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Protein

Bifunctional uridylyltransferase/uridylyl-removing enzyme

Gene

glnD

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

Functioni

Modifies, by uridylylation and deuridylylation, the PII regulatory proteins GlnB and GlnK, in response to the nitrogen status of the cell that GlnD senses through the glutamine level. Under low glutamine levels, catalyzes the conversion of the PII proteins and UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls uridylylation state and activity of the PII proteins, and plays an important role in the regulation of nitrogen assimilation and metabolism.5 Publications

Catalytic activityi

UTP + [protein-PII] = diphosphate + uridylyl-[protein-PII].UniRule annotation
Uridylyl-[protein-PII] + H2O = UMP + [protein-PII].UniRule annotation

Cofactori

Mg2+UniRule annotation1 PublicationNote: Mg2+ appears to be the physiologically relevant metal ion cofactor for both transferase and uridylyl-removing activities.UniRule annotation1 Publication

Enzyme regulationi

Uridylyltransferase (UTase) activity is inhibited by glutamine, while glutamine activates uridylyl-removing (UR) activity. Both reactions are activated by ATP and 2-ketoglutarate, via the binding of these effector molecules to the substrates PII and PII-UMP.UniRule annotation4 Publications

Kineticsi

kcat is 137 min(-1) for the UTase reaction. kcat is 2.7 min(-1) for the UR reaction in the absence of glutamine, and 6.5 min(-1) in the presence of 2.5 mM glutamine.

  1. KM=3.0 µM for GlnB protein1 Publication
  2. KM=40 µM for UTP1 Publication
  3. KM=2.3 µM for uridylyl-[protein-PII] (in the absence of glutamine)1 Publication
  4. KM=0.82 µM for uridylyl-[protein-PII] (in the presence of 2.5 mM glutamine)1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Nucleotidyltransferase, Transferase

    Keywords - Ligandi

    Magnesium

    Enzyme and pathway databases

    BioCyciEcoCyc:GLND-MONOMER.
    ECOL316407:JW0162-MONOMER.
    MetaCyc:GLND-MONOMER.
    BRENDAi2.7.7.59. 2026.
    SABIO-RKP27249.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Bifunctional uridylyltransferase/uridylyl-removing enzymeUniRule annotation
    Short name:
    UTase/URUniRule annotation
    Alternative name(s):
    Bifunctional [protein-PII] modification enzymeUniRule annotation
    Bifunctional nitrogen sensor proteinUniRule annotation
    Including the following 2 domains:
    [Protein-PII] uridylyltransferaseUniRule annotation (EC:2.7.7.59UniRule annotation)
    Short name:
    PII uridylyltransferaseUniRule annotation
    Short name:
    UTaseUniRule annotation
    [Protein-PII]-UMP uridylyl-removing enzymeUniRule annotation (EC:3.1.4.-UniRule annotation)
    Short name:
    URUniRule annotation
    Gene namesi
    Name:glnDUniRule annotation
    Ordered Locus Names:b0167, JW0162
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11411. glnD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi93 – 931G → L or V: Loss of UTase activity, while no significant effect on UR activity. 1 Publication
    Mutagenesisi94 – 941G → D: Loss of UTase activity, while no significant effect on UR activity. 1 Publication
    Mutagenesisi107 – 1071D → A, V or Y: Loss of UTase activity, while no significant effect on UR activity. 1 Publication
    Mutagenesisi514 – 5152HD → AA or QN: Loss of UR activity, while no significant effect on UTase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 890890Bifunctional uridylyltransferase/uridylyl-removing enzymePRO_0000192732Add
    BLAST

    Proteomic databases

    PaxDbiP27249.
    PRIDEiP27249.

    Interactioni

    Subunit structurei

    Monomer. Can also form homooligomers that are much less active.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    glnBP0A9Z13EBI-552032,EBI-551053
    glnKP0AC553EBI-552032,EBI-559503

    Protein-protein interaction databases

    DIPiDIP-9779N.
    IntActiP27249. 24 interactions.
    MINTiMINT-1252261.
    STRINGi511145.b0167.

    Structurei

    3D structure databases

    ProteinModelPortaliP27249.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini468 – 601134HDUniRule annotationAdd
    BLAST
    Domaini709 – 78981ACT 1UniRule annotationAdd
    BLAST
    Domaini816 – 89075ACT 2UniRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 349349UridylyltransferaseAdd
    BLAST
    Regioni350 – 708359Uridylyl-removingAdd
    BLAST

    Domaini

    Has four distinct domains: an N-terminal nucleotidyltransferase (NT) domain responsible for UTase activity, a central HD domain that encodes UR activity, and two C-terminal ACT domains that seem to have a role in glutamine sensing.UniRule annotation1 Publication

    Sequence similaritiesi

    Belongs to the GlnD family.UniRule annotation
    Contains 2 ACT domains.UniRule annotation
    Contains 1 HD domain.UniRule annotation

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiCOG2844.
    HOGENOMiHOG000261778.
    InParanoidiP27249.
    KOiK00990.
    OMAiHTLFWIA.
    OrthoDBiEOG6CCH44.
    PhylomeDBiP27249.

