rppH:Gene Product(s): Difference between revisions

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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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	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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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

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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Name	URL	Comments
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References

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

↑ ^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
↑ ^2.0 ^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)
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^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
↑ ^7.00 ^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
↑ ^8.00 ^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
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46aac1bf8d3ee"  class=" tableEdit GO_table_product sortable dataTable"
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- MALDI(Z-score):20.443930
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-[[ybcJ:Gene_Product(s)|ybcJ]]
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-{|  class="sortable" id="116930"  id="W46a85802582cf"  class=" tableEdit Product_localization_table sortable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a85802582cf"  class=" tableEdit Product_localization_table sortable"
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-{|  class="sortable" id="172209"  id="I46aac1c412b0c"  class=" tableEdit Product_motif_table sortable dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46aac1c412b0c"  class=" tableEdit Product_motif_table sortable dataTable"
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 View models at:
 * [http://www.proteinmodelportal.org/query/uniprot/P0A776 Protein Model Portal]
-* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
+* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0A776 PSI-PRED (P0A776)]
-* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)
+* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0A776 Genomes TO Protein (P0A776)] (GTOP)
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-[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWiki Page]])
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-[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0009276&formSubmitReturn=1 ASAP:ABE-0009276]
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+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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-[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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-[http://ecogene.org/geneinfo.php?eg_id=EG13091 EcoGene:EG13091]
+EcoGene:EG13091
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 Escherichia coli str. K-12 substr. MG1655
+|-
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+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
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+[[EchoBASE]]
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rppH:Gene Product(s): Difference between revisions

Latest revision as of 20:19, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

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rppH:Gene Product(s): Difference between revisions

Latest revision as of 20:19, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

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