Difference between revisions of "YoaD"

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|style="background:#ABCDEF;" align="center"|'''Function''' || methionine biosynthesis
 
|style="background:#ABCDEF;" align="center"|'''Function''' || methionine biosynthesis
 
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU18560 yoaD]
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|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=BSU18560 yoaD]
 
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|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/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation]'''
 
|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/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation]'''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yoaC]]'', ''[[yoaE]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yoaC]]'', ''[[yoaE]]''
 
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13749&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU18560 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU18560 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU18560 Advanced_DNA]
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:yoaD_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:yoaD_context.gif]]

Revision as of 12:58, 13 May 2013

  • Description: similar to phosphoglycerate dehydrogenase

Gene name yoaD
Synonyms
Essential no
Product unknown
Function methionine biosynthesis
Gene expression levels in SubtiExpress: yoaD
Metabolic function and regulation of this protein in SubtiPathways:
Cys, Met & Sulfate assimilation
MW, pI 38 kDa, 5.62
Gene length, protein length 1032 bp, 344 aa
Immediate neighbours yoaC, yoaE
Sequences Protein DNA Advanced_DNA
Genetic context
YoaD context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YoaD expression.png















Categories containing this gene/protein

biosynthesis/ acquisition of amino acids

This gene is a member of the following regulons

S-box

The gene

Basic information

  • Locus tag: BSU18560

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: YoaD is likely to convert 3-phosphoglycerate to serine for use in methionine biosynthesis (based on S-box regulation)
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

The gene is annotated in KEGG as an ortholog of D-3-phosphoglycerate dehydrogenase EC 1.1.1.95. No EC annotation is available in Swiss-Prot. In MetaCyc the protein is marked as “similar to phosphorglycerate dehydrogenase”. No literature/experimental evidence supporting the annotation is available. PubMed

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
    • S-box: transcription termination/ antitermination, the S-box riboswitch binds S-adenosylmethionine resulting in termination 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

Ana Gutiérrez-Preciado, Tina M Henkin, Frank J Grundy, Charles Yanofsky, Enrique Merino
Biochemical features and functional implications of the RNA-based T-box regulatory mechanism.
Microbiol Mol Biol Rev: 2009, 73(1);36-61
[PubMed:19258532] [WorldCat.org] [DOI] (I p)

Jerneja Tomsic, Brooke A McDaniel, Frank J Grundy, Tina M Henkin
Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro.
J Bacteriol: 2008, 190(3);823-33
[PubMed:18039762] [WorldCat.org] [DOI] (I p)

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

F J Grundy, T M Henkin
The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria.
Mol Microbiol: 1998, 30(4);737-49
[PubMed:10094622] [WorldCat.org] [DOI] (P p)