YdaO

• Description: putative transporter
  
  

Gene name	ydaO
Synonyms
Essential	no
Product	unknown
Function	unknown
Gene expression levels in SubtiExpress: ydaO
MW, pI	66 kDa, 9.929
Gene length, protein length	1821 bp, 607 aa
Immediate neighbours	ydaN, mutT
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

membrane proteins, proteins of unknown function

This gene is a member of the following regulons

YdaO riboswitch

The gene

Basic information

• Locus tag: BSU04320

Database entries

• BsubCyc: BSU04320

• DBTBS entry: no entry

• SubtiList entry: [1]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity:

• Protein family:
  • amino acid, polyamine, organocation (APC) superfamily of transporters, TC 2.A.3

• Paralogous protein(s):

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:

• Cofactors:

• Effectors of protein activity:

• Interactions:

• Localization:
  • cell membrane (according to UniProt)

Database entries

• BsubCyc: BSU04320

• Structure:

• UniProt: P96589

• KEGG entry: [2]

• E.C. number:

Expression and regulation

• Operon: ydaO PubMed

• Expression browser: ydaO PubMed

• Sigma factor:

• Regulation:

• Regulatory mechanism:
  • expression is controlled via termination antitermination by the ydaO riboswitch, expression is switched off upon binding od c-di-AMP PubMed

• Additional information:

Biological materials

• Mutant:
  • 1A688 (ydaO::erm), PubMed, available at BGSC
  • GP93 (DydaO::cat), available in Jörg Stülke's lab

• Expression vector:

• lacZ fusion: available in Fabian Commichau's lab

• GFP fusion:

• two-hybrid system:

• Antibody:

References

Aiming Ren, Dinshaw J Patel
c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.
Nat Chem Biol: 2014, 10(9);780-6
[PubMed:25086509] [WorldCat.org] [DOI] (I p)

Ang Gao, Alexander Serganov
Structural insights into recognition of c-di-AMP by the ydaO riboswitch.
Nat Chem Biol: 2014, 10(9);787-92
[PubMed:25086507] [WorldCat.org] [DOI] (I p)

James W Nelson, Narasimhan Sudarsan, Kazuhiro Furukawa, Zasha Weinberg, Joy X Wang, Ronald R Breaker
Riboswitches in eubacteria sense the second messenger c-di-AMP.
Nat Chem Biol: 2013, 9(12);834-9
[PubMed:24141192] [WorldCat.org] [DOI] (I p)

Peter Y Watson, Martha J Fedor
The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis.
Nat Chem Biol: 2012, 8(12);963-5
[PubMed:23086297] [WorldCat.org] [DOI] (I p)

Kirsten F Block, Ming C Hammond, Ronald R Breaker
Evidence for widespread gene control function by the ydaO riboswitch candidate.
J Bacteriol: 2010, 192(15);3983-9
[PubMed:20511502] [WorldCat.org] [DOI] (I p)

Jeffrey E Barrick, Keith A Corbino, Wade C Winkler, Ali Nahvi, Maumita Mandal, Jennifer Collins, Mark Lee, Adam Roth, Narasimhan Sudarsan, Inbal Jona, J Kenneth Wickiser, Ronald R Breaker
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.
Proc Natl Acad Sci U S A: 2004, 101(17);6421-6
[PubMed:15096624] [WorldCat.org] [DOI] (P p)