RegulonDB RegulonDB 11.0: Gene Form
   

rppH gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ptsP rppH ygdT rppHp rppHp TSS_3131 TSS_3131 TSS_3130 TSS_3130

Gene      
Name: rppH    Texpresso search in the literature
Synonym(s): ECK2826, G7459, b2830, nudH, ygdP
Genome position(nucleotides): 2968447 <-- 2968977
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.34
External database links:  
ASAP:
 ABE-0009276
ECHOBASE:
 EB2896
ECOLIHUB:
 rppH
OU-MICROARRAY:
 b2830
STRING:
 511145.b2830
COLOMBOS: rppH


Product      
Name: RNA pyrophosphohydrolase
Synonym(s): NudH, RppH, YgdP
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 20.795
Isoelectric point: 10.555
Motif(s):
 
Type Positions Sequence Comment
6 -> 149 GYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQAMYRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKWFLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMK UniProt: Nudix hydrolase.
7 -> 146 YRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQAMYRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKWFLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRR
38 -> 59 GGINPGESAEQAMYRELFEEVG UniProt: Nudix box; Sequence Annotation Type: short sequence motif.
53 -> 53 E UniProt: Loss of function..

 
Classification:
Multifun Terms (GenProtEC)  
  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:0110153 - RNA NAD-cap (NMN-forming) hydrolase activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0000287 - magnesium ion binding
GO:0034353 - RNA pyrophosphohydrolase activity
biological_process GO:0110155 - NAD-cap decapping
GO:0110154 - RNA decapping
GO:0006402 - mRNA catabolic process
GO:0008033 - tRNA processing
GO:0050779 - RNA destabilization
Note(s): Note(s): ...[more].
Reference(s): [1] Aguilar C., et al., 2015
[2] Almeida MV., et al., 2019
[3] Anupama K., et al., 2019
[4] Bessman MJ. 2019
[5] Bi Y., et al., 2009
[6] Carmona SB., et al., 2020
[7] Cetnar DP., et al., 2021
[8] Luciano DJ., et al., 2019
[9] Morigasaki S., et al., 2021
[10] Qi D., et al., 2015
External database links:  
ALPHAFOLD:
 P0A776
DIP:
 DIP-47855N
ECOCYC:
 G7459-MONOMER
ECOLIWIKI:
 b2830
INTERPRO:
 IPR000086
INTERPRO:
 IPR015797
INTERPRO:
 IPR020084
INTERPRO:
 IPR020476
INTERPRO:
 IPR022927
MODBASE:
 P0A776
PDB:
 6VCO
PDB:
 6VCP
PDB:
 6VCQ
PDB:
 6VCR
PDB:
 6VCN
PDB:
 6VCM
PDB:
 6VCK
PDB:
 5YGU
PDB:
 4S2Y
PDB:
 4S2X
PDB:
 4S2W
PDB:
 4S2V
PDB:
 2KDW
PDB:
 2KDV
PDB:
 6VCL
PFAM:
 PF00293
PRIDE:
 P0A776
PRINTS:
 PR00502
PRODB:
 PRO_000023853
PROSITE:
 PS00893
PROSITE:
 PS51462
REFSEQ:
 NP_417307
SMR:
 P0A776
UNIPROT:
 P0A776


Operon      
Name: rppH-ptsP         
Operon arrangement:
Transcription unit        Promoter
rppH-ptsP


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_3130 2967019 reverse nd [RS-EPT-CBR] [11]
  promoter TSS_3131 2967163 reverse nd [RS-EPT-CBR] [11]


Evidence    

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


Reference(s)    

 [1] Aguilar C., Flores N., Riveros-McKay F., Sahonero-Canavesi D., Carmona SB., Geiger O., Escalante A., Bolivar F., 2015, Deletion of the 2-acyl-glycerophosphoethanolamine cycle improve glucose metabolism in Escherichia coli strains employed for overproduction of aromatic compounds., Microb Cell Fact 14(1):194

 [2] Almeida MV., de Jesus Domingues AM., Lukas H., Mendez-Lago M., Ketting RF., 2019, RppH can faithfully replace TAP to allow cloning of 5'-triphosphate carrying small RNAs., MethodsX 6:265-272

 [3] Anupama K., Leela JK., Gowrishankar J., 2019, Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination., Mol Microbiol 112(4):1371

 [4] Bessman MJ., 2019, A cryptic activity in the Nudix hydrolase superfamily., Protein Sci 28(8):1494-1500

 [5] Bi Y., Li H., Fan S., Xia B., Jin C., 2009, 1H, 13C and 15N resonance assignments of RNA pyrophosphohydrolase RppH from Escherichia coli., Biomol NMR Assign 3(1):149-51

 [6] Carmona SB., Flores N., Martinez-Romero E., Gosset G., Bolivar F., Escalante A., 2020, Evolution of an Escherichia coli PTS- strain: a study of reproducibility and dynamics of an adaptive evolutive process., Appl Microbiol Biotechnol 104(21):9309-9325

 [7] Cetnar DP., Salis HM., 2021, Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons., ACS Synth Biol 10(2):318-332

 [8] Luciano DJ., Levenson-Palmer R., Belasco JG., 2019, Stresses that Raise Np4 A Levels Induce Protective Nucleoside Tetraphosphate Capping of Bacterial RNA., Mol Cell 75(5):957-966.e8

 [9] Morigasaki S., Umeyama A., Kawano Y., Aizawa Y., Ohtsu I., 2021, Defect of RNA pyrophosphohydrolase RppH enhances fermentative production of L-cysteine in Escherichia coli., J Gen Appl Microbiol 66(6):307-314

 [10] Qi D., Alawneh AM., Yonesaki T., Otsuka Y., 2015, Rapid Degradation of Host mRNAs by Stimulation of RNase E Activity by Srd of Bacteriophage T4., Genetics 201(3):977-87

 [11] 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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