    Family and domain databases

    Gene3Di1.10.3210.10. 1 hit.
    HAMAPiMF_00277. PII_uridylyl_transf.
    InterProiIPR002912. ACT_dom.
    IPR003607. HD/PDEase_dom.
    IPR006674. HD_domain.
    IPR002934. Nucleotidyltransferase.
    IPR013546. PII_UdlTrfase/GS_AdlTrfase.
    IPR010043. UTase/UR.
    [Graphical view]
    PfamiPF01842. ACT. 2 hits.
    PF08335. GlnD_UR_UTase. 1 hit.
    PF01966. HD. 1 hit.
    PF01909. NTP_transf_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006288. PII_uridyltransf. 1 hit.
    SMARTiSM00471. HDc. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01693. UTase_glnD. 1 hit.
    PROSITEiPS51671. ACT. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P27249-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNTLPEQYAN TALPTLPGQP QNPCVWPRDE LTVGGIKAHI DTFQRWLGDA
    60 70 80 90 100
    FDNGISAEQL IEARTEFIDQ LLQRLWIEAG FSQIADLALV AVGGYGRGEL
    110 120 130 140 150
    HPLSDVDLLI LSRKKLPDDQ AQKVGELLTL LWDVKLEVGH SVRTLEECML
    160 170 180 190 200
    EGLSDLTVAT NLIESRLLIG DVALFLELQK HIFSEGFWPS DKFYAAKVEE
    210 220 230 240 250
    QNQRHQRYHG TSYNLEPDIK SSPGGLRDIH TLQWVARRHF GATSLDEMVG
    260 270 280 290 300
    FGFLTSAERA ELNECLHILW RIRFALHLVV SRYDNRLLFD RQLSVAQRLN
    310 320 330 340 350
    YSGEGNEPVE RMMKDYFRVT RRVSELNQML LQLFDEAILA LPADEKPRPI
    360 370 380 390 400
    DDEFQLRGTL IDLRDETLFM RQPEAILRMF YTMVHNSAIT GIYSTTLRQL
    410 420 430 440 450
    RHARRHLQQP LCNIPEARKL FLSILRHPGA VRRGLLPMHR HSVLGAYMPQ
    460 470 480 490 500
    WSHIVGQMQF DLFHAYTVDE HTIRVMLKLE SFASEETRQR HPLCVDVWPR
    510 520 530 540 550
    LPSTELIFIA ALFHDIAKGR GGDHSILGAQ DVVHFAELHG LNSRETQLVA
    560 570 580 590 600
    WLVRQHLLMS VTAQRRDIQD PEVIKQFAEE VQTENRLRYL VCLTVADICA
    610 620 630 640 650
    TNETLWNSWK QSLLRELYFA TEKQLRRGMQ NTPDMRERVR HHQLQALALL
    660 670 680 690 700
    RMDNIDEEAL HQIWSRCRAN YFVRHSPNQL AWHARHLLQH DLSKPLVLLS
    710 720 730 740 750
    PQATRGGTEI FIWSPDRPYL FAAVCAELDR RNLSVHDAQI FTTRDGMAMD
    760 770 780 790 800
    TFIVLEPDGN PLSADRHEVI RFGLEQVLTQ SSWQPPQPRR QPAKLRHFTV
    810 820 830 840 850
    ETEVTFLPTH TDRKSFLELI ALDQPGLLAR VGKIFADLGI SLHGARITTI
    860 870 880 890
    GERVEDLFII ATADRRALNN ELQQEVHQRL TEALNPNDKG
    Length:890
    Mass (Da):102,390
    Last modified:June 1, 1994 - v2
    Checksum:i6FF0006341A71D34
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti47 – 471L → S in AAA23878 (Ref. 1) Curated
    Sequence conflicti225 – 2251G → A (PubMed:8202364).Curated
    Sequence conflicti357 – 3582RG → TR in AAA23878 (Ref. 1) Curated
    Sequence conflicti523 – 5231D → H in AAA23878 (Ref. 1) Curated
    Sequence conflicti703 – 7031A → R in CAA79887 (PubMed:8412694).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M96431 Genomic DNA. Translation: AAA23878.1.
    Z21842 Genomic DNA. Translation: CAA79887.1.
    U70214 Genomic DNA. Translation: AAB08596.1.
    U00096 Genomic DNA. Translation: AAC73278.1.
    AP009048 Genomic DNA. Translation: BAE76045.1.
    PIRiG64740.
    RefSeqiNP_414709.1. NC_000913.3.
    WP_001094586.1. NZ_CP010445.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73278; AAC73278; b0167.
    BAE76045; BAE76045; BAE76045.
    GeneIDi944863.
    KEGGieco:b0167.
    PATRICi32115441. VBIEscCol129921_0172.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M96431 Genomic DNA. Translation: AAA23878.1.
    Z21842 Genomic DNA. Translation: CAA79887.1.
    U70214 Genomic DNA. Translation: AAB08596.1.
    U00096 Genomic DNA. Translation: AAC73278.1.
    AP009048 Genomic DNA. Translation: BAE76045.1.
    PIRiG64740.
    RefSeqiNP_414709.1. NC_000913.3.
    WP_001094586.1. NZ_CP010445.1.

