ID   GLND_NITOC              Reviewed;         892 AA.
AC   Q3JCX7;
DT   04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   08-NOV-2005, sequence version 1.
DT   27-MAR-2024, entry version 107.
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=Noc_0806;
OS   Nitrosococcus oceani (strain ATCC 19707 / BCRC 17464 / JCM 30415 / NCIMB
OS   11848 / C-107).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales; Chromatiaceae;
OC   Nitrosococcus.
OX   NCBI_TaxID=323261;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 19707 / BCRC 17464 / JCM 30415 / NCIMB 11848 / C-107;
RX   PubMed=16957257; DOI=10.1128/aem.00463-06;
RA   Klotz M.G., Arp D.J., Chain P.S.G., El-Sheikh A.F., Hauser L.J.,
RA   Hommes N.G., Larimer F.W., Malfatti S.A., Norton J.M., Poret-Peterson A.T.,
RA   Vergez L.M., Ward B.B.;
RT   "Complete genome sequence of the marine, chemolithoautotrophic, ammonia-
RT   oxidizing bacterium Nitrosococcus oceani ATCC 19707.";
RL   Appl. Environ. Microbiol. 72:6299-6315(2006).
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 assimilation and
CC       metabolism. {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; CP000127; ABA57319.1; -; Genomic_DNA.
DR   RefSeq; WP_002811130.1; NC_007484.1.
DR   AlphaFoldDB; Q3JCX7; -.
DR   SMR; Q3JCX7; -.
DR   STRING; 323261.Noc_0806; -.
DR   KEGG; noc:Noc_0806; -.
DR   eggNOG; COG2844; Bacteria.
DR   HOGENOM; CLU_012833_0_0_6; -.
DR   InParanoid; Q3JCX7; -.
DR   Proteomes; UP000006838; Chromosome.
DR   GO; GO:0008773; F:[protein-PII] uridylyltransferase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0008081; F:phosphoric diester hydrolase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0006807; P:nitrogen compound metabolic process; IEA:InterPro.
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; 3.30.460.10; Beta Polymerase, domain 2; 1.
DR   Gene3D; 1.10.3090.10; cca-adding enzyme, 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; 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; SSF81301; Nucleotidyltransferase; 1.
DR   SUPFAM; SSF81593; Nucleotidyltransferase substrate binding subunit/domain; 1.
DR   SUPFAM; SSF81891; Poly A polymerase C-terminal region-like; 1.
DR   PROSITE; PS51671; ACT; 2.
DR   PROSITE; PS51831; HD; 1.
PE   3: Inferred from homology;
KW   Hydrolase; Magnesium; Multifunctional enzyme; Nucleotidyltransferase;
KW   Reference proteome; Repeat; Transferase.
FT   CHAIN           1..892
FT                   /note="Bifunctional uridylyltransferase/uridylyl-removing
FT                   enzyme"
FT                   /id="PRO_0000231683"
FT   DOMAIN          467..589
FT                   /note="HD"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT   DOMAIN          711..786
FT                   /note="ACT 1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00277"
FT   DOMAIN          822..892
FT                   /note="ACT 2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00277"
FT   REGION          1..348
FT                   /note="Uridylyltransferase"
FT   REGION          349..710
FT                   /note="Uridylyl-removing"
SQ   SEQUENCE   892 AA;  103332 MW;  01DF936D6F5B286B CRC64;
     MPNFTGNTRP DPTLFEPAAF AKWIDTSEAP LLLLRSFLKE GIENLKQRFL TGTSAAELLP
     LHAWLVDQIL VQACRLHTKK CPERVALVAV GGYGRGTLHP YSDIDILLLL TEETDSILQN
     SIGHFISFLW DTGLEMGHSV RTVAECQQAA RDDLSFITSL MEARLLFGPE LLFKNLQTAI
     APEQIWNSRQ FFLAKQAEQI TRHHKYHDTA YNLEPNLKEG PGGLRDIQMI QWVSKRYFNT
     WSFDSLLQHD FLTVSERKEL LESQSFLWQL RYGLHTLTGR REDRLLFDHQ IALAKQLGYH
     DQGPHLAVEQ LMKDYYRTAE NTGRLNEMLL QLLEERILLV DAKVHVRPIN ERFQARNGFL
     EVINPSVFKH TPSALLEVFL LLQQHPEIKG VRASTIRLIR EHRHLIDDNF RADSFNRALF
     MEIMRQSRGI TRELRRMNKY GILGAYLPVF GKIVGQMQYD MFHAYTVDEH TLFLIHNLRR
     FALPKYAQEL PLCSEIFQRI SKPELLYLAG LFHDIAKGRG GDHSKLGAKD ALRFCLYHGL
     SRDDSRLVAW LVAHHLLMSM TAQRRDINDP KVIQRFAREV GDERRLNHLY LLTAADIRAT
     NPNLWNSWKD ALLNKLYTAT QQALRQGLEY PVDKKEHIRD IQNEARQALL KDGWTEQKLD
     ILWSQIDADY FLRHTPNEIR WHIKALAQKE PHDGAPRILV RIHNQEPGTM EVFIYARAHA
     LIFTVTTRTM AQLDLDVLDA RIITTGHGFV LESFVVREAA TIRAEADLEF RLQEIQEVLT
     QRLTQPDRAP PYRPGFIPRK LKLFKFPTTI TFTKDRRNQC TVMELTTNNW PGLLSRVCRA
     LASCQVRLVN AKITTLGTQV VDVFFICNQQ DKPLTPEQQQ QLKEAIYTYL ER
//