RegulonDB RegulonDB 10.6.3: Gene Form
   

nrdA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nrdA nrdB ypaB NrdR NrdR DnaA DnaA DnaA Fis CRP Fis ArgP terminator anti-anti-terminator anti-terminator yfaEp1 yfaEp1 yfaEp2 yfaEp2 TSS_2515 TSS_2515 TSS_2514 TSS_2514 TSS_2513 TSS_2513 TSS_2512 TSS_2512 TSS_2511 TSS_2511 TSS_2510 TSS_2510 TSS_2509 TSS_2509 nrdAp nrdAp

Gene      
Name: nrdA    Texpresso search in the literature
Synonym(s): ECK2226, EG10660, b2234, dnaF
Genome position(nucleotides): 2344865 --> 2347150 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.67
External database links:  
ASAP:
ABE-0007383
CGSC:
445
ECHOBASE:
EB0654
ECOCYC:
EG10660
ECOLIHUB:
nrdA
OU-MICROARRAY:
b2234
REGULONDB:
b2234
STRING:
511145.b2234
M3D: nrdA
COLOMBOS: nrdA
PortEco: b2234


Shine dalgarno      
Sequence: aattccaaaaACAGGTacgacatacATG


Product      
Name: ribonucleoside-diphosphate reductase 1 subunit α
Synonym(s): DnaF, NrdA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 85.775
Isoelectric point: 6.097
Motif(s):
 
Type Positions Sequence
223 -> 659 SSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDY
731 -> 731 Y
441 -> 441 E
621 -> 625 PSETS
662 -> 731 LHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYY

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.33 - nucleotide and nucleoside conversions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0005971 - ribonucleoside-diphosphate reductase complex
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0016491 - oxidoreductase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0042802 - identical protein binding
GO:0042803 - protein homodimerization activity
biological_process GO:0008152 - metabolic process
GO:0006260 - DNA replication
GO:0009263 - deoxyribonucleotide biosynthetic process
GO:0015949 - nucleobase-containing small molecule interconversion
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-584N
ECOCYC:
NRDA-MONOMER
ECOLIWIKI:
b2234
INTERPRO:
IPR000788
INTERPRO:
IPR013346
INTERPRO:
IPR008926
INTERPRO:
IPR039718
INTERPRO:
IPR013509
INTERPRO:
IPR005144
MINT:
MINT-1233906
MODBASE:
P00452
PANTHER:
PTHR11573
PDB:
5R1R
PDB:
6R1R
PDB:
5CNT
PDB:
7R1R
PDB:
5CNS
PDB:
4R1R
PDB:
5CNV
PDB:
5CNU
PDB:
1QFN
PDB:
1R1R
PDB:
1RLR
PDB:
2R1R
PDB:
2X0X
PDB:
2XAK
PDB:
2XAP
PDB:
2XAV
PDB:
2XAW
PDB:
2XAX
PDB:
2XAY
PDB:
2XAZ
PDB:
2XO4
PDB:
2XO5
PDB:
3R1R
PDB:
3UUS
PDB:
4ERM
PDB:
4ERP
PFAM:
PF03477
PFAM:
PF02867
PFAM:
PF00317
PRIDE:
P00452
PRINTS:
PR01183
PRODB:
PRO_000023402
PROSITE:
PS00089
PROSITE:
PS51161
PROTEINMODELPORTAL:
P00452
REFSEQ:
NP_416737
SMR:
P00452
UNIPROT:
P00452


Operon      
Name: nrdAB-yfaE         
Operon arrangement:
Transcription unit        Promoter
nrdAB-yfaE
yfaE


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, DnaA, ArgP, Fis
Repressed by: H-NS, DnaA, NrdR


RNA cis-regulatory element    
Attenuation: Transcriptional


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_2509 2344861 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2510 2344875 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2511 2345253 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2512 2345987 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2513 2346007 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2514 2347352 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2515 2347642 forward nd [RS-EPT-CBR] [1]
  promoter yfaEp2 2348338 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yfaEp1 2348341 forward Similarity to the consensus
Read more >
[ICWHO] [2]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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.

 [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


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