Escherichia coli K-12 substr. MG1655 Enzyme: c-di-GMP phosphodiesterase, heme-regulated

Gene: dosP Accession Numbers: G6783 (EcoCyc), b1489, ECK1483

Synonyms: yddU, dos

Regulation Summary Diagram: ?

Regulation summary diagram for dosP

Component of: DosC-DosP complex (summary available)

DosP acts a direct sensor of oxygen; the protein has an N-terminal heme-binding PAS domain and a C-terminal phosphodiesterase domain [DelgadoNixon00]. DosP, together with the oxygen-sensing diguanylate cyclase DosC, appears to control production and removal of the second messenger molecule c-di-GMP in response to oxygen [Tuckerman09].

Conformational changes within the N-terminal domain of DosP regulate the enzymatic activity of the C-terminal domain [DelgadoNixon00]. Binding of O2 or CO to the reduced heme ligand [Takahashi06] and cyanide or imidazole to the oxidized heme ligand [Tanaka08] enhances c-di-GMP phosphodiesterase activity. It is proposed that the heme sensor domain inhibits phosphodiesterase catalytic activity, and ligand binding to the heme releases catalytic suppression [Tanaka08]. O2-dependent catalytic activity is allosterically regulated [Kobayashi10]. Hydrogen sulfide stimulates catalytic activity of DosP under aerobic conditions [Takahashi12].

Dos was initially shown to exhibit cAMP phosphodiesterase activity using a fluorescent substrate; the ferrous form was enzymatically active and the ferric form was not [Sasakura02]. Under different assay conditions using c-di-GMP and cAMP, the C-terminal EAL domain of Dos exhibits c-di-GMP-specific phosphodiesterase activity, but no cAMP-dependent phosphodiesterase activity [Schmidt05]. The rate of cAMP hydrolysis reported in [Sasakura02] is three orders of magnitude lower than the rate of c-di-GMP hydrolysis; thus, c-di-GMP appears to be the physiological substrate [Schmidt05].

Dos forms a homotetramer [Sasakura02], with the C-terminal region responsible for tetramerization [Yoshimura03]. In contrast, later experiments indicate that the full-length protein forms a homodimer [Lechauve09]. Oxygen binding appears to be cooperative [Lechauve09]. Crystal structures of the N-terminal heme-binding domain of Dos, which forms a homodimer, have been solved [Kurokawa04, Park04a].

The physical characteristics of the heme-binding domain and binding of O2, CO, and NO have been studied in detail [DelgadoNixon00, Tomita02, Sato02, Gonzalez02, Park02, Liebl02, Watanabe02a, Liebl03, Taguchi04a, ElMashtoly07, Yamashita08a, ElMashtoly08, Vos08, Ishitsuka08, Bidwai08, Ito09, Tuckerman09, Ito09a]. Binding to heme is not necessary for tetramerization or for enzymatic activity [Yoshimura03]. The Asp40 residue appears to play a role in the electronic structure of the haem iron; mutations in Asp40 abolish catalytic activity [Watanabe04a]. The hydrogen bonding network of the heme group is important for signal transmission to the catalytic phosphodiesterase domain [ElMashtoly07].

Residues His77 [Sasakura02, Sato02] and Met95 coordinate the heme group [Sato02]. Coordination by Met95 appears to be indirect, probably water-mediated [Hirata03]. When O2 or CO is bound, the heme-Met95 interaction is disrupted, causing a conformational change [Sato02]. Met95 coordination of the Fe(II) heme group is critical for the structural change regulating catalysis [Tanaka07a], and Arg97 plays a role in O2 recognition and redox switching [Ishitsuka08]. Leu99 and Leu115 are important for determining the characteristics of the heme iron [Yokota06]. Mg2+ is required for activity [Sasakura02] and appears to bind at residues His590 and His594 [Yoshimura03].

Overexpression of dosP inhibits curli and biofilm formation [Tagliabue10a]. Expression of dosCP is regulated by σS and is increased at low temperature and in stationary phase [Sommerfeldt09].

