RegulonDB RegulonDB 11.1: Gene Form
   

mrdA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mrdA mrdB rlmH TSS_760 TSS_760 TSS_759 TSS_759 TSS_758 TSS_758 TSS_757 TSS_757 rlpAp5 rlpAp5 rlpAp7 rlpAp7

Gene      
Name: mrdA    Texpresso search in the literature
Synonym(s): ECK0628, EG10606, b0635, pbpA
Genome position(nucleotides): 666316 <-- 668217
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.52
External database links:  
ASAP:
 ABE-0002178
CGSC:
 18148
ECHOBASE:
 EB0601
ECOLIHUB:
 mrdA
OU-MICROARRAY:
 b0635
STRING:
 511145.b0635
COLOMBOS: mrdA


Product      
Name: peptidoglycan DD-transpeptidase MrdA
Synonym(s): MrdA, PBP2, PbpA, penicillin-binding protein 2
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space,inner membrane
Molecular weight: 70.857
Isoelectric point: 9.165
Motif(s):
 
Type Positions Sequence Comment
21 -> 45 ALVAFLGILLLTGVLIANLYNLQIV
22 -> 42 LVAFLGILLLTGVLIANLYNL UniProt: Helical.
51 -> 51 Q Q → L: suppresses the slow growth phenotype of a rodZ deletion mutant; restores rod shape to this mutant in L broth
52 -> 52 T T → N: suppresses the slow growth phenotype of a rodZ deletion mutant; restores rod shape to this mutant in L broth
61 -> 61 L L → R: suppresses the growth defect (and partially restores shape) to Rod system mutants (mreC missense mutants, ΔrodZ cells, ΔmreCD cells, and ΔrodZΔmreCD cells); mutant protein stimulates RodA peptidoglycan polymerase activity

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.7 - murein (peptidoglycan)
  5 - cell processes --> 5.6 - protection --> 5.6.4 - drug resistance/sensitivity
  6 - cell structure --> 6.2 - murein
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0005515 - protein binding
GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0004180 - carboxypeptidase activity
GO:0009002 - serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0008658 - penicillin binding
GO:0071972 - peptidoglycan L,D-transpeptidase activity
biological_process GO:0006508 - proteolysis
GO:0009252 - peptidoglycan biosynthetic process
GO:0046677 - response to antibiotic
GO:0008360 - regulation of cell shape
GO:0071555 - cell wall organization
Note(s): Note(s): ...[more].
Reference(s): [1] Anderson JW., et al., 2003
[2] Asoh S., et al., 1983
[3] Begg KJ., et al., 1985
[4] Begg KJ., et al., 1990
[5] Bendezu FO., et al., 2009
[6] Bendezu FO., et al., 2008
[7] Buchnik D., et al., 1987
[8] Bylund JE., et al., 1991
[9] Denome SA., et al., 1999
[10] Garcia del Portillo F., et al., 1991
[11] Georgopapadakou NH., et al., 1982
[12] Ishiguro M., et al., 2001
[13] Ishino F., et al., 1986
[14] Iwaya M., et al., 1978
[15] Jamieson CE., et al., 2003
[16] Karczmarek A., et al., 2007
[17] Khattar MM., et al., 2006
[18] Lange F., et al., 2019
[19] Lee TK., et al., 2014
[20] Legaree BA., et al., 2007
[21] Mueller EA., et al., 2019
[22] Navarro F., et al., 1998
[23] Pas E., et al., 2001
[24] Pradel N., et al., 2007
[25] Santini CL., et al., 2001
[26] Schneider D., et al., 2000
[27] Shiomi D., et al., 2013
[28] Signoretto C., et al., 1996
[29] Sougakoff W., et al., 2000
[30] Sougakoff W., et al., 2000
[31] Spratt BG., et al., 1980
[32] Uehara T., et al., 2002
[33] Uehara T., et al., 2008
[34] Varma A., et al., 2009
[35] Vinella D., et al., 2005
[36] Vinella D., et al., 2000
[37] Vinella D., et al., 1993
[38] Wientjes FB., et al., 1991
[39] Woods R., et al., 2006
[40] de Pedro MA., et al., 2001
External database links:  
ALPHAFOLD:
 P0AD65
DIP:
 DIP-48190N
ECOCYC:
 EG10606-MONOMER
ECOLIWIKI:
 b0635
INTERPRO:
 IPR012338
INTERPRO:
 IPR005311
INTERPRO:
 IPR001460
INTERPRO:
 IPR036138
INTERPRO:
 IPR017790
MODBASE:
 P0AD65
PDB:
 6G9F
PDB:
 6G9P
PDB:
 6G9S
PFAM:
 PF03717
PFAM:
 PF00905
PRIDE:
 P0AD65
PRODB:
 PRO_000023287
REFSEQ:
 NP_415168
SMR:
 P0AD65
UNIPROT:
 P0AD65


Operon      
Name: rsfS-rlmH-mrdAB-rlpA         
Operon arrangement:
Transcription unit        Promoter
rsfS-rlmH-mrdAB-rlpA


