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Protein

Oxygen sensor protein DosP

Gene

dosP

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Heme-based oxygen sensor protein displaying phosphodiesterase (PDE) activity toward c-di-GMP in response to oxygen availability. Involved in the modulation of intracellular c-di-GMP levels, in association with DosC which catalyzes the biosynthesis of c-di-GMP (diguanylate cyclase activity). Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria. Has very poor PDE activity on cAMP (PubMed:15995192) but is not active with cGMP, bis(p-nitrophenyl) phosphate or p-nitrophenyl phosphate (PubMed:11970957). Via its PDE activity on c-di-GMP, DosP regulates biofilm formation through the repression of transcription of the csgBAC operon, which encodes curli structural subunits.3 Publications

Catalytic activityi

Cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine.1 Publication

Cofactori

Protein has several cofactor binding sites:

Enzyme regulationi

Has c-di-GMP PDE activity in both Fe2+ and Fe3+-bound forms; this activity is increased 6-7 fold by binding of O2 and CO (PubMed:15995192) and NO (PubMed:17535805). Has cAMP PDE activity only when the heme is in the Fe2+ form. cAMP PDE activity is inhibited by oxidation of the heme iron and by binding of external ligands such as CO and NO. Also strongly inhibited by etazolate hydrochloride, a selective cAMP PDE inhibitor. PDE activity is inhibited in the absence of oxygen.3 Publications

Kineticsi

For the EAL domain, residues 532-799.1 Publication

Manual assertion based on experiment ini

  1. KM=36 µM for c-di-GMP

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi69Iron (heme proximal ligand)1
    Metal bindingi87Iron (heme distal ligand)1

    GO - Molecular functioni

    • cyclic-guanylate-specific phosphodiesterase activity Source: EcoCyc
    • heme binding Source: EcoCyc
    • magnesium ion binding Source: EcoCyc
    • oxygen sensor activity Source: CACAO
    • phosphorelay sensor kinase activity Source: InterPro

    GO - Biological processi

    • regulation of transcription, DNA-templated Source: UniProtKB-KW
    • response to oxygen levels Source: EcoCyc
    • transcription, DNA-templated Source: UniProtKB-KW
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Sensory transduction, Transcription, Transcription regulation

    Keywords - Ligandi

    c-di-GMP, Heme, Iron, Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G6783-MONOMER.
    ECOL316407:JW1484-MONOMER.
    MetaCyc:G6783-MONOMER.
    SABIO-RKP76129.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Oxygen sensor protein DosP (EC:3.1.4.52)
    Alternative name(s):
    Direct oxygen-sensing phosphodiesterase
    Short name:
    Direct oxygen sensor protein
    Ec DOS
    Heme-regulated cyclic di-GMP phosphodiesterase
    Gene namesi
    Name:dosP
    Synonyms:dos, yddU
    Ordered Locus Names:b1489, JW1484
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13792. dosP.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi69H → A or G: Loss of heme binding. 2 Publications1
    Mutagenesisi75H → A or G: No loss of heme binding. 1 Publication1
    Mutagenesisi87M → 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). 3 Publications1
    Mutagenesisi87M → 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. 3 Publications1
    Mutagenesisi89R → 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. 2 Publications1
    Mutagenesisi91L → F: Alters O(2) binding, increases auto-oxidation. 1 Publication1
    Mutagenesisi91L → T: Increases auto-oxidation. 1 Publication1
    Mutagenesisi107L → F: Significantly reduces heme-binding affinity; increases auto-oxidation. 1 Publication1
    Mutagenesisi107L → T: Increases auto-oxidation. 1 Publication1
    Mutagenesisi582H → A: Loss of cAMP PDE activity. 1 Publication1
    Mutagenesisi586H → A: Loss of cAMP PDE activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000799821 – 799Oxygen sensor protein DosPAdd BLAST799

    Post-translational modificationi

    The heme distal ligand is coordinated by Met-87 in the active Fe2+ (ferrous) form, by O2 in the O(2)-bound form and by H2O in the inactive Fe3+ (ferric) form.

    Proteomic databases

    PaxDbiP76129.
    PRIDEiP76129.

