RegulonDB RegulonDB 11.1: Gene Form
   

dsdA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

emrY dsdX dsdA TSS_2664 TSS_2664 dsdAp dsdAp TSS_2663 TSS_2663

Gene      
Name: dsdA    Texpresso search in the literature
Synonym(s): ECK2362, EG10249, b2366
Genome position(nucleotides): 2479202 --> 2480530
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.87
External database links:  
ASAP:
 ABE-0007804
CGSC:
 834
ECHOBASE:
 EB0245
ECOLIHUB:
 dsdA
OU-MICROARRAY:
 b2366
STRING:
 511145.b2366
COLOMBOS: dsdA


Product      
Name: D-serine ammonia-lyase
Synonym(s): DsdA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 47.901
Isoelectric point: 5.766
Motif(s):
 
Type Positions Sequence Comment
34 -> 34 S UniProt: In Ref. 5; AA sequence..
73 -> 404 TGGIIESELVAIPAMQKRLEKEYQQPISGQLLLKKDSHLPISGSIKARGGIYEVLAHAEKLALEAGLLTLDDDYSKLLSPEFKQFFSQYSIAVGSTGNLGLSIGIMSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKAQFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQISVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGFYTLSDQTMYDMLGWLAQEEGIRLEPSALAGMAGPQRVCASVSYQ
85 -> 85 P UniProt: In Ref. 1; AAA87975..
204 -> 204 S UniProt: In Ref. 1; AAA87975..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.3 - amino acids
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0016829 - lyase activity
GO:0016836 - hydro-lyase activity
GO:0030170 - pyridoxal phosphate binding
GO:0003941 - L-serine ammonia-lyase activity
GO:0004794 - L-threonine ammonia-lyase activity
GO:0008721 - D-serine ammonia-lyase activity
biological_process GO:0006520 - cellular amino acid metabolic process
GO:0006974 - cellular response to DNA damage stimulus
GO:0006565 - L-serine catabolic process
GO:0006567 - threonine catabolic process
GO:0046416 - D-amino acid metabolic process
GO:0070178 - D-serine metabolic process
GO:0036088 - D-serine catabolic process
GO:0051410 - detoxification of nitrogen compound
Note(s): Note(s): ...[more].
Reference(s): [1] Carothers AM., et al., 1980
[2] Federiuk CS., et al., 1981
[3] Heincz MC., et al., 1975
[4] Heincz MC., et al., 1976
[5] McFall E. 1975
[6] McFall E. 1967
[7] McFall E., et al., 1970
[8] McFall E., et al., 1983
[9] Metzler CM., et al., 1991
[10] Schiltz E., et al., 1981
[11] Schnackerz KD., et al., 1980
[12] Schonbeck ND., et al., 1975
External database links:  
ALPHAFOLD:
 P00926
ECOCYC:
 DSERDEAM-MONOMER
ECOLIWIKI:
 b2366
INTERPRO:
 IPR011780
INTERPRO:
 IPR036052
INTERPRO:
 IPR001926
INTERPRO:
 IPR000634
MODBASE:
 P00926
PANTHER:
 PTHR48078:SF9
PDB:
 3SS7
PDB:
 3SS9
PFAM:
 PF00291
PRIDE:
 P00926
PRODB:
 PRO_000022485
PROSITE:
 PS00165
REFSEQ:
 NP_416867
SMR:
 P00926
UNIPROT:
 P00926


Operon      
Name: dsdXA         
Operon arrangement:
Transcription unit        Promoter
dsdXA
dsdA


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, DsdC


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_2663 2479114 forward nd [RS-EPT-CBR] [13]
  promoter TSS_2664 2480013 forward nd [RS-EPT-CBR] [13]


Evidence    

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


Reference(s)    

 [1] Carothers AM., McFall E., Palchaudhuri S., 1980, Physical mapping of the Escherichia coli D-serine deaminase region: contiguity of the dsd structural and regulatory genes., J Bacteriol 142(1):174-84

 [2] Federiuk CS., Shafer JA., 1981, Inactivation of D-serine dehydratase by alkylamines via a transimination of enzyme-linked cofactor., J Biol Chem 256(14):7416-23

 [3] Heincz MC., McFall E., 1975, N-terminal amino acid sequences of D-serine deaminases of wild-type and operator-constitutive strains of Escherichia coli K-12., J Bacteriol 123(3):1163-8

 [4] Heincz MC., McFall E., 1976, Specific in vivo cleavage of D-serine deaminase and properties of tetrameric polypeptide aggregates of the fragments., J Bacteriol 126(1):132-9

 [5] McFall E., 1975, Escherichia coli K-12 mutant forming a temperature-sensitive D-serine deaminase., J Bacteriol 121(3):1074-7

 [6] McFall E., 1967, Mapping of the d-serine deaminase region in Escherichia coli K-12., Genetics 55(1):91-9

 [7] McFall E., Heincz MC., 1970, Thermosensitive regulation of D-serine deaminase synthesis in a mutant of Escherichia coli K 12., Mol Gen Genet 106(4):371-7

 [8] McFall E., Runkel L., 1983, DNA sequences of the D-serine deaminase control region and N-terminal portion of the structural gene., J Bacteriol 154(3):1508-12

 [9] Metzler CM., Metzler DE., Kintanar A., Scott RD., Marceau M., 1991, NMR spectra of exchangeable protons of pyridoxal phosphate-dependent enzymes., Biochem Biophys Res Commun 178(1):385-92

 [10] Schiltz E., Schmitt W., 1981, Sequence of Escherichia coli D-serine dehydratase. Location of the pyridoxal-phosphate binding site., FEBS Lett 134(1):57-62

 [11] Schnackerz KD., Feldmann K., 1980, Pyridoxal-5'-deoxymethylenephosphonate reconstituted D-serine dehydratase: a phosphorus-31 nuclear magnetic resonance study., Biochem Biophys Res Commun 95(4):1832-8

 [12] Schonbeck ND., Skalski M., Shafer JA., 1975, Resolution of D-serine dehydratase by cysteine. An analytical treatment., J Biol Chem 250(14):5352-8

 [13] 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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