Difference between revisions of "YwlF"

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|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
 
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
 
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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/BSU36920 ywlF]
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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=BSU36920 ywlF]
 
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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/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/pathways/carbon_flow.html Central C-metabolism]'''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywlG]]'', ''[[ywlE]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywlG]]'', ''[[ywlE]]''
 
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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:CAB15709&#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=BSU36920 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36920 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36920 Advanced_DNA]
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:ywlF_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ywlF_context.gif]]

Revision as of 14:05, 13 May 2013

  • Description: ribose-5-phosphate isomerase

Gene name ywlF
Synonyms ipc-32d
Essential no
Product ribose-5-phosphate isomerase
Function pentose phosphate pathway
Gene expression levels in SubtiExpress: ywlF
Metabolic function and regulation of this protein in SubtiPathways:
Central C-metabolism
MW, pI 16 kDa, 5.416
Gene length, protein length 447 bp, 149 aa
Immediate neighbours ywlG, ywlE
Sequences Protein DNA Advanced_DNA
Genetic context
YwlF context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YwlF expression.png




























Categories containing this gene/protein

carbon core metabolism

This gene is a member of the following regulons

TnrA regulon

The gene

Basic information

  • Locus tag: BSU36920

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: lacAB/rpiB family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information: Reversible Mass Action Kinetics PubMed PubMed
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
    • Inhibited by 6-phosphogluconate and AMP PubMed
    • Inhibited by divalent ions such as Ag2+, Mg2+, Co2+ and Zn2+ PubMed
    • Activated by EDTA and 2-mercaptoethanol PubMed
  • Interactions:
  • Localization:

Database entries

  • Structure: 3HEE (from Clostridium thermocellum, 55% identity, 72% similarity)
  • KEGG entry: [3]

Additional information

The enzyme has probably more than one active site, but with no cooperativity described PubMed

Expression and regulation

  • Sigma factor:
  • Regulation:
    • repressed in the absence of good nitrogen sources (glutamine or ammonium) (TnrA) PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:
  • FLAG-tag construct: GP1404 (spc, based on pGP1331), available in the Stülke lab

Labs working on this gene/protein

Your additional remarks

References

Shuobo Shi, Tao Chen, Zhigang Zhang, Xun Chen, Xueming Zhao
Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production.
Metab Eng: 2009, 11(4-5);243-52
[PubMed:19446032] [WorldCat.org] [DOI] (I p)

Ken-ichi Yoshida, Hirotake Yamaguchi, Masaki Kinehara, Yo-hei Ohki, Yoshiko Nakaura, Yasutaro Fujita
Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box.
Mol Microbiol: 2003, 49(1);157-65
[PubMed:12823818] [WorldCat.org] [DOI] (P p)

R D MacElroy, C R Middaugh
Bacterial ribosephosphate isomerase.
Methods Enzymol: 1982, 89 Pt D;571-9
[PubMed:7144591] [WorldCat.org] [DOI] (P p)

C R Middaugh, R D MacElroy
The effect of temperature on ribose-5-phosphate isomerase from a mesophile, Thiobacillus thioparus, and a thermophile, Bacillus caldolyticus.
J Biochem: 1976, 79(6);1331-44
[PubMed:956158] [WorldCat.org] [DOI] (P p)