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Protein

GTPase Der

Gene

der

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

Functioni

GTPase that plays an essential role in the late steps of ribosome biogenesis. GTPase point mutations (but not a deletion mutant) are suppressed by mild overexpression of RelA, probably due to increased levels of the stringent response mediator (p)ppGpp. 50S subunits assembled in the absence of Der are defective and unable to assemble into 70S ribosomes. GTPase activity is stimulated by YihI. Overexpression rescues an rrmJ deletion, stabilizing the 70S ribosome. Der and RrmJ are likely to share a mechanism to stabilize 50S ribosomal subunits at a very late stage of 50S subunit maturation possibly by interacting with 23S rRNA or 23S rRNA/r-protein complex.2 Publications

Kineticsi

Vmax increases 35% in the presence of full length YihI and 90% in the presence of YihI missing the first 45 residues.

  1. KM=125 µM for GTP (to 143 µM) in the absence of YihI2 Publications
  2. KM=59.2 µM for GTP in the presence of full-length YihI2 Publications
  3. KM=50.1 µM for GTP in the presence of N-terminally truncated YihI2 Publications

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi9 – 16GTP 1Sequence analysis8
    Nucleotide bindingi56 – 60GTP 1Sequence analysis5
    Nucleotide bindingi118 – 121GTP 1Sequence analysis4
    Nucleotide bindingi209 – 216GTP 2Sequence analysis8
    Nucleotide bindingi256 – 260GTP 2Sequence analysis5
    Nucleotide bindingi321 – 324GTP 2Sequence analysis4

    GO - Molecular functioni

    • GTPase activating protein binding Source: EcoCyc
    • GTPase activity Source: EcoCyc
    • GTP binding Source: GO_Central
    • ribosome binding Source: EcoCyc

    GO - Biological processi

    • ribosomal large subunit assembly Source: EcoCyc
    Complete GO annotation...

    Keywords - Biological processi

    Ribosome biogenesis

    Keywords - Ligandi

    GTP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G7319-MONOMER.
    ECOL316407:JW5403-MONOMER.
    MetaCyc:G7319-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    GTPase Der
    Alternative name(s):
    Double era-like domain protein
    GTP-binding protein EngA
    Gene namesi
    Name:der
    Synonyms:engA, yfgK
    Ordered Locus Names:b2511, JW5403
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG14207. der.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Pathology & Biotechi

    Disruption phenotypei

    Lethality. In a depletion experiment cells grow normally for 4 hours, at which time there is no detectable protein left. After 4 hours cell growth decreases rapidly, the amount of 50S ribosomal subunit decreases, rRNA precursors accumulate. A 40S ribosomal subunit is detected which is missing proteins L9 and L18 and has slightly reduced amounts of L2 and L6 compared to wild-type ribosomes.3 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi15K → A: Complements a disruption mutant, KM for GTP 695 uM. 1 Publication1
    Mutagenesisi16S → A: Does not complement a disruption mutant, KM for GTP 4.9 mM. Decreased GTPase activity, no stimulation by YihI. 2 Publications1
    Mutagenesisi118N → D: Complements a disruption mutant at 42 degrees Celsius, very poor complementation at 30 degrees Celsius. Reduces affinity for the 50S ribosomal subunit at 30 degrees Celsius. RelA suppresses this point mutation at 30 degrees Celsius. 1 Publication1
    Mutagenesisi118N → D: Does not complement a disruption mutant at 42 degrees Celsius, diminished association with 50S ribosomal subunits; when associated with D-321. 1 Publication1
    Mutagenesisi215K → A: Does not complement a disruption mutant, KM for GTP 6.7 mM. 1 Publication1
    Mutagenesisi216S → A: Does not complement a disruption mutant, considerably decreased GTPase activity, KM for GTP 4.8 mM, no stimulation by YihI. 2 Publications1
    Mutagenesisi321N → D: Complements a disruption mutant at 42 degrees Celsius, no complementation at 30 degrees Celsius. Greatly reduces affinity for the 50S ribosomal subunit at 30 degrees Celsius. RelA suppresses this point mutation at 30 degrees Celsius. 1 Publication1
    Mutagenesisi414G → R: Does not complement rrmJ deletion, complements der disruption at 42 degrees Celsius. 1 Publication1
    Mutagenesisi424G → D: Does not complement rrmJ deletion, nor the der disruption at 42 degrees Celsius. 1 Publication1
    Mutagenesisi469N → K: Does not complement rrmJ deletion, complements der disruption at 42 degrees Celsius. 1 Publication1
    Mutagenesisi472T → A: Does not complement rrmJ deletion, complements der disruption at 42 degrees Celsius. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001789911 – 490GTPase DerAdd BLAST490

