SucD - Revision history

134.76.70.252 at 14:15, 17 April 2014

2014-04-17T14:15:21Z

134.76.70.252 at 09:46, 17 April 2014

2014-04-17T09:46:28Z

134.76.38.147 at 13:42, 2 April 2014

2014-04-02T13:42:59Z

Jstuelk at 16:15, 5 March 2014

2014-03-05T16:15:55Z

134.76.70.252 at 10:46, 7 January 2014

2014-01-07T10:46:47Z

134.76.70.252 at 16:16, 11 November 2013

2013-11-11T16:16:43Z

Jstuelk: /* Biological materials */

2013-08-13T14:18:07Z

‎Biological materials

Aklewing: /* Biological materials */

2013-08-13T12:05:21Z

‎Biological materials

134.76.70.252 at 13:20, 16 May 2013

2013-05-16T13:20:59Z

134.76.70.252 at 10:13, 14 May 2013

2013-05-14T10:13:21Z

← Older revision		Revision as of 14:15, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' succinyl-CoA synthetase (alpha subunit) <br/><br/>~~	+	{{#bank: SucD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''sucD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| succinyl-CoA synthetase (alpha subunit)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| TCA cycle~~
−	\|-
−	\|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=BSU16100 sucD]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SucD SucD]
−	\|-
−	\|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=sucD sucD]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 31 kDa, 5.587~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 900 bp, 300 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[sucC]], [[dprA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16100 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:sucD_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=sucD_1681617_1682519_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:sucD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16100]]
−	\|-
−	\|}
−
−	~~__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]] =~~
−	~~{{SubtiWiki regulon\|[[CcpA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU16100
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16100&redirect=T BSU16100]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12681]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)
−
−	* '''Protein family:''' succinate/malate CoA ligase alpha subunit family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' phosphorylation on (Ser-19 OR Thr-20) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−	** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
−	** GTP is not accepted by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[SucC]]-[[SucD]] {{PubMed\|20933603}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16100&redirect=T BSU16100]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P80865 P80865]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16100]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]
−
−	~~=== Additional information===~~
−	* extensive information on the structure and enzymatic properties of succinyl-CoA synthetase can be found at [http://www.proteopedia.org/wiki/index.php/Succinyl-Coa_Synthetase Proteopedia]
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[sucC]]''-''[[sucD]]'' {{PubMed\|11976317}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucD_1681617_1682519_1 sucD] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) {{PubMed\|12850135}}
−
−	* '''Regulatory mechanism:''' [[CcpA]]: transcription repression {{PubMed\|12850135}}
−
−	* '''Additional information:'''
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 7489 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 26678 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP720 (spc), available in [[Jörg Stülke]]'s lab
−	** 1A1008 ( ''sucD''::''spec''), {{PubMed\| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1008&Search=1A1008 BGSC]
−	** GP791 (''[[sucC]]-[[sucD]]''::''tet''), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:''' GP1435 (spc, based on [[pGP1870]]), available in [[Jörg Stülke]]'s lab
−
−	* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	* '''FLAG-tag construct:''' GP1425 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>12850135 17218307 11976317 20933603 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 124: / Line 124: @@
 * '''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/sucCD.html]
@@ Line 96: / Line 97: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

@@ Line 39: / Line 39: @@
 <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]]}}
+{{SubtiWiki category|[[phosphoproteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 68: / Line 65: @@
 === Additional information===
 =The protein=
@@ Line 86: / Line 80: @@
 * '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:''' phosphorylation on (Ser-19 OR Thr-20) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 120: / Line 114: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucD_1681617_1682519_1 sucD] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) {{PubMed|12850135}}
@@ Line 127: / Line 121: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 153: / Line 148: @@
 =References=
-<pubmed>12850135 17218307 11976317 20933603</pubmed>
+<pubmed>12850135 17218307 11976317 20933603 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 18: / Line 18: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SucD SucD]
 |-
-|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=sucD sucD]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.587

@@ 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=BSU16100 sucD]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SucD SucD]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SucD SucD]
 |-
 |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]'''

@@ Line 130: / Line 130: @@
 =Biological materials =
-* '''Mutant:''' GP720 (spc), available in [[Stülke]] lab
+* '''Mutant:'''
 ** 1A1008 ( ''sucD''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1008&Search=1A1008 BGSC]
-** GP791 (''sucCD''::''tet''), available in [[Jörg Stülke]]'s lab
+** GP791 (''[[sucC]]-[[sucD]]''::''tet''), available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''
@@ Line 138: / Line 139: @@
 * '''lacZ fusion:'''
-* '''GFP fusion:''' GP1435 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab
+* '''GFP fusion:''' GP1435 (spc, based on [[pGP1870]]), available in [[Jörg Stülke]]'s lab
-* '''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:'''
-* '''FLAG-tag construct:''' GP1425 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
+* '''FLAG-tag construct:''' GP1425 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
 =Labs working on this gene/protein=

@@ Line 31: / Line 31: @@
   <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=sucD_1681617_1682519_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sucD_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucD_1681617_1682519_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sucD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16100]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sucC]], [[dprA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16100 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16100 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:sucD_context.gif]]