    Expressioni

    Inductioni

    Expressed in the late exponential growth phase and at higher levels in the stationary phase. A member of the dosCP operon. Expression is RpoS dependent and is higher at 28 degrees Celsius than at 37 degrees Celsius.2 Publications

    Interactioni

    Subunit structurei

    Homodimer (PubMed:19864414); has been previously suggested to be a homotetramer based on size exclusion chromatography (PubMed:11970957). Forms a complex with DosC.3 Publications

    Protein-protein interaction databases

    BioGridi4259419. 16 interactors.
    IntActiP76129. 3 interactors.
    STRINGi511145.b1489.

    Structurei

    Secondary structure

    1799
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi14 – 19Combined sources6
    Beta strandi22 – 28Combined sources7
    Beta strandi32 – 37Combined sources6
    Helixi39 – 45Combined sources7
    Helixi49 – 51Combined sources3
    Turni52 – 54Combined sources3
    Helixi57 – 60Combined sources4
    Helixi63 – 65Combined sources3
    Turni66 – 68Combined sources3
    Helixi69 – 77Combined sources9
    Beta strandi90 – 94Combined sources5
    Beta strandi96 – 98Combined sources3
    Beta strandi100 – 112Combined sources13
    Beta strandi115 – 123Combined sources9
    Helixi544 – 549Combined sources6
    Turni552 – 555Combined sources4
    Beta strandi557 – 569Combined sources13
    Beta strandi572 – 583Combined sources12
    Turni584 – 586Combined sources3
    Beta strandi587 – 589Combined sources3
    Helixi591 – 594Combined sources4
    Turni595 – 597Combined sources3
    Helixi607 – 623Combined sources17
    Beta strandi632 – 636Combined sources5
    Turni637 – 640Combined sources4
    Helixi648 – 656Combined sources9
    Beta strandi657 – 659Combined sources3
    Beta strandi664 – 668Combined sources5
    Helixi670 – 672Combined sources3
    Turni675 – 677Combined sources3
    Helixi680 – 688Combined sources9
    Turni689 – 691Combined sources3
    Beta strandi693 – 696Combined sources4
    Helixi703 – 707Combined sources5
    Turni708 – 711Combined sources4
    Beta strandi715 – 719Combined sources5
    Helixi721 – 729Combined sources9
    Helixi731 – 746Combined sources16
    Beta strandi750 – 754Combined sources5
    Helixi759 – 767Combined sources9
    Beta strandi772 – 775Combined sources4
    Turni776 – 778Combined sources3
    Helixi784 – 786Combined sources3
    Helixi787 – 793Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1S66X-ray1.80L/U8-126[»]
    1S67X-ray1.50L/U8-126[»]
    1V9YX-ray1.32A/B1-139[»]
    1V9ZX-ray1.90A/B1-139[»]
    1VB6X-ray1.56A/B1-139[»]
    4HU3X-ray3.30A529-799[»]
    4HU4X-ray2.40A/B529-799[»]
    ProteinModelPortaliP76129.
    SMRiP76129.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP76129.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini10 – 81PAS 1PROSITE-ProRule annotationAdd BLAST72
    Domaini134 – 207PAS 2PROSITE-ProRule annotationAdd BLAST74
    Domaini208 – 260PACPROSITE-ProRule annotationAdd BLAST53
    Domaini402 – 532GGDEFPROSITE-ProRule annotationAdd BLAST131
    Domaini541 – 795EALPROSITE-ProRule annotationAdd BLAST255

    Domaini

    The EAL domain (residues 532 to 799) is a cyclic dinucleotide di-GMP (c-di-GMP) PDE hydrolyzing c-di-GMP to 5'pGpG; it has no activity on cAMP.1 Publication
    Binding of an external ligand to the heme located in the N-terminal sensory domain displaces the distal heme ligand from Met-87 to the ligand and triggers a conformational change that regulates the activity of the C-terminal catalytic domain.
    The heme-PAS domain (residues 1-139) forms homodimers.