A dosP mutant has a slower growth rate than wild type under aerobic growth conditions [YoshimuraSuzuki05]; the cells are longer than wild type [YoshimuraSuzuki05, MendezOrtiz06].

Dos: "direct oxygen sensor" [DelgadoNixon00]

DosP: "direct oxygen sensing phosphodiesterase" [Tuckerman09]

Reviews: [Sasakura06, Yamashita10]

Gene Citations: [Jonas08]

Locations: inner membrane

Map Position: [1,561,358 <- 1,563,757] (33.65 centisomes, 121°)
Length: 2400 bp / 799 aa

Molecular Weight of Polypeptide: 90.26 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004963 , EchoBASE:EB3553 , EcoGene:EG13792 , EcoliWiki:b1489 , ModBase:P76129 , OU-Microarray:b1489 , PortEco:dosP , PR:PRO_000022470 , Protein Model Portal:P76129 , RefSeq:NP_416006 , RegulonDB:G6783 , SMR:P76129 , String:511145.b1489 , UniProt:P76129

Relationship Links: EcoO157Cyc:Homolog:Z2220 , EcoO157Cyc:Homolog:Z2220-MONOMER , EcoO157Cyc:Homolog:Z2221 , EcoO157Cyc:Homolog:Z2221-MONOMER , InterPro:IN-FAMILY:IPR000014 , InterPro:IN-FAMILY:IPR000160 , InterPro:IN-FAMILY:IPR000700 , InterPro:IN-FAMILY:IPR001610 , InterPro:IN-FAMILY:IPR001633 , InterPro:IN-FAMILY:IPR012226 , InterPro:IN-FAMILY:IPR029787 , PDB:Structure:1S66 , PDB:Structure:1S67 , PDB:Structure:1V9Y , PDB:Structure:1V9Z , PDB:Structure:1VB6 , PDB:Structure:4HU3 , PDB:Structure:4HU4 , Pfam:IN-FAMILY:PF00563 , Pfam:IN-FAMILY:PF00990 , Pfam:IN-FAMILY:PF13426 , Prosite:IN-FAMILY:PS50112 , Prosite:IN-FAMILY:PS50113 , Prosite:IN-FAMILY:PS50883 , Prosite:IN-FAMILY:PS50887 , Smart:IN-FAMILY:SM00052 , Smart:IN-FAMILY:SM00086 , Smart:IN-FAMILY:SM00091 , Smart:IN-FAMILY:SM00267

In Paralogous Gene Group: 97 (15 members) , 527 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0000160 - phosphorelay signal transduction system Inferred by computational analysis [GOA01]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0007165 - signal transduction Inferred by computational analysis [GOA01]
GO:0023014 - signal transduction by protein phosphorylation Inferred by computational analysis [GOA01]
GO:0050896 - response to stimulus Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Yoshimura03]
GO:0005515 - protein binding Inferred from experiment [Tuckerman09]
GO:0019826 - oxygen sensor activity Inferred from experiment [Tuckerman09]
GO:0020037 - heme binding Inferred from experiment [DelgadoNixon00]
GO:0042803 - protein homodimerization activity Inferred from experiment [Lechauve09]
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity Inferred from experiment Inferred by computational analysis [GOA01a, Schmidt05]
GO:0000155 - phosphorelay sensor kinase activity Inferred by computational analysis [GOA01]
GO:0004871 - signal transducer activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005886 - plasma membrane Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes adaptations

Essentiality data for dosP knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Last-Curated ? 16-Aug-2012 by Keseler I , SRI International

Enzymatic reaction of: c-di-GMP phosphodiesterase

EC Number:

cyclic di-3',5'-guanylate + H2O <=> linear dimeric GMP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Citations: [Takahashi12]

Cofactors or Prosthetic Groups: Mg2+

Activators (Unknown Mechanism): hydrogen sulfide [Takahashi12]

Kinetic Parameters:

Km (μM)
cyclic di-3',5'-guanylate

Subunit of: DosC-DosP complex

Subunit composition of DosC-DosP complex = [DosP][DosC]
         c-di-GMP phosphodiesterase, heme-regulated = DosP (extended summary available)
         diguanylate cyclase = DosC (extended summary available)

Slightly overexpressed DosC and DosP proteins copurify in a complex [Tuckerman09]. In addition, a ribonucleoprotein complex containing DosC, DosP and other proteins, including PNPase, enolase, and RNase E, can be purified [Tuckerman11]. PNPase within the complex is active under anaerobic, but not aerobic conditions [Tuckerman11].