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 rlpAp7 665213 reverse nd [COMP-AINF] [41]
  promoter rlpAp5 665222 reverse nd [COMP-AINF] [41]
  promoter TSS_757 665332 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_758 665461 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_759 667132 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_760 668468 reverse nd [RS-EPT-CBR] [42]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Anderson JW., Adediran SA., Charlier P., Nguyen-Disteche M., Frere JM., Nicholas RA., Pratt RF., 2003, On the substrate specificity of bacterial DD-peptidases: evidence from two series of peptidoglycan-mimetic peptides., Biochem J 373(Pt 3):949-55

 [2] Asoh S., Matsuzawa H., Matsuhashi M., Ohta T., 1983, Molecular cloning and characterization of the genes (pbpA and rodA) responsible for the rod shape of Escherichia coli K-12: analysis of gene expression with transposon Tn5 mutagenesis and protein synthesis directed by constructed plasmids., J Bacteriol 154(1):10-6

 [3] Begg KJ., Donachie WD., 1985, Cell shape and division in Escherichia coli: experiments with shape and division mutants., J Bacteriol 163(2):615-22

 [4] Begg KJ., Takasuga A., Edwards DH., Dewar SJ., Spratt BG., Adachi H., Ohta T., Matsuzawa H., Donachie WD., 1990, The balance between different peptidoglycan precursors determines whether Escherichia coli cells will elongate or divide., J Bacteriol 172(12):6697-703

 [5] Bendezu FO., Hale CA., Bernhardt TG., de Boer PA., 2009, RodZ (YfgA) is required for proper assembly of the MreB actin cytoskeleton and cell shape in E. coli., EMBO J 28(3):193-204

 [6] Bendezu FO., de Boer PA., 2008, Conditional lethality, division defects, membrane involution, and endocytosis in mre and mrd shape mutants of Escherichia coli., J Bacteriol 190(5):1792-811

 [7] Buchnik D., Woldringh CL., Zaritsky A., 1987, Effects of temperature inactivation of penicillin-binding protein 2 on envelope growth in Escherichia coli., Ann Inst Pasteur Microbiol 138(5):537-47

 [8] Bylund JE., Haines MA., Walsh K., Bouloc P., D'Ari R., Higgins ML., 1991, Buoyant density studies of several mecillinam-resistant and division mutants of Escherichia coli., J Bacteriol 173(17):5396-402

 [9] Denome SA., Elf PK., Henderson TA., Nelson DE., Young KD., 1999, Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: viability, characteristics, and implications for peptidoglycan synthesis., J Bacteriol 181(13):3981-93

 [10] Garcia del Portillo F., de Pedro MA., 1991, Penicillin-binding protein 2 is essential for the integrity of growing cells of Escherichia coli ponB strains., J Bacteriol 173(14):4530-2

 [11] Georgopapadakou NH., Smith SA., Sykes RB., 1982, Mode of action of azthreonam., Antimicrob Agents Chemother 21(6):950-6

 [12] Ishiguro M., Nishihara T., Tanaka R., 2001, [New orally active penem antibiotic: Farom], Yakugaku Zasshi 121(12):915-27

 [13] Ishino F., Park W., Tomioka S., Tamaki S., Takase I., Kunugita K., Matsuzawa H., Asoh S., Ohta T., Spratt BG., 1986, Peptidoglycan synthetic activities in membranes of Escherichia coli caused by overproduction of penicillin-binding protein 2 and rodA protein., J Biol Chem 261(15):7024-31

 [14] Iwaya M., Jones CW., Khorana J., Strominger JL., 1978, Mapping of the mecillinam-resistant, round morphological mutants of Escherichia coli., J Bacteriol 133(1):196-202

 [15] Jamieson CE., Lambert PA., Simpson IN., 2003, In vitro and in vivo activities of AM-112, a novel oxapenem., Antimicrob Agents Chemother 47(5):1652-7

 [16] Karczmarek A., Martinez-Arteaga R., Baselga RM., Alexeeva S., Hansen FG., Vicente M., Nanninga N., den Blaauwen T., 2007, DNA and origin region segregation are not affected by the transition from rod to sphere after inhibition of Escherichia coli MreB by A22., Mol Microbiol 65(1):51-63

 [17] Khattar MM., Bazzi S., Kogan J., Talhouk RS., 2006, Bacterial cell shape-dependent inflammatory response in mammary epithelial cells., Curr Microbiol 52(6):424-9

 [18] Lange F., Pfennigwerth N., Hofken LM., Gatermann SG., Kaase M., 2019, Characterization of mutations in Escherichia coli PBP2 leading to increased carbapenem MICs., J Antimicrob Chemother 74(3):571-576

 [19] Lee TK., Tropini C., Hsin J., Desmarais SM., Ursell TS., Gong E., Gitai Z., Monds RD., Huang KC., 2014, A dynamically assembled cell wall synthesis machinery buffers cell growth., Proc Natl Acad Sci U S A 111(12):4554-9

