SubtiBank SubtiBank
ycbC
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ycbC

5-dehydro-4-deoxyglucarate dehydratase
locus
BSU_02460
pI
5.38
mw
33.89 kDa
protein length
308 aa Sequence Blast
gene length
927 bp Sequence Blast
function
utilization of D-glucarate/galactarate
product
5-dehydro-4-deoxyglucarate dehydratase
essential
no
ec
4.2.1.41
synonyms
Outlinks
KEGGBsubCycSubtiListUniProtExpression Browser

Genomic Context

      

categories

  • [category|SW 2|Metabolism] → [category|SW 2.2|Carbon metabolism] → [category|SW 2.2.2|Utilization of specific carbon sources] → [category|SW 2.2.2.14|Utilization of glucarate/galactarate]

    • Gene

    Coordinates
    267,890 268,816

    The protein

    Catalyzed reaction/ biological activity

  • 5-dehydro-4-deoxy-D-glucarate + H+ --> 2,5-dioxopentanoate + CO2 + H2O (according to UniProt)

    • Protein family

  • DapA family (with [protein|00B4CA4E25858A56F9D4E0ADEE2643F203FEC613|DapA], according to UniProt)

    • Structure

  • [PDB|4UR8] (from Agrobacterium fabrum, 38% identity) [pubmed|25454257]

    • Expression and Regulation

    Operons

    genes
    [gene|3542BC20C11985B3CFAA4F930E8D794700ADFD2E|ycbC]-[gene|5B66ADB81AB141982F187B1C5E3A9346AA064DE2|ycbD]-[gene|9C4932DA4DEF99263E57871A99684E3DAD93E1EC|ycbE]-[gene|372F2A420309DB0193AEF36A740EBA26410F97F2|ycbF]-[gene|1A65880F68898002EE8774F34EDC47F0243B7273|ycbG]-[gene|BA556E144975921DFDD598B0A7480C65176F0F14|ycbH]-[gene|349C99C258331962455100E2662DA2272E946C8A|ycbJ]
    description
    [Pubmed|12044674]

    regulatory mechanism

  • [protein|1A65880F68898002EE8774F34EDC47F0243B7273|YcbG]: repression, [Pubmed|12044674], in [regulon|1A65880F68898002EE8774F34EDC47F0243B7273|YcbG regulon]
  • [protein|E5110D9C36E8C55AFD1419987B14A53232165F20|AbrB]: repression, [Pubmed|18840696], in [regulon|E5110D9C36E8C55AFD1419987B14A53232165F20|AbrB regulon]

    • regulation

  • induced by D-glucarate/galactarate ([protein|search|YcbG]) [Pubmed|12044674]
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    Biological materials

    Mutant

  • MGNA-C027 (ycbC::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/2025 NBRP B. subtilis, Japan]
  • BKE02460 ([gene|3542BC20C11985B3CFAA4F930E8D794700ADFD2E|ycbC]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE02460 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATCAACATAACCTCCTGTT, downstream forward: _UP4_TGACCAGAAAAAACACGAAA
  • BKK02460 ([gene|3542BC20C11985B3CFAA4F930E8D794700ADFD2E|ycbC]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK02460 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATCAACATAACCTCCTGTT, downstream forward: _UP4_TGACCAGAAAAAACACGAAA

    • References

  • 12044674,25454257