RegulonDB RegulonDB 11.1: Gene Form
   

pnp gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pnp nlpI sraG SraG anti-terminator terminator pnpp pnpp TSS_3451 TSS_3451 sraGp sraGp TSS_3450 TSS_3450 TSS_3449 TSS_3449 TSS_3448 TSS_3448 TSS_3447 (cluster) TSS_3447 (cluster) TSS_3446 (cluster) TSS_3446 (cluster) TSS_3445 TSS_3445 TSS_3444 TSS_3444 TSS_3443 TSS_3443 TSS_3442 TSS_3442 TSS_3441 TSS_3441 TSS_3440 TSS_3440 TSS_3439 TSS_3439 nlpIp2 nlpIp2 TSS_3438 TSS_3438 yrbNp2 yrbNp2 TSS_3437 TSS_3437 TSS_3436 TSS_3436 yrbNp1 yrbNp1 TSS_3435 TSS_3435

Gene      
Name: pnp    Texpresso search in the literature
Synonym(s): ECK3152, EG10743, b3164, bfl
Genome position(nucleotides): 3309033 <-- 3311168
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.07
External database links:  
ASAP:
 ABE-0010397
CGSC:
 379
ECHOBASE:
 EB0736
ECOLIHUB:
 pnp
MIM:
 614932
MIM:
 614934
OU-MICROARRAY:
 b3164
STRING:
 511145.b3164
COLOMBOS: pnp


Product      
Name: polynucleotide phosphorylase
Synonym(s): Bfl, Pnp
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,membrane
Molecular weight: 77.101
Isoelectric point: 4.851
Motif(s):
 
Type Positions Sequence Comment
16 -> 144 VTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIP
77 -> 80 FFRR UniProt: FFRR loop; important for RNA binding; Sequence Annotation Type: region of interest.
79 -> 80 RR UniProt: Strongly reduces RNA binding. Reduces RNA degradation..
83 -> 83 R UniProt: No effect on RNA-binding. No effect on degradation of long RNA molecules. Impairs degradation of short RNA molecules..
100 -> 100 R UniProt: Abolishes enzyme activity..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.1 - RNA
  2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
Gene Ontology Terms (GO)  
cellular_component GO:1990061 - bacterial degradosome
GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane
molecular_function GO:0003676 - nucleic acid binding
GO:0016779 - nucleotidyltransferase activity
GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0000175 - 3'-5'-exoribonuclease activity
GO:0003723 - RNA binding
GO:0004654 - polyribonucleotide nucleotidyltransferase activity
GO:0000287 - magnesium ion binding
GO:0042802 - identical protein binding
GO:0035438 - cyclic-di-GMP binding
biological_process GO:0006401 - RNA catabolic process
GO:0009408 - response to heat
GO:0006402 - mRNA catabolic process
GO:0006396 - RNA processing
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic
Reference(s): [1] McBroom AJ., et al., 2006
External database links:  
ALPHAFOLD:
 P05055
DIP:
 DIP-10522N
ECOCYC:
 EG10743-MONOMER
ECOLIWIKI:
 b3164
INTERPRO:
 IPR004087
INTERPRO:
 IPR036612
INTERPRO:
 IPR036456
INTERPRO:
 IPR036345
INTERPRO:
 IPR027408
INTERPRO:
 IPR022967
INTERPRO:
 IPR020568
INTERPRO:
 IPR015848
INTERPRO:
 IPR001247
INTERPRO:
 IPR003029
INTERPRO:
 IPR004088
INTERPRO:
 IPR012162
INTERPRO:
 IPR015847
INTERPRO:
 IPR012340
MINT:
 P05055
MODBASE:
 P05055
PANTHER:
 PTHR11252
PDB:
 3H1C
PDB:
 3GME
PDB:
 3GLL
PDB:
 3GCM
PDB:
 3CDJ
PDB:
 1SRO
PDB:
 3CDI
PFAM:
 PF00575
PFAM:
 PF01138
PFAM:
 PF03725
PFAM:
 PF00013
PFAM:
 PF03726
PRIDE:
 P05055
PRODB:
 PRO_000023561
PROSITE:
 PS50126
PROSITE:
 PS50084
REFSEQ:
 NP_417633
SMART:
 SM00316
SMART:
 SM00322
SMR:
 P05055
UNIPROT:
 P05055


Operon      
Name: metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp         
Operon arrangement:
Transcription unit        Promoter
pnp
rpsO
rpsO-pnp
infB
nusA-infB
rimP-nusA-infB
metY
metY-yhbC-nusA-infB
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp
metY
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp


Transcriptional Regulation      
Display Regulation             
Activated by: Fis
Repressed by: CRP, ArgR


RNA cis-regulatory element    
Attenuation: Transcriptional


Regulation by small RNA    
  Display Regulation
small RNA sraG


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_3435 3308055 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3436 3308214 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3437 3308694 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3438 3308871 reverse nd [RS-EPT-CBR] [2]
  promoter nlpIp2 3309040 reverse nd [COMP-AINF] [3]
  promoter TSS_3439 3309284 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3440 3309502 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3441 3309519 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3442 3309525 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3443 3309527 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3444 3309617 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3445 3310026 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3446 (cluster) 3310204 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3447 (cluster) 3310283 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3448 3310380 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3449 3310391 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3450 3310952 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3451 3311249 reverse nd [RS-EPT-CBR] [2]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] McBroom AJ., Johnson AP., Vemulapalli S., Kuehn MJ., 2006, Outer membrane vesicle production by Escherichia coli is independent of membrane instability., J Bacteriol 188(15):5385-92

 [2] 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.

 [3] 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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