ID   GLND_RUEPO              Reviewed;         908 AA.
AC   Q5LWE5;
DT   08-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-2005, sequence version 1.
DT   27-MAR-2024, entry version 118.
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=SPO0397;
OS   Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter
OS   pomeroyi).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC   Roseobacteraceae; Ruegeria.
OX   NCBI_TaxID=246200;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX   PubMed=15602564; DOI=10.1038/nature03170;
RA   Moran M.A., Buchan A., Gonzalez J.M., Heidelberg J.F., Whitman W.B.,
RA   Kiene R.P., Henriksen J.R., King G.M., Belas R., Fuqua C., Brinkac L.M.,
RA   Lewis M., Johri S., Weaver B., Pai G., Eisen J.A., Rahe E., Sheldon W.M.,
RA   Ye W., Miller T.R., Carlton J., Rasko D.A., Paulsen I.T., Ren Q.,
RA   Daugherty S.C., DeBoy R.T., Dodson R.J., Durkin A.S., Madupu R.,
RA   Nelson W.C., Sullivan S.A., Rosovitz M.J., Haft D.H., Selengut J., Ward N.;
RT   "Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine
RT   environment.";
RL   Nature 432:910-913(2004).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX   PubMed=25780504; DOI=10.1186/1944-3277-9-11;
RA   Rivers A.R., Smith C.B., Moran M.A.;
RT   "An updated genome annotation for the model marine bacterium Ruegeria
RT   pomeroyi DSS-3.";
RL   Stand. Genomic Sci. 9:11-11(2014).
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; CP000031; AAV93715.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q5LWE5; -.
DR   SMR; Q5LWE5; -.
DR   STRING; 246200.SPO0397; -.
DR   PaxDb; 246200-SPO0397; -.
DR   KEGG; sil:SPO0397; -.
DR   eggNOG; COG2844; Bacteria.
DR   HOGENOM; CLU_012833_1_0_5; -.
DR   Proteomes; UP000001023; 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; 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   PIRSF; PIRSF006288; PII_uridyltransf; 1.
DR   SMART; SM00471; HDc; 1.
DR   SUPFAM; SSF55021; ACT-like; 2.
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..908
FT                   /note="Bifunctional uridylyltransferase/uridylyl-removing
FT                   enzyme"
FT                   /id="PRO_0000192769"
FT   DOMAIN          477..599
FT                   /note="HD"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT   DOMAIN          719..801
FT                   /note="ACT 1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00277"
FT   DOMAIN          829..904
FT                   /note="ACT 2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00277"
FT   REGION          1..360
FT                   /note="Uridylyltransferase"
FT   REGION          361..718
FT                   /note="Uridylyl-removing"
SQ   SEQUENCE   908 AA;  102501 MW;  AA6C869FD08E01F5 CRC64;
     MFDTPAVFAR ITEAAAEAAD NAALRGAVVA ILRDVQNAGR AAIAEGFAED PFAARPLTRA
     YTYLTDGMVK TAMYVASEIL HPLATPTQGE RIAVLAVGGF GRGEMAPFSD VDLLFLTPYK
     ITAWAESVIE SMLYILWDLR LKVGHSSRTV KDCIRLGRDD FTIRTAMLEH RFLAGHAPLA
     RSLDQRLKSE LYKDTQREFI EAKLEERDAR HRKQGERYMV EPNVKEGKGG LRDLQSLYWI
     AKYIYEVKET AELVPLGLFT PSEYRTFVQA EEFLWAVRAH LHLVTGRATE QLTFDLQVEV
     AARMGYQDRA GRRGVEVFMQ KYFREATRVG ELTRIFLTKL EAAHMKGAPL LERIFRRRRR
     IKQGYKVVRG RLDVVDPEAF LADKLNLLRI FEEALRTGML IHPDAMRLVT ANLDLIDDGM
     RNDKEARRIF LDLLLKHGNP ERALRRMNEL GVLSAFVPEF EPIVAMMQFN MYHSYTVDEH
     TIQTIVNLAQ IEKGELVESL PLASSILKAG VNRKVLYVAL LLHDIGKGRP EDHSILGARI
     ARKVAPRLGL SKADCETVEW LVRYHLLMSD MAQKRDISDP RTVRDFAKAV QTTKRLDLLT
     VLTVCDIRGV GPNTWNNWKA TLLRALHAET KRALEMGMEA LNREGRGNEA KKALRTALSD
     WPAGEVKTEI ARHYPPYWQG FNVETHVTFA EMLRQLEHSG DPGGIEIRLD PDEDRDATRA
     CFAMADHPGI FSRMAGALAL VGANVVDARS YTTKDGYVTD AFWIQDAEGH PYEAARLPRL
     SQMILKTLKG EVVARDALKS RDKIKKREKA FNVPTHITFD NEGSDIYTII EVDTRDRPGL
     LYDLARALAA ANVYIANAVI ATYGEQVVDS FYVKDMFGLK YHSEAKQRTL ETKLRKAITE
     GAERAAAS
//