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PutA DNA-binding transcriptional repressor

Synonyms: PutA
Summary:
PutA is a flavoprotein with mutually exclusive functions as a transcriptional repressor and membrane-associated enzyme. The switch between the two activities is due to conformational changes triggered by the redox state of FAD. In the presence of proline, PutA is associated with the cytoplasmic membrane and acts a bifunctional enzyme catalyzing both reactions of the |FRAME: PROUT-PWY-I| pathway: the oxidation of proline by proline dehydrogenase and subsequent oxidation to glutamate by pyrroline-5-carboxylate (P5C) dehydrogenase. The kinetics of the coupled reaction is best described by substrate channeling. In the absence of proline, PutA is cytoplasmic and functions as a transcriptional repressor of the put regulon. The N-terminal 47 residues with a ribbon-helix-helix fold contain the dimerization domain and the specific DNA-binding activity of PutA [3]. The Lys9 residue is essential for recognition of put promoter DNA []. Crystal structures of this domain have been solved [3]. In the absence of proline, PutA binds to operator sequences in the putA-putP intergenic region and represses transcription, most likely by keeping RNA polymerase from binding to the putA promoter [3].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PutA Functional   nd [1]
Evolutionary Family: PutA
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: putA
  Genome position: 1074920-1078882
  Length: 3963 bp / 1320 aa
Operon name: putA
TU(s) encoding the TF:
Transcription unit        Promoter
putA
putAp


Regulon       
Regulated gene(s) putA, putP
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
amino acids (1)
electron donors (1)
Transcription related (1)
repressor (1)
Porters (Uni-, Sym- and Antiporters) (1)
Regulated operon(s) putA, putP
First gene in the operon(s) putA, putP
Simple and complex regulons BasR,MarA,PutA
PutA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[PutA,-](2)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  PutA repressor putAp Sigma70 -31.5 -74.5 putA
catttaacatGGTTGCAcaaagttgca
1078954 1078959 [BPP], [GEA], [SM] [1], [2], [3]
  PutA repressor putAp Sigma70 -21.5 -64.5 putA
ggttgcacaaAGTTGCAacatcatgga
1078944 1078949 [BPP], [GEA], [SM] [3]
  PutA repressor putAp Sigma70 14.5 -29.5 putA
gataacgttaAGTTGCAcctttctgaa
1078909 1078914 [BPP], [GEA], [SM] [3]
  PutA repressor putPp1 Sigma70 -81.5 -218.5 putP
atttttgaaaGGTGCAAccgcaaaaaa
1079084 1079089 [BPP], [GEA], [SM] [3]
  PutA repressor putPp1 Sigma70 -54.5 -191.5 putP
tgtgagagagTGCAACCtgatgaaaaa
1079111 1079116 [BPP], [GEA], [SM] [3]


Alignment and PSSM for PutA TFBSs    

Aligned TFBS of PutA   
  Sequence
  TGCAAC
  TGCAAC
  TGCAAC
  TGCAAC
  TGCAAC

Position weight matrix (PWM). PutA matrix-quality result   
A	0	0	0	5	5	0
C	0	0	5	0	0	5
G	0	5	0	0	0	0
T	5	0	0	0	0	0

Consensus   
;	consensus.strict             	TGCAAC
;	consensus.strict.rc          	GTTGCA
;	consensus.IUPAC              	TGCAAC
;	consensus.IUPAC.rc           	GTTGCA
;	consensus.regexp             	TGCAAC
;	consensus.regexp.rc          	GTTGCA

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation






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