    Sequence similaritiesi

    Contains 1 EAL domain.PROSITE-ProRule annotation
    Contains 1 GGDEF domain.PROSITE-ProRule annotation
    Contains 1 PAC (PAS-associated C-terminal) domain.PROSITE-ProRule annotation
    Contains 2 PAS (PER-ARNT-SIM) domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiENOG4105BZU. Bacteria.
    COG2199. LUCA.
    COG2200. LUCA.
    COG2202. LUCA.
    HOGENOMiHOG000136246.
    InParanoidiP76129.
    KOiK13243.
    OMAiCHEVERI.
    PhylomeDBiP76129.

    Family and domain databases

    CDDicd01948. EAL. 1 hit.
    cd01949. GGDEF. 1 hit.
    Gene3Di3.20.20.450. 1 hit.
    InterProiIPR001633. EAL_dom.
    IPR000160. GGDEF_dom.
    IPR029787. Nucleotide_cyclase.
    IPR001610. PAC.
    IPR000014. PAS.
    IPR000700. PAS-assoc_C.
    [Graphical view]
    PfamiPF00563. EAL. 1 hit.
    PF00990. GGDEF. 1 hit.
    PF13426. PAS_9. 2 hits.
    [Graphical view]
    SMARTiSM00052. EAL. 1 hit.
    SM00267. GGDEF. 1 hit.
    SM00086. PAC. 2 hits.
    SM00091. PAS. 2 hits.
    [Graphical view]
    SUPFAMiSSF141868. SSF141868. 1 hit.
    SSF55073. SSF55073. 1 hit.
    SSF55785. SSF55785. 2 hits.
    TIGRFAMsiTIGR00254. GGDEF. 1 hit.
    TIGR00229. sensory_box. 2 hits.
    PROSITEiPS50883. EAL. 1 hit.
    PS50887. GGDEF. 1 hit.
    PS50113. PAC. 1 hit.
    PS50112. PAS. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P76129-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKLTDADNAA DGIFFPALEQ NMMGAVLINE NDEVMFFNPA AEKLWGYKRE
    60 70 80 90 100
    EVIGNNIDML IPRDLRPAHP EYIRHNREGG KARVEGMSRE LQLEKKDGSK
    110 120 130 140 150
    IWTRFALSKV SAEGKVYYLA LVRDASVEMA QKEQTRQLII AVDHLDRPVI
    160 170 180 190 200
    VLDPERHIVQ CNRAFTEMFG YCISEASGMQ PDTLLNIPEF PADNRIRLQQ
    210 220 230 240 250
    LLWKTARDQD EFLLLTRTGE KIWIKASISP VYDVLAHLQN LVMTFSDITE
    260 270 280 290 300
    ERQIRQLEGN ILAAMCSSPP FHEMGEIICR NIESVLNESH VSLFALRNGM
    310 320 330 340 350
    PIHWASSSHG AEIQNAQSWS ATIRQRDGAP AGILQIKTSS GAETSAFIER
    360 370 380 390 400
    VADISQHMAA LALEQEKSRQ HIEQLIQFDP MTGLPNRNNL HNYLDDLVDK
    410 420 430 440 450
    AVSPVVYLIG VDHIQDVIDS LGYAWADQAL LEVVNRFREK LKPDQYLCRI
    460 470 480 490 500
    EGTQFVLVSL ENDVSNITQI ADELRNVVSK PIMIDDKPFP LTLSIGISYD
    510 520 530 540 550
    LGKNRDYLLS TAHNAMDYIR KNGGNGWQFF SPAMNEMVKE RLVLGAALKE
    560 570 580 590 600
    AISNNQLKLV YQPQIFAETG ELYGIEALAR WHDPLHGHVP PSRFIPLAEE
    610 620 630 640 650
    IGEIENIGRW VIAEACRQLA EWRSQNIHIP ALSVNLSALH FRSNQLPNQV
    660 670 680 690 700
    SDAMHAWGID GHQLTVEITE SMMMEHDTEI FKRIQILRDM GVGLSVDDFG
    710 720 730 740 750
    TGFSGLSRLV SLPVTEIKID KSFVDRCLTE KRILALLEAI TSIGQSLNLT
    760 770 780 790
    VVAEGVETKE QFEMLRKIHC RVIQGYFFSR PLPAEEIPGW MSSVLPLKI
    Length:799
    Mass (Da):90,260
    Last modified:December 4, 2007 - v4
    Checksum:i4CE770D2A6B39D5F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74562.2.
    AP009048 Genomic DNA. Translation: BAA15154.1.
    PIRiD64902.
    RefSeqiNP_416006.4. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC74562; AAC74562; b1489.
    BAA15154; BAA15154; BAA15154.
    GeneIDi945815.
    KEGGiecj:JW1484.
    eco:b1489.
    PATRICi32118272. VBIEscCol129921_1556.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74562.2.
    AP009048 Genomic DNA. Translation: BAA15154.1.
    PIRiD64902.
    RefSeqiNP_416006.4. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1S66X-ray1.80L/U8-126[»]
    1S67X-ray1.50L/U8-126[»]
    1V9YX-ray1.32A/B1-139[»]
    1V9ZX-ray1.90A/B1-139[»]
    1VB6X-ray1.56A/B1-139[»]
    4HU3X-ray3.30A529-799[»]
    4HU4X-ray2.40A/B529-799[»]
    ProteinModelPortaliP76129.
    SMRiP76129.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259419. 16 interactors.
    IntActiP76129. 3 interactors.
    STRINGi511145.b1489.

