RegulonDB RegulonDB 10.10: Gene Form
   

minD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

minD minC minE TSS_1504 TSS_1504 TSS_1503 TSS_1503 TSS_1502 TSS_1502 minEp3 minEp3

Gene      
Name: minD    Texpresso search in the literature
Synonym(s): ECK1163, EG10597, b1175, minB
Genome position(nucleotides): 1224549 <-- 1225361 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.94
External database links:  
ASAP:
 ABE-0003938
CGSC:
 31326
ECHOBASE:
 EB0592
ECOLIHUB:
 minD
OU-MICROARRAY:
 b1175
STRING:
 511145.b1175
COLOMBOS: minD


Product      
Name: Z-ring positioning protein MinD
Synonym(s): MinB, MinD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,cytosol
Molecular weight: 29.614
Isoelectric point: 4.991
Motif(s):
 
Type Positions Sequence
16 -> 17 KT
154 -> 154 D
10 -> 17 GKGGVGKT
15 -> 15 G
2 -> 270 ARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFDIGLRNLDLIMGCERRVVYDFVNVIQGDATLNQALIKDKRTENLYILPASQTRDKDALTREGVAKVLDDLKAMDFEFIVCDSPAGIETGALMALYFADEAIITTNPEVSSVRDSDRILGILASKSRRAENGEEPIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVGVIPEDQSVLRASNQGEPVILDINADAGKAYADTVERLLGEERPFRFIEEEKKGFLKRLFGG

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.1 - cell division
  5 - cell processes --> 5.2 - cell cycle physiology
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0009898 - cytoplasmic side of plasma membrane
GO:0031226 - intrinsic component of plasma membrane
GO:0060187 - cell pole
molecular_function GO:0005515 - protein binding
GO:0016887 - ATP hydrolysis activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0042802 - identical protein binding
biological_process GO:0051301 - cell division
GO:0007049 - cell cycle
GO:0000917 - division septum assembly
GO:0007059 - chromosome segregation
GO:0051782 - negative regulation of cell division
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[AUPEINH] Assay of unpurified protein expressed in its native host
[HIFS] Human inference of function from sequence
[IFC] Inferred by functional complementation
Reference(s): [1] Akerlund T., et al., 2002
[2] Akerlund T., et al., 1993
[3] Bi E., et al., 1993
[4] Bonny M., et al., 2013
[5] Dassain M., et al., 1994
[6] Davie E., et al., 1984
[7] Denk J., et al., 2018
[8] Fu M., et al., 2020
[9] Fu X., et al., 2001
[10] Galperin MY., et al., 2000
[11] Gullbrand B., et al., 2000
[12] Heermann T., et al., 2020
[13] Howard M., et al., 2003
[14] Hu Z., et al., 1999
[15] Jaffe A., et al., 1990
[16] Jaffe A., et al., 1997
[17] Juarez JR., et al., 2010
[18] Kohyama S., et al., 2020
[19] Kohyama S., et al., 2020
[20] Kretschmer S., et al., 2021
[21] LaBreck CJ., et al., 2020
[22] Labie C., et al., 1990
[23] Mizuuchi K., et al., 2018
[24] Motallebi-Veshareh M., et al., 1990
[25] Mulder E., et al., 1991
[26] Park KT., et al., 2017
[27] Pichoff S., et al., 1997
[28] Ramm B., et al., 2018
[29] Roos M., et al., 2001
[30] Schaumberg TH., et al., 1983
[31] Shih YL., et al., 2002
[32] Thalmeier D., et al., 2016
[33] Touhami A., et al., 2006
[34] Vecchiarelli AG., et al., 2016
[35] Wettmann L., et al., 2018
[36] Xiong L., et al., 2015
[37] Yu XC., et al., 2001
[38] Zieske K., et al., 2013
[39] Zieske K., et al., 2014
[40] de Boer PA., et al., 1991
[41] de Boer PA., et al., 1990
[42] de Boer PA., et al., 1989
External database links:  
DIP:
 DIP-35946N
ECOCYC:
 EG10597-MONOMER
ECOLIWIKI:
 b1175
INTERPRO:
 IPR002586
INTERPRO:
 IPR010223
INTERPRO:
 IPR025501
INTERPRO:
 IPR027417
MINT:
 P0AEZ3
PDB:
 3R9J
PDB:
 3R9I
PDB:
 3Q9L
PFAM:
 PF01656
PRIDE:
 P0AEZ3
PRODB:
 PRO_000023238
REFSEQ:
 NP_415693
SMR:
 P0AEZ3
UNIPROT:
 P0AEZ3