GO Terms:

Molecular Function: GO:0052621 - diguanylate cyclase activity Inferred from experiment [Tuckerman11, Tuckerman09]
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity Inferred from experiment [Tuckerman11]

Created 28-Sep-2009 by Keseler I , SRI International

Sequence Features

Protein sequence of c-di-GMP phosphodiesterase, heme-regulated with features indicated

Feature Class Location Citations Comment
Conserved-Region 10 -> 81
UniProt: PAS 1;
Metal-Binding-Site 69
UniProt: Iron (heme proximal ligand).
Mutagenesis-Variant 69
[Yoshimura03, Sasakura02, UniProt11]
H → A or G: Loss of heme binding.
Mutagenesis-Variant 75
[Sasakura02, UniProt11]
H → A or G: No loss of heme binding.
Metal-Binding-Site 87
UniProt: Iron (heme distal ligand).
Mutagenesis-Variant 87
[Tanaka07a, Sato02, Gonzalez02, UniProt11]
[Tanaka07a, Sato02, Gonzalez02, UniProt11]
M → A or 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).
M → H: 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.
Mutagenesis-Variant 89
[Tanaka07a, Gonzalez02, UniProt11]
R → A, E or 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.
Mutagenesis-Variant 91
[Yokota06, UniProt11]
[Yokota06, UniProt11]
L → F: Alters O(2) binding, increases auto-oxidation.
L → T: Increases auto-oxidation.
Mutagenesis-Variant 107
[Yokota06, UniProt11]
[Yokota06, UniProt11]
L → T: Increases auto-oxidation.
L → F: Significantly reduces heme-binding affinity; increases auto-oxidation.
Conserved-Region 134 -> 207
UniProt: PAS 2;
Conserved-Region 208 -> 260
UniProt: PAC;
Conserved-Region 402 -> 532
UniProt: GGDEF;
Conserved-Region 541 -> 795
UniProt: EAL;
Mutagenesis-Variant 582
[Yoshimura03, UniProt11]
UniProt: Loss of cAMP PDE activity.
Mutagenesis-Variant 586
[Yoshimura03, UniProt11]
UniProt: Loss of cAMP PDE activity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bidwai08: Bidwai AK, Ok EY, Erman JE (2008). "pH dependence of cyanide binding to the ferric heme domain of the direct oxygen sensor from Escherichia coli and the effect of alkaline denaturation." Biochemistry 47(39);10458-70. PMID: 18771281

DelgadoNixon00: Delgado-Nixon VM, Gonzalez G, Gilles-Gonzalez MA (2000). "Dos, a heme-binding PAS protein from Escherichia coli, is a direct oxygen sensor." Biochemistry 39(10);2685-91. PMID: 10704219

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

ElMashtoly07: El-Mashtoly SF, Takahashi H, Shimizu T, Kitagawa T (2007). "Ultraviolet resonance Raman evidence for utilization of the heme 6-propionate hydrogen-bond network in signal transmission from heme to protein in Ec DOS protein." J Am Chem Soc 129(12);3556-63. PMID: 17335280

ElMashtoly08: El-Mashtoly SF, Nakashima S, Tanaka A, Shimizu T, Kitagawa T (2008). "Roles of Arg-97 and Phe-113 in regulation of distal ligand binding to heme in the sensor domain of Ec DOS protein. Resonance Raman and mutation study." J Biol Chem 283(27);19000-10. PMID: 18450754

