '''Additional information:'''
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]
@@ Line 101: / Line 102: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2E28 2E28] (Geobacillus stearothermophilus)

@@ Line 42: / Line 42: @@
 {{SubtiWiki category|[[ATP synthesis]]}},
 {{SubtiWiki category|[[carbon core metabolism]]}},
-{{SubtiWiki category|[[phosphoproteins]]}}
+{{SubtiWiki category|[[phosphoproteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 126: / Line 127: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 155: / Line 157: @@
 =References=
-<pubmed>17726680 16493705 11489127 17505547 10966427 17218307 3711058 4623707 21821766 22846916 23420519 24158146 24571712</pubmed>
+<pubmed>17726680 16493705 11489127 17505547 10966427 17218307 3711058 4623707 21821766 22846916 23420519 24158146 24571712 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 79: / Line 79: @@
 === Extended information on the protein ===
-* '''Kinetic information:''' Allosteric Regulation [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
+* '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:''' phosphorylation on Ser36 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], phosphorylation on Ser536 or Ser546 [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], please note that the Ser is not on position 536 but rather at 538
-* '''Cofactor(s):''' Mg2+, K+
+* '''[[Cofactors]]:''' Mg2+, K+
 * '''Effectors of protein activity:'''
@@ Line 153: / Line 155: @@
 =References=
-<pubmed>17726680 16493705 11489127 17505547 10966427 17218307 3711058 4623707 21821766 22846916 23420519 24158146 </pubmed>
+<pubmed>17726680 16493705 11489127 17505547 10966427 17218307 3711058 4623707 21821766 22846916 23420519 24158146 24571712</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 16: / Line 16: @@
 |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=BSU29180 pyk]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=pyk pyk]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61,9 kDa, 4.88

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 120: / Line 116: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pyk_2984788_2986545_-1 pyk] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 132: / Line 128: @@
 *  '''Mutant:'''
-* GP589 (''pyk''::''cat''), available in [[Stülke]] lab
+* GP589 (''pyk''::''cat''), available in [[Jörg Stülke]]'s lab, {{PubMed|23420519}}
-* GP600 (''pyk''::''erm''), available in [[Stülke]] lab
+* GP600 (''pyk''::''erm''), available in [[Jörg Stülke]]'s lab, {{PubMed|23420519}}
 * '''Expression vector:'''
-** expression in ''E. coli'', N-terminal His-tag: pGP1100 (in [[pWH844]]), available in [[Stülke]] lab
+** expression in ''E. coli'', N-terminal His-tag: pGP1100 (in [[pWH844]]), available in [[Jörg Stülke]]'s lab
-** expression in ''B. subtilis'', native protein: pGP1411 (in [[pBQ200]]), available in [[Stülke]] lab
+** expression in ''B. subtilis'', native protein: pGP1411 (in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
-** expression in ''B. subtilis'', N-terminal Strep-tag: pGP1409 (in [[pGP380]]), available in [[Stülke]] lab
+** expression in ''B. subtilis'', N-terminal Strep-tag: pGP1409 (in [[pGP380]]), available in [[Jörg Stülke]]'s lab
-** expression in ''B. subtilis'', C-terminal Strep-tag: pGP1410 (in [[pGP382]]), available in [[Stülke]] lab
+** expression in ''B. subtilis'', C-terminal Strep-tag: pGP1410 (in [[pGP382]]), available in [[Jörg Stülke]]'s lab
 * '''lacZ fusion:''' see ''[[pfkA]]''
@@ Line 145: / Line 141: @@
 * '''GFP fusion:'''
-* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
 * '''Antibody:'''
@@ Line 157: / Line 153: @@
 =References=
-<pubmed>17726680 16493705 11489127 17505547 10966427 17218307 3711058 4623707 21821766 22846916 </pubmed>
+<pubmed>17726680 16493705 11489127 17505547 10966427 17218307 3711058 4623707 21821766 22846916 23420519</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 29: / Line 29: @@
   <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=pyk_2984788_2986545_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pyk_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pyk_2984788_2986545_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pyk_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29180]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytzA]]'', ''[[pfkA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29180 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29180 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29180 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29180 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29180 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29180 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:pyk_context.gif]]