RegulonDB RegulonDB 10.8: Gene Form
   

pnp gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pnp nlpI 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 TSS_3437 TSS_3437 TSS_3436 TSS_3436 yrbNp yrbNp TSS_3435 TSS_3435

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


Product      
Name: polynucleotide phosphorylase
Synonym(s): Bfl, Pnp
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 77.101
Isoelectric point: 4.851
Motif(s):
 
Type Positions Sequence
77 -> 80 FFRR
450 -> 450 L
16 -> 144 VTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIP
241 -> 320 ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLAEDETLDENELGEILHAIEKNVVRSRVLAGEPRIDGRE
319 -> 319 R

 

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:0005737 - cytoplasm
GO:0005829 - cytosol
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:  
DIP:
DIP-10522N
ECOCYC:
EG10743-MONOMER
ECOLIWIKI:
b3164
INTERPRO:
IPR001247
INTERPRO:
IPR036612
INTERPRO:
IPR036456
INTERPRO:
IPR036345
INTERPRO:
IPR027408
INTERPRO:
IPR022967
INTERPRO:
IPR020568
INTERPRO:
IPR015848
INTERPRO:
IPR015847
INTERPRO:
IPR012340
INTERPRO:
IPR012162
INTERPRO:
IPR004088
INTERPRO:
IPR004087
INTERPRO:
IPR003029
MINT:
P05055
MODBASE:
P05055
PANTHER:
PTHR11252
PDB:
3GLL
PDB:
1SRO
PDB:
3CDI
PDB:
3CDJ
PDB:
3GCM
PDB:
3H1C
PDB:
3GME
PFAM:
PF03726
PFAM:
PF01138
PFAM:
PF00013
PFAM:
PF00575
PFAM:
PF03725
PRIDE:
P05055
PRODB:
PRO_000023561
PROSITE:
PS50084
PROSITE:
PS50126
REFSEQ:
NP_417633
SMART:
SM00322
SMART:
SM00316
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


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 Similarity to the consensus
Read more >
[ICWHO] [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 For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_3447 (cluster) 3310283 reverse For this promoter, there
Read more >
[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

 [ICWHO] 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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