Difference between revisions of "YmdB"
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===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
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* strong overexpression of ''[[hag]]'' {{PubMed|21856853}} | * strong overexpression of ''[[hag]]'' {{PubMed|21856853}} | ||
| − | * defective in [[biofilm formation]] {{PubMed|21856853}} | + | * defective in [[biofilm formation]] {{PubMed|21856853,22113911}} |
* the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[[slrR]]'' {{PubMed|21856853}} | * the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[[slrR]]'' {{PubMed|21856853}} | ||
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=References= | =References= | ||
| + | <pubmed> 22113911 </pubmed> | ||
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big> | <big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big> | ||
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big> | <big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big> | ||
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J Bacteriol.: 2011, 193(21):5997-6007. | J Bacteriol.: 2011, 193(21):5997-6007. | ||
[http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853] | [http://www.ncbi.nlm.nih.gov/pubmed/21856853 PubMed:21856853] | ||
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==Functional and structural analysis of orthologs in other organisms== | ==Functional and structural analysis of orthologs in other organisms== | ||
Revision as of 17:44, 25 November 2011
- Description: putative phosphatase/ phosphodiesterase, controls bistable gene expression
| Gene name | ymdB |
| Synonyms | |
| Essential | no |
| Product | putative phosphatase/ phosphodiesterase |
| Function | control of bistable gene expression |
| MW, pI | 29,1 kDa, 6.50 |
| Gene length, protein length | 792 bp, 264 amino acids |
| Immediate neighbours | rny, spoVS |
| Get the DNA and protein sequences (Barbe et al., 2009) | |
Genetic context 
This image was kindly provided by SubtiList
| |
Contents
Categories containing this gene/protein
This gene is a member of the following regulons
The gene
Basic information
- Locus tag: BSU16970
Phenotypes of a mutant
- strong overexpression of hag PubMed
- defective in biofilm formation PubMed
- the phenotypes of the ymdB mutant can be suppressed by overexpression of slrR PubMed
Database entries
- DBTBS entry: no entry
- SubtiList entry: [1]
Additional information
The protein
Basic information/ Evolution
- Catalyzed reaction/ biological activity: phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP (the Deinococcus ortholog) PubMed
- Protein family:
- Paralogous protein(s):
Extended information on the protein
- Kinetic information:
- Domains:
- Modification:
- Cofactor(s):
- Effectors of protein activity:
Database entries
- UniProt: O31775
- KEGG entry: [2]
- E.C. number:
Additional information
Expression and regulation
- Regulation: constitutive
- Regulatory mechanism:
- Additional information: there is a terminator between rny and ymdB, most transcripts terminate there PubMed
Biological materials
- Mutant:
- Expression vector:
- for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP1041, available in Stülke lab
- for expression/ purification from B. subtilis with C-terminal Strep-tag, for SPINE, in pGP382: pGP1919, available in Stülke lab
- for expression/ purification from E. coli with N-terminal His-tag, in pWH844: pGP1040, available in Stülke lab
- for expression/ purification from E. coli with N-terminal Strep-tag, in pGP172: pGP1917, available in Stülke lab
- GP970 (ymdB-Strep (cat)), purification from B. subtilis, for SPINE, available in Stülke lab
- lacZ fusion:
- GFP fusion:
- two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
- Antibody:
Labs working on this gene/protein
Jörg Stülke, University of Göttingen, Germany Homepage
Your additional remarks
References
Eric R Pozsgai, Kris M Blair, Daniel B Kearns
Modified mariner transposons for random inducible-expression insertions and transcriptional reporter fusion insertions in Bacillus subtilis.
Appl Environ Microbiol: 2012, 78(3);778-85
[PubMed:22113911]
[WorldCat.org]
[DOI]
(I p)
Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J A Novel Factor Controlling Bistability in Bacillus subtilis: The YmdB Protein Affects Flagellin Expression and Biofilm Formation. J Bacteriol.: 2011, 193(21):5997-6007. PubMed:21856853
Functional and structural analysis of orthologs in other organisms
Jason Zemansky, Benjamin C Kline, Joshua J Woodward, Jess H Leber, Hélène Marquis, Daniel A Portnoy
Development of a mariner-based transposon and identification of Listeria monocytogenes determinants, including the peptidyl-prolyl isomerase PrsA2, that contribute to its hemolytic phenotype.
J Bacteriol: 2009, 191(12);3950-64
[PubMed:19376879]
[WorldCat.org]
[DOI]
(I p)
Dong Hae Shin, Michael Proudfoot, Hyo Jin Lim, In-Kyu Choi, Hisao Yokota, Alexander F Yakunin, Rosalind Kim, Sung-Hou Kim
Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans.
Proteins: 2008, 70(3);1000-9
[PubMed:17847097]
[WorldCat.org]
[DOI]
(I p)