Operon      
Name: minCDE         
Operon arrangement:
Transcription unit        Promoter
minCDE


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter minEp3 1224711 reverse nd [ICWHO] [43]
  promoter TSS_1502 1224778 reverse nd [RS-EPT-CBR] [44]
  promoter TSS_1503 1225451 reverse nd [RS-EPT-CBR] [44]
  promoter TSS_1504 1225647 reverse nd [RS-EPT-CBR] [44]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Akerlund T., Gullbrand B., Nordstrom K., 2002, Effects of the Min system on nucleoid segregation in Escherichia coli., Microbiology 148(Pt 10):3213-22

 [2] Akerlund T., Nordstrom K., Bernander R., 1993, Branched Escherichia coli cells., Mol Microbiol 10(4):849-58

 [3] Bi E., Lutkenhaus J., 1993, Cell division inhibitors SulA and MinCD prevent formation of the FtsZ ring., J Bacteriol 175(4):1118-25

 [4] Bonny M., Fischer-Friedrich E., Loose M., Schwille P., Kruse K., 2013, Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation., PLoS Comput Biol 9(12):e1003347

 [5] Dassain M., Bouche JP., 1994, The min locus, which confers topological specificity to cell division, is not involved in its coupling with nucleoid separation., J Bacteriol 176(19):6143-5

 [6] Davie E., Sydnor K., Rothfield LI., 1984, Genetic basis of minicell formation in Escherichia coli K-12., J Bacteriol 158(3):1202-3

 [7] Denk J., Kretschmer S., Halatek J., Hartl C., Schwille P., Frey E., 2018, MinE conformational switching confers robustness on self-organized Min protein patterns., Proc Natl Acad Sci U S A 115(18):4553-4558

 [8] Fu M., Franquelim HG., Kretschmer S., Schwille P., 2020, Non-equilibrium large-scale membrane transformations driven by MinDE biochemical reaction cycles., Angew Chem Int Ed Engl

 [9] Fu X., Shih YL., Zhang Y., Rothfield LI., 2001, The MinE ring required for proper placement of the division site is a mobile structure that changes its cellular location during the Escherichia coli division cycle., Proc Natl Acad Sci U S A 98(3):980-5

 [10] Galperin MY., Grishin NV., 2000, The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase., Proteins 41(2):238-47

 [11] Gullbrand B., Nordstrom K., 2000, FtsZ ring formation without subsequent cell division after replication runout in Escherichia coli., Mol Microbiol 36(6):1349-59

 [12] Heermann T., Ramm B., Glaser S., Schwille P., 2020, Local Self-Enhancement of MinD Membrane Binding in Min Protein Pattern Formation., J Mol Biol 432(10):3191-3204

 [13] Howard M., Rutenberg AD., 2003, Pattern formation inside bacteria: fluctuations due to the low copy number of proteins., Phys Rev Lett 90(12):128102

 [14] Hu Z., Lutkenhaus J., 1999, Topological regulation of cell division in Escherichia coli involves rapid pole to pole oscillation of the division inhibitor MinC under the control of MinD and MinE., Mol Microbiol 34(1):82-90

 [15] Jaffe A., Boye E., D'Ari R., 1990, Rule governing the division pattern in Escherichia coli minB and wild-type filaments., J Bacteriol 172(6):3500-2

 [16] Jaffe A., Vinella D., D'Ari R., 1997, The Escherichia coli histone-like protein HU affects DNA initiation, chromosome partitioning via MukB, and cell division via MinCDE., J Bacteriol 179(11):3494-9

 [17] Juarez JR., Margolin W., 2010, Changes in the Min oscillation pattern before and after cell birth., J Bacteriol 192(16):4134-42

 [18] Kohyama S., Fujiwara K., Yoshinaga N., Doi N., 2020, Conformational equilibrium of MinE regulates the allowable concentration ranges of a protein wave for cell division., Nanoscale 12(22):11960-11970

 [19] Kohyama S., Fujiwara K., Yoshinaga N., Doi N., 2020, Self-organization Assay for Min Proteins of Escherichia coli in Micro-droplets Covered with Lipids., Bio Protoc 10(6):e3561

 [20] Kretschmer S., Heermann T., Tassinari A., Glock P., Schwille P., 2021, Increasing MinD's Membrane Affinity Yields Standing Wave Oscillations and Functional Gradients on Flat Membranes., ACS Synth Biol

 [21] LaBreck CJ., Trebino CE., Ferreira CN., Morrison JJ., DiBiasio EC., Conti J., Camberg JL., 2020, Degradation of MinD oscillator complexes by Escherichia coli ClpXP., J Biol Chem

