Difference between revisions of "XynC"

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* '''Description:''' write here <br/><br/>
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* '''Description:''' endo-xylanase, preference for methylglucurono-xylan <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ynfF''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ynfF''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' ||  
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|style="background:#ABCDEF;" align="center"| '''Product''' || endo-xylanase
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
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|style="background:#ABCDEF;" align="center"|'''Function''' || xylan degradation
 +
|-
 +
|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=BSU18150 xynC]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 9.078   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 9.078   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1266 bp, 422 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1266 bp, 422 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ynfE]]'', ''[[xynD]]''
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ynfF_nucleotide.txt    Gene sequence     (+200bp)  ]'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU18150 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU18150 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU18150 DNA_with_flanks]
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ynfF_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ynfF_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ynfF_context.gif]]
 +
<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=xynC_1942714_1943982_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:xynC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU18150]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/>
  
−
<br/><br/>
+
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[utilization of specific carbon sources]]}}
 +
 
 +
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[AbrB regulon]]}}
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU18150
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU18150&redirect=T BSU18150]
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ynfF.html]
+
* '''DBTBS entry:''' no entry
  
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11830]
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11830]
  
 
=== Additional information===
 
=== Additional information===
 +
 +
  
  
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Endohydrolysis of (1->4)-beta-D-xylosyl links in some glucuronoarabinoxylans (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' glycosyl hydrolase 30 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''[[SubtInteract|Interactions]]:'''  
  
−
* '''Localization:'''
+
* '''[[Localization]]:'''
 +
** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU18150&redirect=T BSU18150]
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3GTN 3GTN] {{PubMed|19407387,21256135}}
  
−
* '''Swiss prot entry:'''
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45070 Q45070]
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18150]
  
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* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.136 3.2.1.136]
  
 
=== Additional information===
 
=== Additional information===
  
 
=Expression and regulation=
 
=Expression and regulation=
 +
* '''Operon:''' ''[[xynD]]-[[xynC]]'' {{PubMed|20817675}}
  
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* '''Operon:'''  
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* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=xynC_1942714_1943982_-1 xynC] {{PubMed|22383849}}
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[AbrB]]: transcription repression {{PubMed|20817675}}
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
 +
==Reviews==
 +
<pubmed>20735481 </pubmed>
 +
==Original publications==
 +
<pubmed>19407387, 18957862, 17028274 20817675,21256135 24271172 </pubmed>
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
[[Category:Protein-coding genes]]

Latest revision as of 13:51, 2 April 2014

  • Description: endo-xylanase, preference for methylglucurono-xylan

Gene name xynC
Synonyms ynfF
Essential no
Product endo-xylanase
Function xylan degradation
Gene expression levels in SubtiExpress: xynC
MW, pI 47 kDa, 9.078
Gene length, protein length 1266 bp, 422 aa
Immediate neighbours ynfE, xynD
Sequences Protein DNA DNA_with_flanks
Genetic context
YnfF context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
XynC expression.png















Categories containing this gene/protein

utilization of specific carbon sources

This gene is a member of the following regulons

AbrB regulon

The gene

Basic information

  • Locus tag: BSU18150

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Endohydrolysis of (1->4)-beta-D-xylosyl links in some glucuronoarabinoxylans (according to Swiss-Prot)
  • Protein family: glycosyl hydrolase 30 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • KEGG entry: [2]

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • 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

Reviews

Massimiliano Marvasi, Pieter T Visscher, Lilliam Casillas Martinez
Exopolymeric substances (EPS) from Bacillus subtilis: polymers and genes encoding their synthesis.
FEMS Microbiol Lett: 2010, 313(1);1-9
[PubMed:20735481] [WorldCat.org] [DOI] (I p)

Original publications

Mun Su Rhee, Lusha Wei, Neha Sawhney, John D Rice, Franz J St John, Jason C Hurlbert, James F Preston
Engineering the xylan utilization system in Bacillus subtilis for production of acidic Xylooligosaccharides.
Appl Environ Microbiol: 2014, 80(3);917-27
[PubMed:24271172] [WorldCat.org] [DOI] (I p)

Franz J St John, Jason C Hurlbert, John D Rice, James F Preston, Edwin Pozharski
Ligand bound structures of a glycosyl hydrolase family 30 glucuronoxylan xylanohydrolase.
J Mol Biol: 2011, 407(1);92-109
[PubMed:21256135] [WorldCat.org] [DOI] (I p)

Onuma Chumsakul, Hiroki Takahashi, Taku Oshima, Takahiro Hishimoto, Shigehiko Kanaya, Naotake Ogasawara, Shu Ishikawa
Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation.
Nucleic Acids Res: 2011, 39(2);414-28
[PubMed:20817675] [WorldCat.org] [DOI] (I p)

Franz J St John, David K Godwin, James F Preston, Edwin Pozharski, Jason C Hurlbert
Crystallization and crystallographic analysis of Bacillus subtilis xylanase C.
Acta Crystallogr Sect F Struct Biol Cryst Commun: 2009, 65(Pt 5);499-503
[PubMed:19407387] [WorldCat.org] [DOI] (I p)

Birgit Voigt, Haike Antelmann, Dirk Albrecht, Armin Ehrenreich, Karl-Heinz Maurer, Stefan Evers, Gerhard Gottschalk, Jan Maarten van Dijl, Thomas Schweder, Michael Hecker
Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis.
J Mol Microbiol Biotechnol: 2009, 16(1-2);53-68
[PubMed:18957862] [WorldCat.org] [DOI] (I p)

Franz J St John, John D Rice, James F Preston
Characterization of XynC from Bacillus subtilis subsp. subtilis strain 168 and analysis of its role in depolymerization of glucuronoxylan.
J Bacteriol: 2006, 188(24);8617-26
[PubMed:17028274] [WorldCat.org] [DOI] (P p)

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