rppH:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

RppH [1]

Synonyms

NudH,nucleotide hydrolase[2], B2830[3][2], NudH[3][2], YgdP[3][2], ECK2826, JW2798, nudH, ygdP, b2830

Product description

RNA pyrophosphohydrolase (removes the 5'-pyrophosphate from mRNAs and initiates degradation by the 5'-end dependent pathway)[1]; putative invasion protein[3][4] RNA pyrophosphohydrolase, destabilizes primary transcripts[5]

EC number (for enzymes)

3.6.1.-[2]

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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0016818

hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides

PMID:18202662[1]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [2].

Missing: evidence, reference

GO:0050779

RNA destabilization

PMID:18202662[1]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0034353

RNA pyrophosphohydrolase activity

PMID:18202662[1]

IDA: Inferred from Direct Assay

F

Fig. 2

complete

GO:0016818

hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides

PMID:18202662[1]

IDA: Inferred from Direct Assay

F

Fig. 1 and 2.

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

yajQ

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

ycbY

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

rluC

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

dapF

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

deaD

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

rplA

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rplB

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rplC

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rplD

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rplE

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

rplF

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rplI

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rplJ

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

rplM

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rplN

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

rplO

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rplR

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rplS

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rplV

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rpsA

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rpsB

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rpsD

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

rpsE

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rpsG

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rpsM

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

spoT

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

srmB

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

rnr

PMID:15690043[6]

Experiment(s):EBI-885881

Protein

yfiF

PMID:15690043[6]

Experiment(s):EBI-885881, EBI-892437

Protein

rpsD

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

rplC

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

rtcB

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

ynaE

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

slyD

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

ydfH

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

ydfK

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

xapR

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

rplQ

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

rplB

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

groL

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

rpsI

PMID:16606699[7]

Experiment(s):EBI-1144087

Protein

hupA

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rplP

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rplQ

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rplT

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rplU

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rplX

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rplY

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rpmB

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rpsC

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rpsF

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rpsR

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rpsS

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rpsT

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rluB

PMID:15690043[6]

Experiment(s):EBI-892437

Protein

rplE

PMID:19402753[8]

MALDI(Z-score):28.463340

Protein

rpsA

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):26.887059

Protein

rplY

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

rplO

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):25.179672

Protein

hupB

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplT

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplP

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplN

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):7.838609

Protein

rpmB

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpsR

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpsM

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):14.084270

Protein

rplS

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):18.353672

Protein

hupA

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplR

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rplI

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):33.508185

Protein

rpsS

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):12.464277

Protein

rplM

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):25.289364

Protein

rpsD

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):35.519048

Protein

rplF

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):22.038532

Protein

rpsC

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):3.220775

Protein

rplQ

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):3.168755

Protein

rplB

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):19.096082

Protein

rplA

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):22.386967

Protein

rlmL

PMID:19402753[8]

MALDI(Z-score):28.108464

Protein

srmB

PMID:19402753[8]

LCMS(ID Probability):91.3 MALDI(Z-score):27.803343

Protein

aidB

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):19.683372

Protein

prs

PMID:19402753[8]

MALDI(Z-score):20.443930

Protein

dapF

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):33.322088

Protein

yibL

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rnr

PMID:19402753[8]

LCMS(ID Probability):81.9 MALDI(Z-score):27.146759

Protein

yfiF

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):36.478881

Protein

ybcJ

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

deaD

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):27.659514

Protein

rluB

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):19.012086

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Notes

RppH (formerly NudH/YgdP) is an RNA pyrophosphorylase that removes the 5'-pyrophosphate group and initiates mRNA decay ([1]).

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MIDDDGYRPN VGIVICNRQG QVMWARRFGQ HSWQFPQGGI NPGESAEQAM YRELFEEVGL
SRKDVRILAS TRNWLRYKLP KRLVRWDTKP VCIGQKQKWF LLQLVSGDAE INMQTSSTPE
FDGWRWVSYW YPVRQVVSFK RDVYRRVMKE FASVVMSLQE NTPKPQNASA YRRKRG
Length

176

Mol. Wt

20.794 kDa

pI

10.4 (calculated)

Extinction coefficient

54,430 - 54,680 (calc based on 7 Y, 8 W, and 2 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

7..150

PF00293 NUDIX domain

PMID:19920124[9]

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=rppH taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130734

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947300

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009276

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A776

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7459

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13091

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947300

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004022

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2896

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Deana, A et al. (2008) The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal. Nature 451 355-8 PubMed
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  5. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 6.12 6.13 6.14 6.15 6.16 6.17 6.18 6.19 6.20 6.21 6.22 6.23 6.24 6.25 6.26 6.27 6.28 6.29 6.30 6.31 6.32 6.33 6.34 6.35 6.36 6.37 6.38 6.39 6.40 6.41 6.42 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 8.19 8.20 8.21 8.22 8.23 8.24 8.25 8.26 8.27 8.28 8.29 8.30 8.31 8.32 8.33 8.34 8.35 8.36 8.37 8.38 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  9. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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