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Gene |

Product(s) |

Expression|

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Standard Name	dosP
Gene Synonym(s)	ECK1483, b1489, JW1484, yddU, dos^[1], dos, yddU
Product Desc.	phosphodiesterase, heme-regulated^[2]^[3]; Component of phosphodiesterase, heme-regulated^[3] c-di-GMP phosphodiesterase, heme-regulated oxygen sensor; may have weak cAMP PDE activity; tetrameric^[4]
Product Synonyms(s)	cAMP phosphodiesterase, heme-regulated^[1], B1489^[2]^[1], YddU^[2]^[1], DosP^[2]^[1] , dos, ECK1483, JW1484, yddU, b1489
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yddV-dosP^[2]
Regulation/Activity
Quick Links
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Notes

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YddV/Dos may constitute a cyclic-di-GMP synthesis/degradation module (Mendez-Ortiz, 2006). The EAL domain of Dos has been shown to be a c-di-GMP-specific phosphodiesterase and does not have cAMP phosphodiesterase activity, in contrast to an earlier report (Sasakura, 2002; Schmidt, 2005). cAMP hydrolysis by full length Dos found by Sasakura (2002) is three orders of magnitude slower than the rate of c-di-GMP hydrolysis, may not be physiologically relevant, and may be due to the use of 2'-O-anthraniloyl-cAMP instead of cAMP as substrate (Schmidt, 2005). Redox changes in the bound heme result in global 3D structural alterations; this "scissor-type" subunit movement aids in catalytic control. Dos contains 2 N-terminal heme binding PAS domains, a GGDEF domain, and a C-terminal EAL domain. The start codon might be 8 codons upstream. dos expression is elevated under aerobic conditions where it is partially responsible for cAMP degradation. The heme binding domain is called DosH. Asp40 is involved in the electronic structure of the haem iron and redox-dependent catalytic control of the PDE domain because mutations in Asp40 result in lack of catalytic activity. Second gene in yddV-dos operon. A dos mutant is reported to have elevated cAMP under aerobic conditions, but this may be an indirect effect or it may reflect a physiologically relevant cAMP PDE activity in vivo.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	dosP
Mnemonic
Synonyms	ECK1483, b1489, JW1484, yddU, dos^[1], dos, yddU
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	33.65 minutes	MG1655: 1563757..1561358 <gbrowseImage> name=NC_000913:1561358..1563757 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1539671..1537272 <gbrowseImage> name=NC_012967:1537272..1539671 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1453417..1455816 <gbrowseImage> name=NC_012759:1453417..1455816 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1567447..1565048 <gbrowseImage> name=NC_007779:1565048..1567447 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1654352..1651953 <gbrowseImage> name=NC_010473:1651953..1654352 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Description	Reference	Availability	Comments
Δdos (Keio:JW1484)	deletion	deletion		PMID:16738554	Shigen CGSC9289^[5]
dosH582A		H582A	Loss of cAMP PDE activity			seeded from UniProt:P76129
dosH586A		H586A	Loss of cAMP PDE activity			seeded from UniProt:P76129
dosH69A,G		H69A,G	Loss of heme binding			seeded from UniProt:P76129
dosH75A,G		H75A,G	No loss of heme binding			seeded from UniProt:P76129
dosL91T		L91T	Increases auto-oxidation			seeded from UniProt:P76129
dosL107F		L107F	Significantly reduces heme-binding affinity; increases auto-oxidation			seeded from UniProt:P76129
dosL107T		L107T	Increases auto-oxidation			seeded from UniProt:P76129
dosM87A,I		M87A,I	Ferrous heme iron changes from an exclusively hexacoordinate low-spin form to an exclusively pentacoordinate high- spin form. Ferric heme iron remains hexacoordinate but becomes a mixture of high and low spin. Increases c-di-GMP PDE activity 7-fold in absence of O(2), CO or NO, no additional increase upon addition of gases (M-A only)			seeded from UniProt:P76129
dosM87H		M87H	No change in heme coordination; increases c-di-GMP PDE activity 2-fold in absence of O(2), CO or NO, and 2-fold more upon addition of gases			seeded from UniProt:P76129
dosR89A,E,I		R89A,E,I	The Fe(2+)-O(2) form loses c- di-GMP PDE activity, due to reduced O(2) affinity and/or increased auto-oxidation. NO and CO forms are less affected			seeded from UniProt:P76129
dosL91F		L91F	Alters O(2) binding, increases auto-oxidation			seeded from UniProt:P76129
Δdos-782::kan				PMID:16738554	CGSC:100634
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW1484	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGCTAACCGATGCGGATAA Primer 2:CCGATTTTCAGCGGTAACACGCT
9B8	Kohara Phage	Genobase	PMID:3038334
10C7	Kohara Phage	Genobase	PMID:3038334
22E3	Kohara Phage	Genobase	PMID:3038334
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[5]	est. P1 cotransduction: 38% ^[6] Synonyms:zdc-235::Tn10
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: % ^[6] Synonyms:zdh-925::Tn10
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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
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1489
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C1918
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:Z2221
EcoCyc (EcoliWiki Page)	ECOCYC:G6783	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945815	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

