RegulonDB RegulonDB 11.1: Gene Form
   

pyrD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pyrD ycbF zapC ycbV ycbX Fis PurR Cis-reg; leader terminator anti-terminator ycbWp4 ycbWp4 TSS_1247 (cluster) TSS_1247 (cluster) ycbWp6 ycbWp6 pyrDp pyrDp

Gene      
Name: pyrD    Texpresso search in the literature
Synonym(s): ECK0936, EG10807, b0945
Genome position(nucleotides): 1004768 --> 1005778
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 46.98
External database links:  
ASAP:
 ABE-0003201
CGSC:
 328
ECHOBASE:
 EB0800
ECOLIHUB:
 pyrD
MIM:
 263750
OU-MICROARRAY:
 b0945
STRING:
 511145.b0945
COLOMBOS: pyrD


Product      
Name: dihydroorotate dehydrogenase, type 2
Synonym(s): PyrD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,inner membrane
Molecular weight: 36.775
Isoelectric point: 7.966
Motif(s):
 
Type Positions Sequence Comment
47 -> 335 VNCMGLTFKNPLGLAAGLDKDGECIDALGAMGFGSIEIGTVTPRPQPGNDKPRLFRLVDAEGLINRMGFNNLGVDNLVENVKKAHYDGVLGINIGKNKDTPVEQGKDDYLICMEKIYAYAGYIAINISSPNTPGLRTLQYGEALDDLLTAIKNKQNDLQAMHHKYVPIAVKIAPDLSEEELIQVADSLVRHNIDGVIATNTTLDRSLVQGMKNCDQTGGLSGRPLQLKSTEIIRRLSLELNGRLPIIGVGGIDSVIAAREKIAAGASLVQIYSGFIFKGPPLIKEIVTH
62 -> 66 AGLDK UniProt: FMN.
111 -> 115 NRMGF UniProt: Substrate binding; Sequence Annotation Type: region of interest.
175 -> 175 S UniProt: Almost no activity..
246 -> 247 NT UniProt: Substrate binding; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.2 - nucleotides --> 1.5.2.2 - pyrimidine biosynthesis
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane
GO:0005886 - plasma membrane
molecular_function GO:0003824 - catalytic activity
GO:0016491 - oxidoreductase activity
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors
GO:0010181 - FMN binding
GO:0004152 - dihydroorotate dehydrogenase activity
biological_process GO:0006221 - pyrimidine nucleotide biosynthetic process
GO:0009220 - pyrimidine ribonucleotide biosynthetic process
GO:0006207 - 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006222 - UMP biosynthetic process
GO:0044205 - 'de novo' UMP biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] Smyth CJ., et al., 1978
External database links:  
ALPHAFOLD:
 P0A7E1
DIP:
 DIP-35945N
ECOCYC:
 DIHYDROOROTOX-MONOMER
ECOLIWIKI:
 b0945
INTERPRO:
 IPR012135
INTERPRO:
 IPR013785
INTERPRO:
 IPR005720
INTERPRO:
 IPR005719
INTERPRO:
 IPR001295
MODBASE:
 P0A7E1
PDB:
 1F76
PFAM:
 PF01180
PRIDE:
 P0A7E1
PRODB:
 PRO_000023659
PROSITE:
 PS00912
PROSITE:
 PS00911
REFSEQ:
 NP_415465
SMR:
 P0A7E1
UNIPROT:
 P0A7E1


Operon      
Name: pyrD         
Operon arrangement:
Transcription unit        Promoter
pyrD


Transcriptional Regulation      
Display Regulation             
Repressed by: PurR, Fis


RNA cis-regulatory element    
   
Cis-reg; leader PyrD leader
   
   


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 ycbWp6 1005850 forward nd [COMP-AINF] [2]
  promoter TSS_1247 (cluster) 1005852 forward nd [RS-EPT-CBR] [3]
  promoter ycbWp4 1005890 forward nd [COMP-AINF] [2]


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] Smyth CJ., Siegel J., Salton MR., Owen P., 1978, Immunochemical analysis of inner and outer membranes of Escherichia coli by crossed immunoelectrophoresis., J Bacteriol 133(1):306-19

 [2] 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

 [3] 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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