RegulonDB RegulonDB 10.8: Gene Form
   

murD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

murD ftsW mraY murG murF TSS_172 TSS_172 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

Gene      
Name: murD    Texpresso search in the literature
Synonym(s): ECK0089, EG10620, b0088
Genome position(nucleotides): 97087 --> 98403 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.9
External database links:  
ASAP:
 ABE-0000318
CGSC:
 30450
ECHOBASE:
 EB0615
OU-MICROARRAY:
 b0088
PortEco:
 murD
STRING:
 511145.b0088
COLOMBOS: murD


Product      
Name: UDP-N-acetylmuramoyl-L-alanine—D-glutamate ligase
Synonym(s): MurD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 46.974
Isoelectric point: 4.965
Motif(s):
 
Type Positions Sequence
112 -> 118 GSNGKST
174 -> 174 A
28 -> 28 R
2 -> 438 ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELG
110 -> 280 ITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALA

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.7 - murein (peptidoglycan)
  6 - cell structure --> 6.2 - murein
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0016874 - ligase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0008764 - UDP-N-acetylmuramoylalanine-D-glutamate ligase activity
GO:0042802 - identical protein binding
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].
External database links:  
DIP:
 DIP-10279N
ECOCYC:
 UDP-NACMURALA-GLU-LIG-MONOMER
ECOLIWIKI:
 b0088
INTERPRO:
 IPR005762
INTERPRO:
 IPR004101
INTERPRO:
 IPR013221
INTERPRO:
 IPR036615
INTERPRO:
 IPR036565
MINT:
 MINT-1269366
MODBASE:
 P14900
PANTHER:
 PTHR23135:SF2
PDB:
 2UUP
PDB:
 2VTD
PDB:
 2VTE
PDB:
 2WJP
PDB:
 2X5O
PDB:
 2XPC
PDB:
 2Y1O
PDB:
 2Y67
PDB:
 2Y68
PDB:
 3UAG
PDB:
 4UAG
PDB:
 5A5E
PDB:
 5A5F
PDB:
 2UUO
PDB:
 2UAG
PDB:
 2JFH
PDB:
 2JFG
PDB:
 2JFF
PDB:
 1UAG
PDB:
 1EEH
PDB:
 1E0D
PDB:
 2Y66
PFAM:
 PF02875
PFAM:
 PF08245
PRIDE:
 P14900
PRODB:
 PRO_000023315
REFSEQ:
 NP_414630
SMR:
 P14900
UNIPROT:
 P14900


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
mraW-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
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_162 96153 forward nd [RS-EPT-CBR] [1]
  promoter TSS_163 (cluster) 96971 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [1]
  promoter TSS_164 96982 forward nd [RS-EPT-CBR] [1]
  promoter TSS_165 96984 forward nd [RS-EPT-CBR] [1]
  promoter TSS_166 96988 forward nd [RS-EPT-CBR] [1]
  promoter TSS_167 96993 forward nd [RS-EPT-CBR] [1]
  promoter TSS_168 96997 forward nd [RS-EPT-CBR] [1]
  promoter TSS_169 97532 forward nd [RS-EPT-CBR] [1]
  promoter TSS_170 97539 forward nd [RS-EPT-CBR] [1]
  promoter TSS_171 97550 forward nd [RS-EPT-CBR] [1]
  promoter TSS_172 100621 forward nd [RS-EPT-CBR] [1]


Evidence    

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


Reference(s)    

 [1] 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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