    Proteomic databases

    PaxDbiP76129.
    PRIDEiP76129.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74562; AAC74562; b1489.
    BAA15154; BAA15154; BAA15154.
    GeneIDi945815.
    KEGGiecj:JW1484.
    eco:b1489.
    PATRICi32118272. VBIEscCol129921_1556.

    Organism-specific databases

    EchoBASEiEB3553.
    EcoGeneiEG13792. dosP.

    Phylogenomic databases

    eggNOGiENOG4105BZU. Bacteria.
    COG2199. LUCA.
    COG2200. LUCA.
    COG2202. LUCA.
    HOGENOMiHOG000136246.
    InParanoidiP76129.
    KOiK13243.
    OMAiCHEVERI.
    PhylomeDBiP76129.

    Enzyme and pathway databases

    BioCyciEcoCyc:G6783-MONOMER.
    ECOL316407:JW1484-MONOMER.
    MetaCyc:G6783-MONOMER.
    SABIO-RKP76129.

    Miscellaneous databases

    EvolutionaryTraceiP76129.
    PROiP76129.

    Family and domain databases

    CDDicd01948. EAL. 1 hit.
    cd01949. GGDEF. 1 hit.
    Gene3Di3.20.20.450. 1 hit.
    InterProiIPR001633. EAL_dom.
    IPR000160. GGDEF_dom.
    IPR029787. Nucleotide_cyclase.
    IPR001610. PAC.
    IPR000014. PAS.
    IPR000700. PAS-assoc_C.
    [Graphical view]
    PfamiPF00563. EAL. 1 hit.
    PF00990. GGDEF. 1 hit.
    PF13426. PAS_9. 2 hits.
    [Graphical view]
    SMARTiSM00052. EAL. 1 hit.
    SM00267. GGDEF. 1 hit.
    SM00086. PAC. 2 hits.
    SM00091. PAS. 2 hits.
    [Graphical view]
    SUPFAMiSSF141868. SSF141868. 1 hit.
    SSF55073. SSF55073. 1 hit.
    SSF55785. SSF55785. 2 hits.
    TIGRFAMsiTIGR00254. GGDEF. 1 hit.
    TIGR00229. sensory_box. 2 hits.
    PROSITEiPS50883. EAL. 1 hit.
    PS50887. GGDEF. 1 hit.
    PS50113. PAC. 1 hit.
    PS50112. PAS. 2 hits.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDOSP_ECOLI
    AccessioniPrimary (citable) accession number: P76129
    Secondary accession number(s): P76872, P77708
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 15, 1998
    Last sequence update: December 4, 2007
    Last modified: November 2, 2016
    This is version 149 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Binds O2 with a dissociation constant of about 74 µM.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.