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Gonzalez02: Gonzalez G, Dioum EM, Bertolucci CM, Tomita T, Ikeda-Saito M, Cheesman MR, Watmough NJ, Gilles-Gonzalez MA (2002). "Nature of the displaceable heme-axial residue in the EcDos protein, a heme-based sensor from Escherichia coli." Biochemistry 41(26);8414-21. PMID: 12081490

Hirata03: Hirata S, Matsui T, Sasakura Y, Sugiyama S, Yoshimura T, Sagami I, Shimizu T (2003). "Characterization of Met95 mutants of a heme-regulated phosphodiesterase from Escherichia coli. Optical absorption, magnetic circular dichroism, circular dichroism, and redox potentials." Eur J Biochem 270(23);4771-9. PMID: 14622266

Ishitsuka08: Ishitsuka Y, Araki Y, Tanaka A, Igarashi J, Ito O, Shimizu T (2008). "Arg97 at the heme-distal side of the isolated heme-bound PAS domain of a heme-based oxygen sensor from Escherichia coli (Ec DOS) plays critical roles in autoxidation and binding to gases, particularly O2." Biochemistry 47(34);8874-84. PMID: 18672892

Ito09: Ito S, Araki Y, Tanaka A, Igarashi J, Wada T, Shimizu T (2009). "Role of Phe113 at the distal side of the heme domain of an oxygen-sensor (Ec DOS) in the characterization of the heme environment." J Inorg Biochem 103(7);989-96. PMID: 19482359

Ito09a: Ito S, Igarashi J, Shimizu T (2009). "The FG loop of a heme-based gas sensor enzyme, Ec DOS, functions in heme binding, autoxidation and catalysis." J Inorg Biochem 103(10);1380-5. PMID: 19712978

Jonas08: Jonas K, Edwards AN, Simm R, Romeo T, Romling U, Melefors O (2008). "The RNA binding protein CsrA controls cyclic di-GMP metabolism by directly regulating the expression of GGDEF proteins." Mol Microbiol 70(1);236-57. PMID: 18713317

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kobayashi10: Kobayashi K, Tanaka A, Takahashi H, Igarashi J, Ishitsuka Y, Yokota N, Shimizu T (2010). "Catalysis and oxygen binding of Ec DOS: a haem-based oxygen-sensor enzyme from Escherichia coli." J Biochem 148(6);693-703. PMID: 20861024

Kurokawa04: Kurokawa H, Lee DS, Watanabe M, Sagami I, Mikami B, Raman CS, Shimizu T (2004). "A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor." J Biol Chem 279(19);20186-93. PMID: 14982921

Lechauve09: Lechauve C, Bouzhir-Sima L, Yamashita T, Marden MC, Vos MH, Liebl U, Kiger L (2009). "Heme-ligand binding properties and intra-dimer interactions in the full length sensor protein DOS from Escherichia coli and its isolated heme domain." J Biol Chem 284(52):36146-59. PMID: 19864414

Liebl02: Liebl U, Bouzhir-Sima L, Negrerie M, Martin JL, Vos MH (2002). "Ultrafast ligand rebinding in the heme domain of the oxygen sensors FixL and Dos: general regulatory implications for heme-based sensors." Proc Natl Acad Sci U S A 99(20);12771-6. PMID: 12271121

Liebl03: Liebl U, Bouzhir-Sima L, Kiger L, Marden MC, Lambry JC, Negrerie M, Vos MH (2003). "Ligand binding dynamics to the heme domain of the oxygen sensor Dos from Escherichia coli." Biochemistry 42(21);6527-35. PMID: 12767236

MendezOrtiz06: Mendez-Ortiz MM, Hyodo M, Hayakawa Y, Membrillo-Hernandez J (2006). "Genome-wide transcriptional profile of Escherichia coli in response to high levels of the second messenger 3',5'-cyclic diguanylic acid." J Biol Chem 281(12);8090-9. PMID: 16418169

Park02: Park H, Suquet C, Savenkova MI, Satterlee JD, Kang C (2002). "Cloning, purification, crystallization and preliminary X-ray analysis of DOS heme domain, a new heme oxygen sensor in Escherichia coli." Acta Crystallogr D Biol Crystallogr 58(Pt 9);1504-6. PMID: 12198316

