RegulonDB RegulonDB 11.2: Gene Form
   

murF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

murE murF murD mraY ftsI ftsO TSS_171 TSS_171 TSS_170 TSS_170 TSS_169 TSS_169 TSS_168 TSS_168 TSS_167 TSS_167 TSS_166 TSS_166 TSS_165 TSS_165 TSS_164 TSS_164 TSS_163 (cluster) TSS_163 (cluster) TSS_162 TSS_162 TSS_161 (cluster) TSS_161 (cluster) TSS_160 TSS_160 TSS_159 TSS_159

Gene      
Name: murF    Texpresso search in the literature
Synonym(s): ECK0087, EG10622, b0086, mra
Genome position(nucleotides): 94650 --> 96008
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.11
External database links:  
ASAP:
 ABE-0000313
CGSC:
 474
ECHOBASE:
 EB0617
ECOLIHUB:
 murF
OU-MICROARRAY:
 b0086
STRING:
 511145.b0086
COLOMBOS: murF


Product      
Name: D-alanyl-D-alanine-adding enzyme
Synonym(s): Mra, MurF
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 47.447
Isoelectric point: 5.105
Motif(s):
 
Type Positions Sequence Comment
26 -> 79 AVTTDTRKLTPGCLFVALKGERFDAHDFADQAKAGGAGALLVSRPLDIDLPQLI
61 -> 61 G UniProt: In Ref. 1 and 3..
106 -> 292 TGSSGKTSVKEMTAAILSQCGNTLYTAGNLNNDIGVPMTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEAALVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMNADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATNIHVTSHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAAL
107 -> 113 GSSGKTS UniProt: ATP.
178 -> 178 A UniProt: In Ref. 1 and 3..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.7 - murein (peptidoglycan)
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.34 - murein turnover, recycling
  5 - cell processes --> 5.1 - cell division
  6 - cell structure --> 6.2 - murein
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0016874 - ligase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0047480 - UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity
GO:0008766 - UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity
biological_process GO:0051301 - cell division
GO:0007049 - cell cycle
GO:0009058 - biosynthetic process
GO:0009252 - peptidoglycan biosynthetic process
GO:0008360 - regulation of cell shape
GO:0071555 - cell wall organization
Note(s): Note(s): ...[more].
Reference(s): [1] Kuru E., et al., 2019
[2] Maruyama IN., et al., 1988
[3] Miyakawa T., et al., 1972
[4] Murakami R., et al., 2009
[5] Schouten JA., et al., 2006
External database links:  
ALPHAFOLD:
 P11880
DIP:
 DIP-10281N
ECOCYC:
 UDP-NACMURALGLDAPAALIG-MONOMER
ECOLIWIKI:
 b0086
INTERPRO:
 IPR036615
INTERPRO:
 IPR013221
INTERPRO:
 IPR005863
INTERPRO:
 IPR004101
INTERPRO:
 IPR036565
INTERPRO:
 IPR035911
INTERPRO:
 IPR000713
MODBASE:
 P11880
PDB:
 1GG4
PFAM:
 PF08245
PFAM:
 PF02875
PFAM:
 PF01225
PRIDE:
 P11880
PRODB:
 PRO_000023317
REFSEQ:
 NP_414628
SMR:
 P11880
UNIPROT:
 P11880


Operon      
Name: mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC         
Operon arrangement:
Transcription unit        Promoter
mraZW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
ftsQ
ftsQAZ
ftsQAZ
ftsAZ
ftsZ
ftsZ
ftsZ
lpxC
lpxC


Transcriptional Regulation      
Display Regulation             
Repressed by: MraZ, LexA, PdhR


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 TSS_159 92485 forward nd [RS-EPT-CBR] [6]
  promoter TSS_160 94608 forward nd [RS-EPT-CBR] [6]
  promoter TSS_161 (cluster) 94681 forward nd [RS-EPT-CBR] [6]
  promoter TSS_162 96153 forward nd [RS-EPT-CBR] [6]
  promoter TSS_163 (cluster) 96971 forward nd [RS-EPT-CBR] [6]
  promoter TSS_164 96982 forward nd [RS-EPT-CBR] [6]
  promoter TSS_165 96984 forward nd [RS-EPT-CBR] [6]
  promoter TSS_166 96988 forward nd [RS-EPT-CBR] [6]
  promoter TSS_167 96993 forward nd [RS-EPT-CBR] [6]
  promoter TSS_168 96997 forward nd [RS-EPT-CBR] [6]
  promoter TSS_169 97532 forward nd [RS-EPT-CBR] [6]
  promoter TSS_170 97539 forward nd [RS-EPT-CBR] [6]
  promoter TSS_171 97550 forward nd [RS-EPT-CBR] [6]


Evidence    

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


Reference(s)    

 [1] Kuru E., Radkov A., Meng X., Egan A., Alvarez L., Dowson A., Booher G., Breukink E., Roper DI., Cava F., Vollmer W., Brun Y., VanNieuwenhze MS., 2019, Mechanisms of Incorporation for D-Amino Acid Probes That Target Peptidoglycan Biosynthesis., ACS Chem Biol 14(12):2745-2756

 [2] Maruyama IN., Yamamoto AH., Hirota Y., 1988, Determination of gene products and coding regions from the murE-murF region of Escherichia coli., J Bacteriol 170(8):3786-8

 [3] Miyakawa T., Matsuzawa H., Matsuhashi M., Sugino Y., 1972, Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis., J Bacteriol 112(2):950-8

 [4] Murakami R., Muramatsu Y., Minami E., Masuda K., Sakaida Y., Endo S., Suzuki T., Ishida O., Takatsu T., Miyakoshi S., Inukai M., Isono F., 2009, A novel assay of bacterial peptidoglycan synthesis for natural product screening., J Antibiot (Tokyo) 62(3):153-8

 [5] Schouten JA., Bagga S., Lloyd AJ., de Pascale G., Dowson CG., Roper DI., Bugg TD., 2006, Fluorescent reagents for in vitro studies of lipid-linked steps of bacterial peptidoglycan biosynthesis: derivatives of UDPMurNAc-pentapeptide containing d-cysteine at position 4 or 5., Mol Biosyst 2(10):484-91

 [6] 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.

RegulonDB