 [20] Legaree BA., Adams CB., Clarke AJ., 2007, Overproduction of penicillin-binding protein 2 and its inactive variants causes morphological changes and lysis in Escherichia coli., J Bacteriol 189(14):4975-83

 [21] Mueller EA., Egan AJ., Breukink E., Vollmer W., Levin PA., 2019, Plasticity of Escherichia coli cell wall metabolism promotes fitness and antibiotic resistance across environmental conditions., Elife 8

 [22] Navarro F., Robin A., D'Ari R., Joseleau-Petit D., 1998, Analysis of the effect of ppGpp on the ftsQAZ operon in Escherichia coli., Mol Microbiol 29(3):815-23

 [23] Pas E., Einav M., Woldringh CL., Zaritsky A., 2001, Perpendicular planes of FtsZ arcs in spheroidal Escherichia coli cells., Biochimie 83(1):121-4

 [24] Pradel N., Santini CL., Bernadac A., Shih YL., Goldberg MB., Wu LF., 2007, Polar positional information in Escherichia coli spherical cells., Biochem Biophys Res Commun 353(2):493-500

 [25] Santini CL., Bernadac A., Zhang M., Chanal A., Ize B., Blanco C., Wu LF., 2001, Translocation of jellyfish green fluorescent protein via the Tat system of Escherichia coli and change of its periplasmic localization in response to osmotic up-shock., J Biol Chem 276(11):8159-64

 [26] Schneider D., Duperchy E., Coursange E., Lenski RE., Blot M., 2000, Long-term experimental evolution in Escherichia coli. IX. Characterization of insertion sequence-mediated mutations and rearrangements., Genetics 156(2):477-88

 [27] Shiomi D., Toyoda A., Aizu T., Ejima F., Fujiyama A., Shini T., Kohara Y., Niki H., 2013, Mutations in cell elongation genes mreB, mrdA and mrdB suppress the shape defect of RodZ-deficient cells., Mol Microbiol 87(5):1029-44

 [28] Signoretto C., Di Stefano F., Canepari P., 1996, Modified peptidoglycan chemical composition in shape-altered Escherichia coli., Microbiology 142 ( Pt 8):1919-26

 [29] Sougakoff W., Jarlier V., 2000, Comparative potency of mecillinam and other beta-lactam antibiotics against Escherichia coli strains producing different beta-lactamases., J Antimicrob Chemother 46 Suppl A:9-14

 [30] Sougakoff W., Jarlier V., 2000, Comparative potency of mecillinam and other beta-lactam antibiotics against Escherichia coli strains producing different beta-lactamases., J Antimicrob Chemother 46 Suppl 1:9-14: discussion 63-5

 [31] Spratt BG., Boyd A., Stoker N., 1980, Defective and plaque-forming lambda transducing bacteriophage carrying penicillin-binding protein-cell shape genes: genetic and physical mapping and identification of gene products from the lip-dacA-rodA-pbpA-leuS region of the Escherichia coli chromosome., J Bacteriol 143(2):569-81

 [32] Uehara T., Park JT., 2002, Role of the murein precursor UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-meso-diaminopimelic acid-D-Ala-D-Ala in repression of beta-lactamase induction in cell division mutants., J Bacteriol 184(15):4233-9

 [33] Uehara T., Park JT., 2008, Growth of Escherichia coli: significance of peptidoglycan degradation during elongation and septation., J Bacteriol 190(11):3914-22

 [34] Varma A., Young KD., 2009, In Escherichia coli, MreB and FtsZ direct the synthesis of lateral cell wall via independent pathways that require PBP 2., J Bacteriol 191(11):3526-33

 [35] Vinella D., Albrecht C., Cashel M., D'Ari R., 2005, Iron limitation induces SpoT-dependent accumulation of ppGpp in Escherichia coli., Mol Microbiol 56(4):958-70

 [36] Vinella D., Cashel M., D'Ari R., 2000, Selected amplification of the cell division genes ftsQ-ftsA-ftsZ in Escherichia coli., Genetics 156(4):1483-92

 [37] Vinella D., Joseleau-Petit D., Thevenet D., Bouloc P., D'Ari R., 1993, Penicillin-binding protein 2 inactivation in Escherichia coli results in cell division inhibition, which is relieved by FtsZ overexpression., J Bacteriol 175(20):6704-10

 [38] Wientjes FB., Nanninga N., 1991, On the role of the high molecular weight penicillin-binding proteins in the cell cycle of Escherichia coli., Res Microbiol 142(2-3):333-44

 [39] Woods R., Schneider D., Winkworth CL., Riley MA., Lenski RE., 2006, Tests of parallel molecular evolution in a long-term experiment with Escherichia coli., Proc Natl Acad Sci U S A 103(24):9107-12

 [40] de Pedro MA., Donachie WD., Holtje JV., Schwarz H., 2001, Constitutive septal murein synthesis in Escherichia coli with impaired activity of the morphogenetic proteins RodA and penicillin-binding protein 2., J Bacteriol 183(14):4115-26

 [41] 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

 [42] 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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