ID   GLND_METCA              Reviewed;         877 AA.
AC   Q60BB2;
DT   08-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT   23-NOV-2004, sequence version 1.
DT   27-MAR-2024, entry version 110.
DE   RecName: Full=Bifunctional uridylyltransferase/uridylyl-removing enzyme {ECO:0000255|HAMAP-Rule:MF_00277};
DE            Short=UTase/UR {ECO:0000255|HAMAP-Rule:MF_00277};
DE   AltName: Full=Bifunctional [protein-PII] modification enzyme {ECO:0000255|HAMAP-Rule:MF_00277};
DE   AltName: Full=Bifunctional nitrogen sensor protein {ECO:0000255|HAMAP-Rule:MF_00277};
DE   Includes:
DE     RecName: Full=[Protein-PII] uridylyltransferase {ECO:0000255|HAMAP-Rule:MF_00277};
DE              Short=PII uridylyltransferase {ECO:0000255|HAMAP-Rule:MF_00277};
DE              Short=UTase {ECO:0000255|HAMAP-Rule:MF_00277};
DE              EC=2.7.7.59 {ECO:0000255|HAMAP-Rule:MF_00277};
DE   Includes:
DE     RecName: Full=[Protein-PII]-UMP uridylyl-removing enzyme {ECO:0000255|HAMAP-Rule:MF_00277};
DE              Short=UR {ECO:0000255|HAMAP-Rule:MF_00277};
DE              EC=3.1.4.- {ECO:0000255|HAMAP-Rule:MF_00277};
GN   Name=glnD {ECO:0000255|HAMAP-Rule:MF_00277};
GN   OrderedLocusNames=MCA0565;
OS   Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Methylococcales;
OC   Methylococcaceae; Methylococcus.
OX   NCBI_TaxID=243233;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 33009 / NCIMB 11132 / Bath;
RX   PubMed=15383840; DOI=10.1371/journal.pbio.0020303;
RA   Ward N.L., Larsen O., Sakwa J., Bruseth L., Khouri H.M., Durkin A.S.,
RA   Dimitrov G., Jiang L., Scanlan D., Kang K.H., Lewis M.R., Nelson K.E.,
RA   Methe B.A., Wu M., Heidelberg J.F., Paulsen I.T., Fouts D.E., Ravel J.,
RA   Tettelin H., Ren Q., Read T.D., DeBoy R.T., Seshadri R., Salzberg S.L.,
RA   Jensen H.B., Birkeland N.K., Nelson W.C., Dodson R.J., Grindhaug S.H.,
RA   Holt I.E., Eidhammer I., Jonasen I., Vanaken S., Utterback T.R.,
RA   Feldblyum T.V., Fraser C.M., Lillehaug J.R., Eisen J.A.;
RT   "Genomic insights into methanotrophy: the complete genome sequence of
RT   Methylococcus capsulatus (Bath).";
RL   PLoS Biol. 2:1616-1628(2004).
CC   -!- FUNCTION: Modifies, by uridylylation and deuridylylation, the PII
CC       regulatory proteins (GlnB and homologs), in response to the nitrogen
CC       status of the cell that GlnD senses through the glutamine level. Under
CC       low glutamine levels, catalyzes the conversion of the PII proteins and
CC       UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD
CC       hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls
CC       uridylylation state and activity of the PII proteins, and plays an
CC       important role in the regulation of nitrogen fixation and metabolism.
CC       {ECO:0000255|HAMAP-Rule:MF_00277}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=[protein-PII]-L-tyrosine + UTP = [protein-PII]-uridylyl-L-
CC         tyrosine + diphosphate; Xref=Rhea:RHEA:13673, Rhea:RHEA-COMP:12147,
CC         Rhea:RHEA-COMP:12148, ChEBI:CHEBI:33019, ChEBI:CHEBI:46398,
CC         ChEBI:CHEBI:46858, ChEBI:CHEBI:90602; EC=2.7.7.59;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00277};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=[protein-PII]-uridylyl-L-tyrosine + H2O = [protein-PII]-L-
CC         tyrosine + H(+) + UMP; Xref=Rhea:RHEA:48600, Rhea:RHEA-COMP:12147,
CC         Rhea:RHEA-COMP:12148, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:46858, ChEBI:CHEBI:57865, ChEBI:CHEBI:90602;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00277};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00277};
CC   -!- ACTIVITY REGULATION: Uridylyltransferase (UTase) activity is inhibited
CC       by glutamine, while glutamine activates uridylyl-removing (UR)
CC       activity. {ECO:0000255|HAMAP-Rule:MF_00277}.
CC   -!- DOMAIN: Has four distinct domains: an N-terminal nucleotidyltransferase
CC       (NT) domain responsible for UTase activity, a central HD domain that
CC       encodes UR activity, and two C-terminal ACT domains that seem to have a
CC       role in glutamine sensing. {ECO:0000255|HAMAP-Rule:MF_00277}.
CC   -!- SIMILARITY: Belongs to the GlnD family. {ECO:0000255|HAMAP-
CC       Rule:MF_00277}.
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DR   EMBL; AE017282; AAU93245.1; -; Genomic_DNA.
DR   RefSeq; WP_010959913.1; NC_002977.6.
DR   AlphaFoldDB; Q60BB2; -.
DR   SMR; Q60BB2; -.
DR   STRING; 243233.MCA0565; -.
DR   KEGG; mca:MCA0565; -.
DR   eggNOG; COG2844; Bacteria.
DR   HOGENOM; CLU_012833_0_0_6; -.
DR   Proteomes; UP000006821; Chromosome.
DR   GO; GO:0008773; F:[protein-PII] uridylyltransferase activity; ISS:JCVI.
