Difference between revisions of "Sandbox"

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−
* '''Description:''' unknown <br/><br/>
+
* '''Description:''' IMP dehydrogenase <br/><br/>
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''yaaC''
+
|''guaB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''guaA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || IMP dehydrogenase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of GMP
 
|-
 
|-
−
|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=BSU00080 YaaC]
+
|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=BSU00090 GuaB]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 7.788 
+
|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/purine_biosynthesis.html Purine synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 945 bp, 315 aa
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 6.168 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rrnO-5S]]'', ''[[guaB]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1464 bp, 488 aa
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00080 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00080 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00080 DNA_with_flanks]
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaC]]'', ''[[dacA]]''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaC_context.gif]]
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00090 DNA_with_flanks]
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:guaB_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <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=yaaC_14847_15794_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00080]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:guaB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00090]]
 
|-
 
|-
 
|}
 
|}
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<br/><br/><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 =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[sporulation proteins]]}}
+
{{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}},
 +
{{SubtiWiki category|[[essential genes]]}},
 +
{{SubtiWiki category|[[phosphoproteins]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
 
+
{{SubtiWiki regulon|[[CodY regulon]]}}
  
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
−
* '''Locus tag:''' BSU00080
+
 
 +
* '''Locus tag:''' BSU00090
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/guaB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10072]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10073]
  
 
=== Additional information===
 
=== Additional information===
−
 
−
 
  
  
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Inosine 5'-phosphate + NAD<sup>+</sup> + H<sub>2</sub>O = xanthosine 5'-phosphate + NADH (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' IMPDH/GMPR family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:'''  
 +
** phosphorylated (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
 +
** Cys308 is S-cysteinylated after diamide stress [http://www.ncbi.nlm.nih.gov/pubmed/17611193 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
 +
** Cys308 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species [http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
 +
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|22981860,6111556}}
  
 
* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
Line 88: Line 97:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1VRD 1VRD] (from ''Thermotoga maritima msb8'', 60% identity, 80% similarity)
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37526 P37526]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P21879 P21879]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00080]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00090]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.205 1.1.1.205]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''yaaC'' (chromosomal arrangement)
+
* '''Operon:''' ''guaB'' {{PubMed|22383849}}
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaC_14847_15794_-1 yaaC] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 guaB] {{PubMed|22383849}}
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** activated during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[CodY]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
  
−
* '''Additional information:'''
+
* '''Additional information:'''
 +
** the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
 +
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}
  
 
=Biological materials =
 
=Biological materials =
Line 117: Line 130:
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
 +
** purification from ''B. subtilis'' with an N-terminal Strep-tag, for [[SPINE]], (in [[pGP380]]): pGP901, available in [[Stülke]] lab
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
Line 131: Line 145:
  
 
=References=
 
=References=
 +
 +
<pubmed>22938038,17611193,12884008,1722815, 22981860,12618455,17726680 17726680 6111556 </pubmed>
 +
 +
[http://www.ncbi.nlm.nih.gov/pubmed/PMID PubMed]
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:54, 11 November 2013

  • Description: IMP dehydrogenase

Gene name guaB
Synonyms guaA
Essential yes PubMed
Product IMP dehydrogenase
Function biosynthesis of GMP
Gene expression levels in SubtiExpress: GuaB
Metabolic function and regulation of this protein in SubtiPathways:
Purine synthesis, Nucleotides (regulation)
MW, pI 52 kDa, 6.168
Gene length, protein length 1464 bp, 488 aa
Immediate neighbours yaaC, dacA
Sequences Protein DNA DNA_with_flanks
Genetic context
GuaB context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
GuaB expression.png



















Categories containing this gene/protein

biosynthesis/ acquisition of nucleotides, essential genes, phosphoproteins

This gene is a member of the following regulons

CodY regulon

The gene

Basic information

  • Locus tag: BSU00090

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Inosine 5'-phosphate + NAD+ + H2O = xanthosine 5'-phosphate + NADH (according to Swiss-Prot)
  • Protein family: IMPDH/GMPR family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
    • phosphorylated (STY) PubMed
    • Cys308 is S-cysteinylated after diamide stress PubMed, PubMed
    • Cys308 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species PubMed
  • Cofactor(s):
  • Effectors of protein activity:
    • inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´PubMed

Database entries

  • Structure: 1VRD (from Thermotoga maritima msb8, 60% identity, 80% similarity)
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation:
    • activated during growth in the presence of branched chain amino acids (CodY) PubMed
  • Regulatory mechanism:
  • Additional information:
    • the mRNA is very stable (half-life > 15 min) PubMed
    • inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´PubMed

Biological materials

  • Mutant:
  • Expression vector:
    • purification from B. subtilis with an N-terminal Strep-tag, for SPINE, (in pGP380): pGP901, available in Stülke lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Allison Kriel, Alycia N Bittner, Sok Ho Kim, Kuanqing Liu, Ashley K Tehranchi, Winnie Y Zou, Samantha Rendon, Rui Chen, Benjamin P Tu, Jue D Wang
Direct regulation of GTP homeostasis by (p)ppGpp: a critical component of viability and stress resistance.
Mol Cell: 2012, 48(2);231-41
[PubMed:22981860] [WorldCat.org] [DOI] (I p)

Bui Khanh Chi, Alexandra A Roberts, Tran Thi Thanh Huyen, Katrin Bäsell, Dörte Becher, Dirk Albrecht, Chris J Hamilton, Haike Antelmann
S-bacillithiolation protects conserved and essential proteins against hypochlorite stress in firmicutes bacteria.
Antioxid Redox Signal: 2013, 18(11);1273-95
[PubMed:22938038] [WorldCat.org] [DOI] (I p)

Christine Eymann, Dörte Becher, Jörg Bernhardt, Katrin Gronau, Anja Klutzny, Michael Hecker
Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis.
Proteomics: 2007, 7(19);3509-26
[PubMed:17726680] [WorldCat.org] [DOI] (P p)

Falko Hochgräfe, Jörg Mostertz, Dierk-Christoph Pöther, Dörte Becher, John D Helmann, Michael Hecker
S-cysteinylation is a general mechanism for thiol protection of Bacillus subtilis proteins after oxidative stress.
J Biol Chem: 2007, 282(36);25981-5
[PubMed:17611193] [WorldCat.org] [DOI] (P p)

G Hambraeus, C von Wachenfeldt, L Hederstedt
Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs.
Mol Genet Genomics: 2003, 269(5);706-14
[PubMed:12884008] [WorldCat.org] [DOI] (P p)

Virginie Molle, Yoshiko Nakaura, Robert P Shivers, Hirotake Yamaguchi, Richard Losick, Yasutaro Fujita, Abraham L Sonenshein
Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis.
J Bacteriol: 2003, 185(6);1911-22
[PubMed:12618455] [WorldCat.org] [DOI] (P p)

H H Saxild, P Nygaard
Regulation of levels of purine biosynthetic enzymes in Bacillus subtilis: effects of changing purine nucleotide pools.
J Gen Microbiol: 1991, 137(10);2387-94
[PubMed:1722815] [WorldCat.org] [DOI] (P p)

J M Lopez, A Dromerick, E Freese
Response of guanosine 5'-triphosphate concentration to nutritional changes and its significance for Bacillus subtilis sporulation.
J Bacteriol: 1981, 146(2);605-13
[PubMed:6111556] [WorldCat.org] [DOI] (P p)


PubMed

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