    Proteomic databases

    EPDiP0A6P5.
    PaxDbiP0A6P5.
    PRIDEiP0A6P5.

    Interactioni

    Subunit structurei

    Associates with the 50S ribosomal subunit in the presence of GMPPNP, a non-hydrolysable GTP analog, and thus probably also in the presence of GTP, but not in the presence of GDP or in the absence of nucleotide. Interacts with YihI via the last 490 residues.3 Publications

    GO - Molecular functioni

    • GTPase activating protein binding Source: EcoCyc

    Protein-protein interaction databases

    BioGridi4263153. 14 interactors.
    DIPiDIP-48272N.
    IntActiP0A6P5. 7 interactors.
    STRINGi511145.b2511.

    Structurei

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3J8Gelectron microscopy5.00X1-490[»]
    ProteinModelPortaliP0A6P5.
    SMRiP0A6P5.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini3 – 166EngA-type G 1Add BLAST164
    Domaini203 – 376EngA-type G 2Add BLAST174
    Domaini377 – 461KH-likeAdd BLAST85

    Domaini

    The 2 G (guanine nucleotide-binding) domains are essential for activity and function cooperatively. The KH-like domain is required for ribosome recognition.1 Publication

    Sequence similaritiesi

    Contains 1 KH-like domain.Curated

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiENOG4105DKZ. Bacteria.
    COG1160. LUCA.
    HOGENOMiHOG000242862.
    InParanoidiP0A6P5.
    KOiK03977.
    OMAiDVMGTPI.
    PhylomeDBiP0A6P5.

    Family and domain databases

    Gene3Di3.30.300.20. 1 hit.
    3.40.50.300. 2 hits.
    HAMAPiMF_00195. GTPase_Der. 1 hit.
    InterProiIPR031166. G_ENGA.
    IPR016484. GTP-bd_EngA.
    IPR006073. GTP_binding_domain.
    IPR032859. KH_dom-like.
    IPR015946. KH_dom-like_a/b.
    IPR027417. P-loop_NTPase.
    IPR005225. Small_GTP-bd_dom.
    [Graphical view]
    PANTHERiPTHR11649:SF5. PTHR11649:SF5. 1 hit.
    PfamiPF14714. KH_dom-like. 1 hit.
    PF01926. MMR_HSR1. 2 hits.
    [Graphical view]
    PIRSFiPIRSF006485. GTP-binding_EngA. 1 hit.
    PRINTSiPR00326. GTP1OBG.
    SUPFAMiSSF52540. SSF52540. 3 hits.
    TIGRFAMsiTIGR03594. GTPase_EngA. 1 hit.
    TIGR00231. small_GTP. 2 hits.
    PROSITEiPS51712. G_ENGA. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0A6P5-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MVPVVALVGR PNVGKSTLFN RLTRTRDALV ADFPGLTRDR KYGRAEIEGR
    60 70 80 90 100
    EFICIDTGGI DGTEDGVETR MAEQSLLAIE EADVVLFMVD ARAGLMPADE
    110 120 130 140 150
    AIAKHLRSRE KPTFLVANKT DGLDPDQAVV DFYSLGLGEI YPIAASHGRG
    160 170 180 190 200
    VLSLLEHVLL PWMEDLAPQE EVDEDAEYWA QFEAEENGEE EEEDDFDPQS
    210 220 230 240 250
    LPIKLAIVGR PNVGKSTLTN RILGEERVVV YDMPGTTRDS IYIPMERDGR
    260 270 280 290 300
    EYVLIDTAGV RKRGKITDAV EKFSVIKTLQ AIEDANVVML VIDAREGISD
    310 320 330 340 350
    QDLSLLGFIL NSGRSLVIVV NKWDGLSQEV KEQVKETLDF RLGFIDFARV
    360 370 380 390 400
    HFISALHGSG VGNLFESVRE AYDSSTRRVG TSMLTRIMTM AVEDHQPPLV
    410 420 430 440 450
    RGRRVKLKYA HAGGYNPPIV VIHGNQVKDL PDSYKRYLMN YFRKSLDVMG
    460 470 480 490
    SPIRIQFKEG ENPYANKRNT LTPTQMRKRK RLMKHIKKNK
    Length:490
    Mass (Da):55,036
    Last modified:May 10, 2005 - v1
    Checksum:i0321511F5A5A7E3D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC75564.2.
    AP009048 Genomic DNA. Translation: BAA16397.2.
    PIRiF65027.
    RefSeqiNP_417006.2. NC_000913.3.
    WP_000249410.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75564; AAC75564; b2511.
    BAA16397; BAA16397; BAA16397.
    GeneIDi946983.
    KEGGiecj:JW5403.
    eco:b2511.
    PATRICi32120415. VBIEscCol129921_2610.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC75564.2.
    AP009048 Genomic DNA. Translation: BAA16397.2.
    PIRiF65027.
    RefSeqiNP_417006.2. NC_000913.3.
    WP_000249410.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3J8Gelectron microscopy5.00X1-490[»]
    ProteinModelPortaliP0A6P5.
    SMRiP0A6P5.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4263153. 14 interactors.
    DIPiDIP-48272N.
    IntActiP0A6P5. 7 interactors.
    STRINGi511145.b2511.

