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PutA DNA-binding transcriptional repressor

Synonyms: PutA
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, 4, 5]. The Lys9 residue is essential for recognition of put promoter DNA [6]. Crystal structures of this domain have been solved [3, 6]. 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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
PutA Functional   nd nd nd
Evolutionary Family: PutA
TFBs length: 6
TFBs symmetry: asymmetric
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

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
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  PutA repressor putAp Sigma70 -31.5 -74.5 putA
  PutA repressor putAp Sigma70 -21.5 -64.5 putA
  PutA repressor putAp Sigma70 14.5 -29.5 putA
  PutA repressor putPp1 Sigma70 -81.5 -218.5 putP
  PutA repressor putPp1 Sigma70 -54.5 -191.5 putP

Alignment and PSSM for PutA TFBSs    

Aligned TFBS of PutA   

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.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


 [1] Becker DF., Thomas EA., 2001, Redox properties of the PutA protein from Escherichia coli and the influence of the flavin redox state on PutA-DNA interactions., Biochemistry 40(15):4714-21

 [2] Brown ED., Wood JM., 1992, Redesigned purification yields a fully functional PutA protein dimer from Escherichia coli., J Biol Chem 267(18):13086-92

 [3] Zhou Y., Larson JD., Bottoms CA., Arturo EC., Henzl MT., Jenkins JL., Nix JC., Becker DF., Tanner JJ., 2008, Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA., J Mol Biol 381(1):174-88

 [4] Gu D, Zhou Y, Kallhoff V, Baban B, Tanner JJ, Becker DF, 2004, Identification and characterization of the DNA-binding domain of the multifunctional PutA flavoenzyme., J Biol Chem, 279(30):31171 10.1074/jbc.M403701200

 [5] Singh RK, Larson JD, Zhu W, Rambo RP, Hura GL, Becker DF, Tanner JJ, 2011, Small-angle X-ray scattering studies of the oligomeric state and quaternary structure of the trifunctional proline utilization A (PutA) flavoprotein from Escherichia coli., J Biol Chem, 286(50):43144 10.1074/jbc.M111.292474

 [6] Larson JD, Jenkins JL, Schuermann JP, Zhou Y, Becker DF, Tanner JJ, 2006, Crystal structures of the DNA-binding domain of Escherichia coli proline utilization A flavoprotein and analysis of the role of Lys9 in DNA recognition., Protein Sci, 15(11):2630 10.1110/ps.062425706

 [7] Zhang W, Zhou Y, Becker DF, 2004, Regulation of PutA-membrane associations by flavin adenine dinucleotide reduction., Biochemistry, 43(41):13165 10.1021/bi048596g

 [8] Shimada T., Ogasawara H., Kobayashi I., Kobayashi N., Ishihama A., 2021, Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12., Front Microbiol 12:697803

 [9] Vinod MP, Bellur P, Becker DF, 2002, Electrochemical and functional characterization of the proline dehydrogenase domain of the PutA flavoprotein from Escherichia coli., Biochemistry, 41(20):6525 10.1021/bi025706f

 [10] Abrahamson JL, Baker LG, Stephenson JT, Wood JM, 1983, Proline dehydrogenase from Escherichia coli K12. Properties of the membrane-associated enzyme., Eur J Biochem, 134(1):77 10.1111/j.1432-1033.1983.tb07533.x

 [11] Moxley MA, Tanner JJ, Becker DF, 2011, Steady-state kinetic mechanism of the proline:ubiquinone oxidoreductase activity of proline utilization A (PutA) from Escherichia coli., Arch Biochem Biophys, 516(2):113 10.1016/

 [12] Moxley MA, Becker DF, 2012, Rapid reaction kinetics of proline dehydrogenase in the multifunctional proline utilization A protein., Biochemistry, 51(1):511 10.1021/bi201603f

 [13] Moxley MA, Zhang L, Christgen S, Tanner JJ, Becker DF, 2017, Identification of a Conserved Histidine As Being Critical for the Catalytic Mechanism and Functional Switching of the Multifunctional Proline Utilization A Protein., Biochemistry, 56(24):3078 10.1021/acs.biochem.7b00046

 [14] Wood JM, 1987, Membrane association of proline dehydrogenase in Escherichia coli is redox dependent., Proc Natl Acad Sci U S A, 84(2):373 10.1073/pnas.84.2.373

 [15] Brown ED, Wood JM, 1993, Conformational change and membrane association of the PutA protein are coincident with reduction of its FAD cofactor by proline., J Biol Chem, 268(12):8972 None

 [16] Zhu W, Becker DF, 2003, Flavin redox state triggers conformational changes in the PutA protein from Escherichia coli., Biochemistry, 42(18):5469 10.1021/bi0272196

 [17] Zhu W, Becker DF, 2005, Exploring the proline-dependent conformational change in the multifunctional PutA flavoprotein by tryptophan fluorescence spectroscopy., Biochemistry, 44(37):12297 10.1021/bi051026b

 [18] Zhang W, Zhang M, Zhu W, Zhou Y, Wanduragala S, Rewinkel D, Tanner JJ, Becker DF, 2007, Redox-induced changes in flavin structure and roles of flavin N(5) and the ribityl 2'-OH group in regulating PutA--membrane binding., Biochemistry, 46(2):483 10.1021/bi061935g