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

Standard name	DosP
Synonyms	cAMP phosphodiesterase, heme-regulated^[1], B1489^[2]^[1], YddU^[2]^[1], DosP^[2]^[1] , dos, ECK1483, JW1484, yddU, b1489
Product description	phosphodiesterase, heme-regulated^[2]^[3]; Component of phosphodiesterase, heme-regulated^[3] c-di-GMP phosphodiesterase, heme-regulated oxygen sensor; may have weak cAMP PDE activity; tetrameric^[4]
EC number (for enzymes)
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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:0000155	two-component sensor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000700	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000160	two-component signal transduction system (phosphorelay)	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000700	P	Seeded from EcoCyc (v14.0)	complete
	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:0000287	magnesium ion binding	PMID:14551206	IMP: Inferred from Mutant Phenotype		F	Seeded from EcoCyc (v14.0)	complete
	GO:0004871	signal transducer activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000014	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001610	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013767	P	Seeded from EcoCyc (v14.0)	complete
	GO:0007165	signal transduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000014	P	Seeded from EcoCyc (v14.0)	complete
	GO:0007165	signal transduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001610	P	Seeded from EcoCyc (v14.0)	complete
	GO:0020037	heme binding	PMID:10704219	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0050896	response to stimulus	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0716	P	Seeded from EcoCyc (v14.0)	complete
	GO:0071111	cyclic-guanylate-specific phosphodiesterase activity	PMID:15995192	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	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	Subunits of phosphodiesterase, heme-regulated	could be indirect
Protein	kdsD		PMID:16606699	Experiment(s):EBI-1139971
Protein	talA		PMID:16606699	Experiment(s):EBI-1139971
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Notes

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 MRQDAEVIMK LTDADNAADG IFFPALEQNM MGAVLINEND EVMFFNPAAE KLWGYKREEV IGNNIDMLIP RDLRPAHPEY IRHNREGGKA RVEGMSRELQ LEKKDGSKIW TRFALSKVSA EGKVYYLALV RDASVEMAQK EQTRQLIIAV DHLDRPVIVL DPERHIVQCN RAFTEMFGYC ISEASGMQPD TLLNIPEFPA DNRIRLQQLL WKTARDQDEF LLLTRTGEKI WIKASISPVY DVLAHLQNLV MTFSDITEER QIRQLEGNIL AAMCSSPPFH EMGEIICRNI ESVLNESHVS LFALRNGMPI HWASSSHGAE IQNAQSWSAT IRQRDGAPAG ILQIKTSSGA ETSAFIERVA DISQHMAALA LEQEKSRQHI EQLIQFDPMT GLPNRNNLHN YLDDLVDKAV SPVVYLIGVD HIQDVIDSLG YAWADQALLE VVNRFREKLK PDQYLCRIEG TQFVLVSLEN DVSNITQIAD ELRNVVSKPI MIDDKPFPLT LSIGISYDLG KNRDYLLSTA HNAMDYIRKN GGNGWQFFSP AMNEMVKERL VLGAALKEAI SNNQLKLVYQ PQIFAETGEL YGIEALARWH DPLHGHVPPS RFIPLAEEIG EIENIGRWVI AEACRQLAEW RSQNIHIPAL SVNLSALHFR SNQLPNQVSD AMHAWGIDGH QLTVEITESM MMEHDTEIFK RIQILRDMGV GLSVDDFGTG FSGLSRLVSL PVTEIKIDKS FVDRCLTEKR ILALLEAITS IGQSLNLTVV AEGVETKEQF EMLRKIHCRV IQGYFFSRPL PAEEIPGWMS SVLPLKI
Length	807
Mol. Wt	91.205 kDa
pI	5.3 (calculated)
Extinction coefficient	95,340 - 96,340 (calc based on 16 Y, 13 W, and 8 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	References
Domain	376..526	PF00990 GGDEF domain	PMID:19920124
Domain	545..781	PF00563 EAL domain	PMID:19920124
Domain	16..125	PF00989 PAS fold	PMID:19920124
Domain	142..253	PF08448 PAS fold	PMID:19920124
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<motif_map/>

Structure
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Structures

<beststructure> gene=dos 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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Resource type	Source	Notes/Reference
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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:162135902	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945815	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76129	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945815	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	3^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	20	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
yddV-dos
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:1563737..1563777 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b1489 (EcoliWiki Page)	NCBI GEO profiles for dos
microarray	GenExpDB:b1489 (EcoliWiki Page)	Summary of data for dos from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to dosP Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1489
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00563 EAL domain
PFAM (EcoliWiki Page)	PFAM:PF00989
Pfam (EcoliWiki Page)	PF00990 GGDEF domain
Panther (EcoliWiki Page)	PTHR24423:SF199
Superfamily (EcoliWiki Page)	SUPERFAMILY:55073
Superfamily (EcoliWiki Page)	SUPERFAMILY:55785
Superfamily (EcoliWiki Page)	SUPERFAMILY:55785
Superfamily (EcoliWiki Page)	SUPERFAMILY:141868
Pfam (EcoliWiki Page)	PF00989 PAS fold
Pfam (EcoliWiki Page)	PF08448 PAS fold
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

dosP:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

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Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to dosP Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

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