DR   GO; GO:0008081; F:phosphoric diester hydrolase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0006542; P:glutamine biosynthetic process; ISS:JCVI.
DR   GO; GO:0009399; P:nitrogen fixation; IEA:UniProtKB-UniRule.
DR   GO; GO:0006808; P:regulation of nitrogen utilization; IEA:UniProtKB-UniRule.
DR   CDD; cd04899; ACT_ACR-UUR-like_2; 1.
DR   CDD; cd04900; ACT_UUR-like_1; 1.
DR   CDD; cd00077; HDc; 1.
DR   CDD; cd05401; NT_GlnE_GlnD_like; 1.
DR   Gene3D; 1.10.3090.10; cca-adding enzyme, domain 2; 1.
DR   Gene3D; 1.20.120.330; Nucleotidyltransferases domain 2; 1.
DR   HAMAP; MF_00277; PII_uridylyl_transf; 1.
DR   InterPro; IPR045865; ACT-like_dom_sf.
DR   InterPro; IPR002912; ACT_dom.
DR   InterPro; IPR003607; HD/PDEase_dom.
DR   InterPro; IPR006674; HD_domain.
DR   InterPro; IPR043519; NT_sf.
DR   InterPro; IPR013546; PII_UdlTrfase/GS_AdlTrfase.
DR   InterPro; IPR002934; Polymerase_NTP_transf_dom.
DR   InterPro; IPR010043; UTase/UR.
DR   NCBIfam; TIGR01693; UTase_glnD; 1.
DR   PANTHER; PTHR47320; BIFUNCTIONAL URIDYLYLTRANSFERASE/URIDYLYL-REMOVING ENZYME; 1.
DR   PANTHER; PTHR47320:SF1; BIFUNCTIONAL URIDYLYLTRANSFERASE_URIDYLYL-REMOVING ENZYME; 1.
DR   Pfam; PF01842; ACT; 1.
DR   Pfam; PF08335; GlnD_UR_UTase; 1.
DR   Pfam; PF01966; HD; 1.
DR   Pfam; PF01909; NTP_transf_2; 1.
DR   PIRSF; PIRSF006288; PII_uridyltransf; 1.
DR   SMART; SM00471; HDc; 1.
DR   SUPFAM; SSF55021; ACT-like; 1.
DR   SUPFAM; SSF109604; HD-domain/PDEase-like; 1.
DR   SUPFAM; SSF81301; Nucleotidyltransferase; 1.
DR   SUPFAM; SSF81593; Nucleotidyltransferase substrate binding subunit/domain; 1.
DR   PROSITE; PS51671; ACT; 2.
DR   PROSITE; PS51831; HD; 1.
PE   3: Inferred from homology;
KW   Hydrolase; Magnesium; Multifunctional enzyme; Nitrogen fixation;
KW   Nucleotidyltransferase; Reference proteome; Repeat; Transferase.
FT   CHAIN           1..877
FT                   /note="Bifunctional uridylyltransferase/uridylyl-removing
FT                   enzyme"
FT                   /id="PRO_0000192744"
FT   DOMAIN          454..576
FT                   /note="HD"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT   DOMAIN          696..778
FT                   /note="ACT 1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00277"
FT   DOMAIN          805..877
FT                   /note="ACT 2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00277"
FT   REGION          1..335
FT                   /note="Uridylyltransferase"
FT   REGION          336..695
FT                   /note="Uridylyl-removing"
SQ   SEQUENCE   877 AA;  99886 MW;  54954C07DB9E3AE9 CRC64;
     MDGPNSDRAH DRHAFDRVAA CKARIQHNTA ELAERFRTGT PVADLIRERT AFIDHLLSEA
     WDRRIGRGAT DVALVAVGGY GRGELLLHSD VDLLILLDEA APSSRKQDLS DFLRLLWDIG
     LKPGHSVRSP AECAEAARTD QTIITNLLEG RLLVGSAALW EAVRSETAPE RMWSSAAFFE
     AKMAEQRIRY SKYHNTAYNL EPNVKEGPGG LRDIQLIGWI IRRHSDARGL QDLVAHGWLT
     DAEYRELKEA QAFLWRIRFA LHALTGRCED RLLFDYQREL AGLFGYRGET SNEVVEGFMQ
     DYFRTVTGVE RLNELLLQLF NEAVLHRDDA FSPTPVNDHF QAVNDYLEAV HPAVFREHPL
     ALLEVFLILQ KNSALEGVRA ATIRLIRQHI HLIDDAFRND PEACRLFMDI LRQPGGVTHQ
     LRRMNRYGVL AAYLPEFGRV VGRMQYDLFH VYTVDEHTLF VVRNLRRFAL EEFQQENPLC
     YELFQLIEKP ELLYIAALMH DIAKGSDGDH SEVGERIAEE FCRRHRIGPR ETLLVKWLVR
     HHLVMSMTAQ RKDLSDPEVI HEFAQIVRNQ NTLNHLYLLT VADIRATNPS LWNSWKGALL
     QELYTSTSWT LRRGLDTPPD YAEQISAAKD EARTLLQRFG LAEDAITAVW ENIGDDYFLR
     FLPEEIAWHT TAIAACRPEH LPLVLLRPES LRGSVEVFIY ERNRDFLFAQ TTAVLDQLGL
     TVLDAKIIAS RQGFALLSFN VLERSGTAPE GLFRLVQICD RLKEALSGGG APPPAVSRLA
     TRQIRHFTVP TKVFFHDDPQ NRFSILELIA TDRPGLLSKV GQAFMRTGIR LHNAKISTVG
     SRAEDIFFIT DREDRPLDGE ADRAALRRVL IEFVGDQ
//