RegulonDB RegulonDB 10.8: Gene Form
   

dapB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

carA rihC dapB nc9 ArgR ArgR Fis PepA Fis PurR Fis PepA RutR IHF ArgP ArgP carBp carBp carAp2 carAp2 carAp1 carAp1 dapBp1 dapBp1 TSS_75 TSS_75 dapBp2 dapBp2

Gene      
Name: dapB    Texpresso search in the literature
Synonym(s): ECK0032, EG10206, b0031
Genome position(nucleotides): 28374 --> 29195 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.41
External database links:  
ASAP:
ABE-0000112
CGSC:
879
ECHOBASE:
EB0202
OU-MICROARRAY:
b0031
PortEco:
dapB
STRING:
511145.b0031
COLOMBOS: dapB


Product      
Name: 4-hydroxy-tetrahydrodipicolinate reductase
Synonym(s): DHPR, DapB, dihydrodipicolinate reductase
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 28.757
Isoelectric point: 5.55
Motif(s):
 
Type Positions Sequence
126 -> 129 AANF
12 -> 17 GAGGRM
132 -> 268 GVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDLKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFANGAVRSALWLSGKESGLFDMRDVL
169 -> 170 GT
6 -> 129 IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFAANF

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.1 - amino acids --> 1.5.1.7 - lysine
  6 - cell structure --> 6.2 - murein
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0016491 - oxidoreductase activity
GO:0016726 - oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
GO:0008839 - 4-hydroxy-tetrahydrodipicolinate reductase
GO:0042802 - identical protein binding
GO:0050661 - NADP binding
GO:0051287 - NAD binding
biological_process GO:0008652 - cellular amino acid biosynthetic process
GO:0009085 - lysine biosynthetic process
GO:0009089 - lysine biosynthetic process via diaminopimelate
GO:0019877 - diaminopimelate biosynthetic process
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
Reference(s): [1] Boy E., et al., 1976
[2] Ge X., et al., 2007
[3] Mackie GA. 1980
[4] Maringanti S., et al., 1999
[5] Patte JC., et al., 1980
[6] Trigoso YD., et al., 2016
External database links:  
DIP:
DIP-9399N
ECOCYC:
DIHYDROPICRED-MONOMER
ECOLIWIKI:
b0031
INTERPRO:
IPR036291
INTERPRO:
IPR023940
INTERPRO:
IPR022664
INTERPRO:
IPR022663
INTERPRO:
IPR000846
MODBASE:
P04036
PANTHER:
PTHR20836
PDB:
1DRW
PDB:
1DRV
PDB:
1DRU
PDB:
1DIH
PDB:
1ARZ
PFAM:
PF05173
PFAM:
PF01113
PRIDE:
P04036
PRODB:
PRO_000022401
PROSITE:
PS01298
REFSEQ:
NP_414572
SMR:
P04036
UNIPROT:
P04036


Operon      
Name: dapB         
Operon arrangement:
Transcription unit        Promoter
dapB
dapB


Transcriptional Regulation      
Display Regulation             
Activated by: ArgP


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_75 28293 forward nd [RS-EPT-CBR] [7]


Evidence    

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



Reference(s)    

 [1] Boy E., Reinisch F., Richaud C., Patte JC., 1976, Role of lysyl-tRNA in the regulation of lysine biosynthesis in Escherichia coli K12., Biochimie 58(1-2):213-8

 [2] Ge X., Sem DS., 2007, Affinity-based chemical proteomic probe for dehydrogenases: fluorescence and visible binding assays in gels., Anal Biochem 370(2):171-9

 [3] Mackie GA., 1980, Cloning of fragments of lambda dapB2 DNA and identification of the dapB gene product., J Biol Chem 255(18):8928-35

 [4] Maringanti S., Imlay JA., 1999, An intracellular iron chelator pleiotropically suppresses enzymatic and growth defects of superoxide dismutase-deficient Escherichia coli., J Bacteriol 181(12):3792-802

 [5] Patte JC., Morand P., Boy E., Richaud C., Borne F., 1980, The relA locus and the regulation of lysine biosynthesis in Escherichia coli., Mol Gen Genet 179(2):319-25

 [6] Trigoso YD., Evans RC., Karsten WE., Chooback L., 2016, Cloning, Expression, and Purification of Histidine-Tagged Escherichia coli Dihydrodipicolinate Reductase., PLoS One 11(1):e0146525

 [7] 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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