Difference between revisions of "Sandbox"

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−
* '''Description:''' alkyl hydroperoxide reductase (small subunit) <br/><br/>
+
* '''Description:''' alkyl hydroperoxide reductase (large subunit) / NADH 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'''
−
|''ahpC''
+
|''ahpF''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''perR ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ndh ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || alkyl hydroperoxide reductase (small subunit)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || alkyl hydroperoxide reductase (large subunit) / <br/>NADH dehydrogenase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance against peroxide stres  
 
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance against peroxide stres  
 
|-
 
|-
−
|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/stress_response.html Stress]'''
+
|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/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 4.283  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 4.705  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 561 bp, 187 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1527 bp, 509 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gntZ]]'', ''[[ahpF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ahpC]]'', ''[[bglA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16046&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16047&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ahpC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ahpF_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>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU40090
+
* '''Locus tag:''' BSU40100
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 45: Line 45:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ahpCF.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ahpCF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11385]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11204]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 2 R'-SH + ROOH = R'-S-S-R' + H<sub>2</sub>O + ROH (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' NADH + acceptor = NAD<sup>+</sup> + reduced acceptor (according to Swiss-Prot)  
  
−
* '''Protein family:''' ahpC/TSA family (according to Swiss-Prot)
+
* '''Protein family:''' class-II pyridine nucleotide-disulfide oxidoreductase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]  
+
* '''Modification:''' phosphorylation on (Ser-48 OR Ser-49) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 74: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 80:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80239 P80239]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42974 P42974]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40090]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40100]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 122: Line 122:
 
=References=
 
=References=
  
−
<pubmed>11532148,,8932314,8932315,11532148,16493705, </pubmed>
+
<pubmed>11532148,,16232966,8932314,8932315,11532148,17218307, </pubmed>

Revision as of 14:12, 22 June 2009

  • Description: alkyl hydroperoxide reductase (large subunit) / NADH dehydrogenase

Gene name ahpF
Synonyms ndh
Essential no
Product alkyl hydroperoxide reductase (large subunit) /
NADH dehydrogenase
Function resistance against peroxide stres
Metabolic function and regulation of this protein in SubtiPathways:
Stress, Stress
MW, pI 54 kDa, 4.705
Gene length, protein length 1527 bp, 509 aa
Immediate neighbours ahpC, bglA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AhpF context.gif
This image was kindly provided by SubtiList







The gene

Basic information

  • Locus tag: BSU40100

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: NADH + acceptor = NAD+ + reduced acceptor (according to Swiss-Prot)
  • Protein family: class-II pyridine nucleotide-disulfide oxidoreductase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on (Ser-48 OR Ser-49) PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: induced by H2O2 (PerR) PubMed
    • repressed in the absence of hydrogen peroxide (PerR) PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P p)

A Sakai, K Katayama, T Katsuragi, Y Tani
Glycolaldehyde-forming route in Bacillus subtilis in relation to vitamin B6 biosynthesis.
J Biosci Bioeng: 2001, 91(2);147-52
[PubMed:16232966] [WorldCat.org] [DOI] (P p)

A F Herbig, J D Helmann
Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA.
Mol Microbiol: 2001, 41(4);849-59
[PubMed:11532148] [WorldCat.org] [DOI] (P p)

N Bsat, L Chen, J D Helmann
Mutation of the Bacillus subtilis alkyl hydroperoxide reductase (ahpCF) operon reveals compensatory interactions among hydrogen peroxide stress genes.
J Bacteriol: 1996, 178(22);6579-86
[PubMed:8932315] [WorldCat.org] [DOI] (P p)

H Antelmann, S Engelmann, R Schmid, M Hecker
General and oxidative stress responses in Bacillus subtilis: cloning, expression, and mutation of the alkyl hydroperoxide reductase operon.
J Bacteriol: 1996, 178(22);6571-8
[PubMed:8932314] [WorldCat.org] [DOI] (P p)

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