    3D structure databases

    ProteinModelPortaliP27249.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-9779N.
    IntActiP27249. 24 interactions.
    MINTiMINT-1252261.
    STRINGi511145.b0167.

    Proteomic databases

    PaxDbiP27249.
    PRIDEiP27249.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73278; AAC73278; b0167.
    BAE76045; BAE76045; BAE76045.
    GeneIDi944863.
    KEGGieco:b0167.
    PATRICi32115441. VBIEscCol129921_0172.

    Organism-specific databases

    EchoBASEiEB1383.
    EcoGeneiEG11411. glnD.

    Phylogenomic databases

    eggNOGiCOG2844.
    HOGENOMiHOG000261778.
    InParanoidiP27249.
    KOiK00990.
    OMAiHTLFWIA.
    OrthoDBiEOG6CCH44.
    PhylomeDBiP27249.

    Enzyme and pathway databases

    BioCyciEcoCyc:GLND-MONOMER.
    ECOL316407:JW0162-MONOMER.
    MetaCyc:GLND-MONOMER.
    BRENDAi2.7.7.59. 2026.
    SABIO-RKP27249.

    Miscellaneous databases

    PROiP27249.

    Family and domain databases

    Gene3Di1.10.3210.10. 1 hit.
    HAMAPiMF_00277. PII_uridylyl_transf.
    InterProiIPR002912. ACT_dom.
    IPR003607. HD/PDEase_dom.
    IPR006674. HD_domain.
    IPR002934. Nucleotidyltransferase.
    IPR013546. PII_UdlTrfase/GS_AdlTrfase.
    IPR010043. UTase/UR.
    [Graphical view]
    PfamiPF01842. ACT. 2 hits.
    PF08335. GlnD_UR_UTase. 1 hit.
    PF01966. HD. 1 hit.
    PF01909. NTP_transf_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006288. PII_uridyltransf. 1 hit.
    SMARTiSM00471. HDc. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01693. UTase_glnD. 1 hit.
    PROSITEiPS51671. ACT. 2 hits.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Molecular cloning and sequencing of gldD, the gene for uridylyl transferase and uridyl removing enzyme of E. coli."
      Park S.-C., Kim I.H., Rhee S.G.
      Submitted (JUL-1992) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "The genes of the glutamine synthetase adenylylation cascade are not regulated by nitrogen in Escherichia coli."
      van Heeswijk W.C., Rabenberg M., Westerhoff H.V., Kahn D.D.
      Mol. Microbiol. 9:443-458(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. "Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region."
      Fujita N., Mori H., Yura T., Ishihama A.
      Nucleic Acids Res. 22:1637-1639(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Sequence of minutes 4-25 of Escherichia coli."
      Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
      Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    6. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    7. "Cascade control of Escherichia coli glutamine synthetase. Purification and properties of PII uridylyltransferase and uridylyl-removing enzyme."
      Garcia E., Rhee S.G.
      J. Biol. Chem. 258:2246-2253(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.
    8. "An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli."
      van Heeswijk W.C., Hoving S., Molenaar D., Stegeman B., Kahn D., Westerhoff H.V.
      Mol. Microbiol. 21:133-146(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ENZYME REGULATION.
      Strain: K12.
    9. "Enzymological characterization of the signal-transducing uridylyltransferase/uridylyl-removing enzyme (EC 2.7.7.59) of Escherichia coli and its interaction with the PII protein."
      Jiang P., Peliska J.A., Ninfa A.J.
      Biochemistry 37:12782-12794(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, KINETIC PARAMETERS, SUBSTRATE SPECIFICITY, KINETIC MECHANISM.
    10. "Characterization of the GlnK protein of Escherichia coli."
      Atkinson M.R., Ninfa A.J.
      Mol. Microbiol. 32:301-313(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION WITH GLNK AS SUBSTRATE, CATALYTIC ACTIVITY, ENZYME REGULATION.
    11. "Mutagenesis and functional characterization of the four domains of GlnD, a bifunctional nitrogen sensor protein."
      Zhang Y., Pohlmann E.L., Serate J., Conrad M.C., Roberts G.P.
      J. Bacteriol. 192:2711-2721(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, DOMAIN, ENZYME REGULATION, MUTAGENESIS OF GLY-93; GLY-94; ASP-107 AND 514-HIS-ASP-515.

    Entry informationi

    Entry nameiGLND_ECOLI
    AccessioniPrimary (citable) accession number: P27249
    Secondary accession number(s): Q2MCG1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1992
    Last sequence update: June 1, 1994
    Last modified: July 22, 2015
    This is version 146 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The transferase reaction proceeds by an ordered bi-bi kinetic mechanism, with PII binding before UTP and pyrophosphate (PPi) released before PII-UMP. The uridylyl-removing reaction proceeds with rapid equilibrium binding of substrate and random release of products (PubMed:9737855).1 Publication

    Keywords - Technical termi

    Complete proteome, Multifunctional enzyme, Reference proteome

    Documents

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

    External Data

    Dasty 3

    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 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.