    Proteomic databases

    EPDiP0A6P5.
    PaxDbiP0A6P5.
    PRIDEiP0A6P5.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75564; AAC75564; b2511.
    BAA16397; BAA16397; BAA16397.
    GeneIDi946983.
    KEGGiecj:JW5403.
    eco:b2511.
    PATRICi32120415. VBIEscCol129921_2610.

    Organism-specific databases

    EchoBASEiEB3959.
    EcoGeneiEG14207. der.

    Phylogenomic databases

    eggNOGiENOG4105DKZ. Bacteria.
    COG1160. LUCA.
    HOGENOMiHOG000242862.
    InParanoidiP0A6P5.
    KOiK03977.
    OMAiDVMGTPI.
    PhylomeDBiP0A6P5.

    Enzyme and pathway databases

    BioCyciEcoCyc:G7319-MONOMER.
    ECOL316407:JW5403-MONOMER.
    MetaCyc:G7319-MONOMER.

    Miscellaneous databases

    PROiP0A6P5.

    Family and domain databases

    Gene3Di3.30.300.20. 1 hit.
    3.40.50.300. 2 hits.
    HAMAPiMF_00195. GTPase_Der. 1 hit.
    InterProiIPR031166. G_ENGA.
    IPR016484. GTP-bd_EngA.
    IPR006073. GTP_binding_domain.
    IPR032859. KH_dom-like.
    IPR015946. KH_dom-like_a/b.
    IPR027417. P-loop_NTPase.
    IPR005225. Small_GTP-bd_dom.
    [Graphical view]
    PANTHERiPTHR11649:SF5. PTHR11649:SF5. 1 hit.
    PfamiPF14714. KH_dom-like. 1 hit.
    PF01926. MMR_HSR1. 2 hits.
    [Graphical view]
    PIRSFiPIRSF006485. GTP-binding_EngA. 1 hit.
    PRINTSiPR00326. GTP1OBG.
    SUPFAMiSSF52540. SSF52540. 3 hits.
    TIGRFAMsiTIGR03594. GTPase_EngA. 1 hit.
    TIGR00231. small_GTP. 2 hits.
    PROSITEiPS51712. G_ENGA. 2 hits.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDER_ECOLI
    AccessioniPrimary (citable) accession number: P0A6P5
    Secondary accession number(s): P77254, Q8X4Y1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 10, 2005
    Last sequence update: May 10, 2005
    Last modified: November 2, 2016
    This is version 98 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    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.