Park04a: Park H, Suquet C, Satterlee JD, Kang C (2004). "Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia coli Dos heme domain (Ec DosH)." Biochemistry 43(10);2738-46. PMID: 15005609

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Sasakura02: Sasakura Y, Hirata S, Sugiyama S, Suzuki S, Taguchi S, Watanabe M, Matsui T, Sagami I, Shimizu T (2002). "Characterization of a direct oxygen sensor heme protein from Escherichia coli. Effects of the heme redox states and mutations at the heme-binding site on catalysis and structure." J Biol Chem 277(26);23821-7. PMID: 11970957

Sasakura06: Sasakura Y, Yoshimura-Suzuki T, Kurokawa H, Shimizu T (2006). "Structure-function relationships of EcDOS, a heme-regulated phosphodiesterase from Escherichia coli." Acc Chem Res 39(1);37-43. PMID: 16411738

Sato02: Sato A, Sasakura Y, Sugiyama S, Sagami I, Shimizu T, Mizutani Y, Kitagawa T (2002). "Stationary and time-resolved resonance Raman spectra of His77 and Met95 mutants of the isolated heme domain of a direct oxygen sensor from Escherichia coli." J Biol Chem 277(36);32650-8. PMID: 12080073

Schmidt05: Schmidt AJ, Ryjenkov DA, Gomelsky M (2005). "The Ubiquitous Protein Domain EAL Is a Cyclic Diguanylate-Specific Phosphodiesterase: Enzymatically Active and Inactive EAL Domains." J Bacteriol 187(14);4774-81. PMID: 15995192

Sommerfeldt09: Sommerfeldt N, Possling A, Becker G, Pesavento C, Tschowri N, Hengge R (2009). "Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli." Microbiology 155(Pt 4);1318-31. PMID: 19332833

Tagliabue10a: Tagliabue L, Maciag A, Antoniani D, Landini P (2010). "The yddV-dos operon controls biofilm formation through the regulation of genes encoding curli fibers' subunits in aerobically growing Escherichia coli." FEMS Immunol Med Microbiol 59(3);477-84. PMID: 20553324

Taguchi04a: Taguchi S, Matsui T, Igarashi J, Sasakura Y, Araki Y, Ito O, Sugiyama S, Sagami I, Shimizu T (2004). "Binding of oxygen and carbon monoxide to a heme-regulated phosphodiesterase from Escherichia coli: Kinetics and infrared spectra of the full-length wild-type enzyme, isolated PAS domain and Met95 mutants." J Biol Chem 279(5);3340-7. PMID: 14612459

Takahashi06: Takahashi H, Shimizu T (2006). "Phosphodiesterase activity of Ec DOS, a heme-regulated enzyme from Escherichia coli, toward 3',5'-cyclic diguanylic acid is obviously enhanced by O2 and CO binding." Chem Lett 35(8):970.

Takahashi12: Takahashi H, Sekimoto M, Tanaka M, Tanaka A, Igarashi J, Shimizu T (2012). "Hydrogen sulfide stimulates the catalytic activity of a heme-regulated phosphodiesterase from Escherichia coli (Ec DOS)." J Inorg Biochem 109;66-71. PMID: 22387619

Tanaka07a: Tanaka A, Takahashi H, Shimizu T (2007). "Critical role of the heme axial ligand, Met95, in locking catalysis of the phosphodiesterase from Escherichia coli (Ec DOS) toward Cyclic diGMP." J Biol Chem 282(29);21301-7. PMID: 17535805

Tanaka08: Tanaka A, Shimizu T (2008). "Ligand binding to the Fe(III)-protoporphyrin IX complex of phosphodiesterase from Escherichia coli (Ec DOS) markedly enhances catalysis of cyclic di-GMP: roles of Met95, Arg97, and Phe113 of the putative heme distal side in catalytic regulation and ligand binding." Biochemistry 47(50);13438-46. PMID: 19053256