 [22] Labie C., Bouche F., Bouche JP., 1990, Minicell-forming mutants of Escherichia coli: suppression of both DicB- and MinD-dependent division inhibition by inactivation of the minC gene product., J Bacteriol 172(10):5852-5

 [23] Mizuuchi K., Vecchiarelli AG., 2018, Mechanistic insights of the Min oscillator via cell-free reconstitution and imaging., Phys Biol 15(3):031001

 [24] Motallebi-Veshareh M., Rouch DA., Thomas CM., 1990, A family of ATPases involved in active partitioning of diverse bacterial plasmids., Mol Microbiol 4(9):1455-63

 [25] Mulder E., Woldringh CL., 1991, Autoradiographic analysis of diaminopimelic acid incorporation in filamentous cells of Escherichia coli: repression of peptidoglycan synthesis around the nucleoid., J Bacteriol 173(15):4751-6

 [26] Park KT., Villar MT., Artigues A., Lutkenhaus J., 2017, MinE conformational dynamics regulate membrane binding, MinD interaction, and Min oscillation., Proc Natl Acad Sci U S A 114(29):7497-7504

 [27] Pichoff S., Vollrath B., Bouche JP., 1997, MinCD-independent inhibition of cell division by a protein that fuses MalE to the topological specificity factor MinE., J Bacteriol 179(14):4616-9

 [28] Ramm B., Glock P., Schwille P., 2018, In Vitro Reconstitution of Self-Organizing Protein Patterns on Supported Lipid Bilayers., J Vis Exp (137)

 [29] Roos M., van Geel AB., Aarsman ME., Veuskens JT., Woldringh CL., Nanninga N., 2001, The replicated ftsQAZ and minB chromosomal regions of Escherichia coli segregate on average in line with nucleoid movement., Mol Microbiol 39(3):633-40

 [30] Schaumberg TH., Kuempel PL., 1983, Genetic mapping of the minB locus in Escherichia coli K-12., J Bacteriol 153(2):1063-5

 [31] Shih YL., Fu X., King GF., Le T., Rothfield L., 2002, Division site placement in E.coli: mutations that prevent formation of the MinE ring lead to loss of the normal midcell arrest of growth of polar MinD membrane domains., EMBO J 21(13):3347-57

 [32] Thalmeier D., Halatek J., Frey E., 2016, Geometry-induced protein pattern formation., Proc Natl Acad Sci U S A 113(3):548-53

 [33] Touhami A., Jericho M., Rutenberg AD., 2006, Temperature dependence of MinD oscillation in Escherichia coli: running hot and fast., J Bacteriol 188(21):7661-7

 [34] Vecchiarelli AG., Li M., Mizuuchi M., Hwang LC., Seol Y., Neuman KC., Mizuuchi K., 2016, Membrane-bound MinDE complex acts as a toggle switch that drives Min oscillation coupled to cytoplasmic depletion of MinD., Proc Natl Acad Sci U S A 113(11):E1479-88

 [35] Wettmann L., Bonny M., Kruse K., 2018, Effects of geometry and topography on Min-protein dynamics., PLoS One 13(8):e0203050

 [36] Xiong L., Lan G., 2015, An Optimal Free Energy Dissipation Strategy of the MinCDE Oscillator in Regulating Symmetric Bacterial Cell Division., PLoS Comput Biol 11(8):e1004351

 [37] Yu XC., Sun Q., Margolin W., 2001, FtsZ rings in mukB mutants with or without the Min system., Biochimie 83(1):125-9

 [38] Zieske K., Schwille P., 2013, Reconstitution of pole-to-pole oscillations of min proteins in microengineered polydimethylsiloxane compartments., Angew Chem Int Ed Engl 52(1):459-62

 [39] Zieske K., Schwille P., 2014, Reconstitution of self-organizing protein gradients as spatial cues in cell-free systems., Elife 3

 [40] de Boer PA., Crossley RE., Hand AR., Rothfield LI., 1991, The MinD protein is a membrane ATPase required for the correct placement of the Escherichia coli division site., EMBO J 10(13):4371-80

 [41] de Boer PA., Crossley RE., Rothfield LI., 1990, Central role for the Escherichia coli minC gene product in two different cell division-inhibition systems., Proc Natl Acad Sci U S A 87(3):1129-33

 [42] de Boer PA., Crossley RE., Rothfield LI., 1989, A division inhibitor and a topological specificity factor coded for by the minicell locus determine proper placement of the division septum in E. coli., Cell 56(4):641-9

 [43] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [44] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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