 [19] Zhu W, Haile AM, Singh RK, Larson JD, Smithen D, Chan JY, Tanner JJ, Becker DF, 2013, Involvement of the ?3-?3 loop of the proline dehydrogenase domain in allosteric regulation of membrane association of proline utilization A., Biochemistry, 52(26):4482 10.1021/bi400396g

 [20] Christgen SL, Zhu W, Sanyal N, Bibi B, Tanner JJ, Becker DF, 2017, Discovery of the Membrane Binding Domain in Trifunctional Proline Utilization A., Biochemistry, 56(47):6292 10.1021/acs.biochem.7b01008

 [21] Lee YH, Nadaraia S, Gu D, Becker DF, Tanner JJ, 2003, Structure of the proline dehydrogenase domain of the multifunctional PutA flavoprotein., Nat Struct Biol, 10(2):109 10.1038/nsb885

 [22] Zhang M, White TA, Schuermann JP, Baban BA, Becker DF, Tanner JJ, 2004, Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors., Biochemistry, 43(39):12539 10.1021/bi048737e

 [23] Ostrander EL, Larson JD, Schuermann JP, Tanner JJ, 2009, A conserved active site tyrosine residue of proline dehydrogenase helps enforce the preference for proline over hydroxyproline as the substrate., Biochemistry, 48(5):951 10.1021/bi802094k

 [24] Srivastava D, Zhu W, Johnson WH, Whitman CP, Becker DF, Tanner JJ, 2010, The structure of the proline utilization a proline dehydrogenase domain inactivated by N-propargylglycine provides insight into conformational changes induced by substrate binding and flavin reduction., Biochemistry, 49(3):560 10.1021/bi901717s

 [25] Baban BA, Vinod MP, Tanner JJ, Becker DF, 2004, Probing a hydrogen bond pair and the FAD redox properties in the proline dehydrogenase domain of Escherichia coli PutA., Biochim Biophys Acta, 1701(1-2):49 10.1016/j.bbapap.2004.06.001

 [26] Ling M, Allen SW, Wood JM, 1994, Sequence analysis identifies the proline dehydrogenase and delta 1-pyrroline-5-carboxylate dehydrogenase domains of the multifunctional Escherichia coli PutA protein., J Mol Biol, 243(5):950 10.1006/jmbi.1994.1696

 [27] Moxley MA, Sanyal N, Krishnan N, Tanner JJ, Becker DF, 2014, Evidence for hysteretic substrate channeling in the proline dehydrogenase and ?1-pyrroline-5-carboxylate dehydrogenase coupled reaction of proline utilization A (PutA)., J Biol Chem, 289(6):3639 10.1074/jbc.M113.523704

 [28] Deutch CE, Hasler JM, Houston RM, Sharma M, Stone VJ, 1989, Nonspecific inhibition of proline dehydrogenase synthesis in Escherichia coli during osmotic stress., Can J Microbiol, 35(8):779 10.1139/m89-130

 [29] Zhang L, Alfano JR, Becker DF, 2015, Proline metabolism increases katG expression and oxidative stress resistance in Escherichia coli., J Bacteriol, 197(3):431 10.1128/JB.02282-14

 [30] Wood JM., Zadworny D., 1980, Amplification of the put genes and identification of the put gene products in Escherichia coli K12., Can J Biochem 58(10):787-96

 [31] Maloy S, Stewart V, 1993, Autogenous regulation of gene expression., J Bacteriol, 175(2):307 10.1128/jb.175.2.307-316.1993

 [32] Commichau FM, Stülke J, 2008, Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression., Mol Microbiol, 67(4):692 10.1111/j.1365-2958.2007.06071.x

 [33] Zhou Y, Zhu W, Bellur PS, Rewinkel D, Becker DF, 2008, Direct linking of metabolism and gene expression in the proline utilization A protein from Escherichia coli., Amino Acids, 35(4):711 10.1007/s00726-008-0053-6

 [34] Tanner JJ, 2008, Structural biology of proline catabolism., Amino Acids, 35(4):719 10.1007/s00726-008-0062-5

 [35] Becker DF, Zhu W, Moxley MA, 2011, Flavin redox switching of protein functions., Antioxid Redox Signal, 14(6):1079 10.1089/ars.2010.3417

 [36] Singh RK, Tanner JJ, 2012, Unique structural features and sequence motifs of proline utilization A (PutA)., Front Biosci (Landmark Ed), 17(None):556 10.2741/3943

 [37] Arentson BW, Sanyal N, Becker DF, 2012, Substrate channeling in proline metabolism., Front Biosci (Landmark Ed), 17(1):375 10.2741/3932

 [38] Liu LK, Becker DF, Tanner JJ, 2017, Structure, function, and mechanism of proline utilization A (PutA)., Arch Biochem Biophys, 632(None):142 10.1016/

 [39] Tanner JJ, 2019, Structural Biology of Proline Catabolic Enzymes., Antioxid Redox Signal, 30(4):650 10.1089/ars.2017.7374