Tomita02: Tomita T, Gonzalez G, Chang AL, Ikeda-Saito M, Gilles-Gonzalez MA (2002). "A comparative resonance Raman analysis of heme-binding PAS domains: heme iron coordination structures of the BjFixL, AxPDEA1, EcDos, and MtDos proteins." Biochemistry 41(15);4819-26. PMID: 11939776

Tuckerman09: Tuckerman JR, Gonzalez G, Sousa EH, Wan X, Saito JA, Alam M, Gilles-Gonzalez MA (2009). "An Oxygen-Sensing Diguanylate Cyclase and Phosphodiesterase Couple for c-di-GMP Control." Biochemistry 48(41):9764-74. PMID: 19764732

Tuckerman11: Tuckerman JR, Gonzalez G, Gilles-Gonzalez MA (2011). "Cyclic di-GMP activation of polynucleotide phosphorylase signal-dependent RNA processing." J Mol Biol 407(5);633-9. PMID: 21320509

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Vos08: Vos MH, Battistoni A, Lechauve C, Marden MC, Kiger L, Desbois A, Pilet E, de Rosny E, Liebl U (2008). "Ultrafast heme-residue bond formation in six-coordinate heme proteins: implications for functional ligand exchange." Biochemistry 47(21);5718-23. PMID: 18454557

Watanabe02a: Watanabe M, Matsui T, Sasakura Y, Sagami I, Shimizu T (2002). "Unusual cyanide bindings to a heme-regulated phosphodiesterase from Escherichia coli: effect of Met95 mutations." Biochem Biophys Res Commun 299(2);169-72. PMID: 12437964

Watanabe04a: Watanabe M, Kurokawa H, Yoshimura-Suzuki T, Sagami I, Shimizu T (2004). "Critical roles of Asp40 at the haem proximal side of haem-regulated phosphodiesterase from Escherichia coli in redox potential, auto-oxidation and catalytic control." Eur J Biochem 271(19);3937-42. PMID: 15373839

Yamashita08a: Yamashita T, Bouzhir-Sima L, Lambry JC, Liebl U, Vos MH (2008). "Ligand dynamics and early signaling events in the heme domain of the sensor protein Dos from Escherichia coli." J Biol Chem 283(4);2344-52. PMID: 18039668

Yamashita10: Yamashita T (2010). "[Recent studies on gas sensors, CooA, FixL, and Dos]." Yakugaku Zasshi 130(9);1181-7. PMID: 20823675

Yokota06: Yokota N, Araki Y, Kurokawa H, Ito O, Igarashi J, Shimizu T (2006). "Critical roles of Leu99 and Leu115 at the heme distal side in auto-oxidation and the redox potential of a heme-regulated phosphodiesterase from Escherichia coli." FEBS J 273(6);1210-23. PMID: 16519686

Yoshimura03: Yoshimura T, Sagami I, Sasakura Y, Shimizu T (2003). "Relationships between heme incorporation, tetramer formation, and catalysis of a heme-regulated phosphodiesterase from Escherichia coli: a study of deletion and site-directed mutants." J Biol Chem 278(52);53105-11. PMID: 14551206

YoshimuraSuzuki05: Yoshimura-Suzuki T, Sagami I, Yokota N, Kurokawa H, Shimizu T (2005). "DOS(Ec), a heme-regulated phosphodiesterase, plays an important role in the regulation of the cyclic AMP level in Escherichia coli." J Bacteriol 187(19);6678-82. PMID: 16166529

Other References Related to Gene Regulation

Lessard98: Lessard IA, Pratt SD, McCafferty DG, Bussiere DE, Hutchins C, Wanner BL, Katz L, Walsh CT (1998). "Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in Streptomyces toyocaensis, Escherichia coli and Synechocystis: attributes of catalytic efficiency, stereoselectivity and regulation with implications for function." Chem Biol 5(9);489-504. PMID: 9751644

Weber06a: Weber H, Pesavento C, Possling A, Tischendorf G, Hengge R (2006). "Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli." Mol Microbiol 62(4);1014-34. PMID: 17010156

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Mon Oct 5, 2015, biocyc13.