ID D1KDX5_9GAMM Unreviewed; 838 AA.
AC D1KDX5;
DT 19-JAN-2010, integrated into UniProtKB/TrEMBL.
DT 19-JAN-2010, sequence version 1.
DT 24-JAN-2024, entry version 74.
DE RecName: Full=Bifunctional uridylyltransferase/uridylyl-removing enzyme {ECO:0000256|HAMAP-Rule:MF_00277};
DE Short=UTase/UR {ECO:0000256|HAMAP-Rule:MF_00277};
DE AltName: Full=Bifunctional [protein-PII] modification enzyme {ECO:0000256|HAMAP-Rule:MF_00277};
DE AltName: Full=Bifunctional nitrogen sensor protein {ECO:0000256|HAMAP-Rule:MF_00277};
DE Includes:
DE RecName: Full=[Protein-PII] uridylyltransferase {ECO:0000256|HAMAP-Rule:MF_00277};
DE Short=PII uridylyltransferase {ECO:0000256|HAMAP-Rule:MF_00277};
DE Short=UTase {ECO:0000256|HAMAP-Rule:MF_00277};
DE EC=2.7.7.59 {ECO:0000256|HAMAP-Rule:MF_00277};
DE Includes:
DE RecName: Full=[Protein-PII]-UMP uridylyl-removing enzyme {ECO:0000256|HAMAP-Rule:MF_00277};
DE Short=UR {ECO:0000256|HAMAP-Rule:MF_00277};
DE EC=3.1.4.- {ECO:0000256|HAMAP-Rule:MF_00277};
GN Name=glnD {ECO:0000256|HAMAP-Rule:MF_00277};
GN ORFNames=Sup05_0972 {ECO:0000313|EMBL:EEZ79673.1};
OS uncultured Candidatus Thioglobus sp.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Candidatus Thioglobus;
OC environmental samples.
OX NCBI_TaxID=655186 {ECO:0000313|EMBL:EEZ79673.1, ECO:0000313|Proteomes:UP000009383};
RN [1] {ECO:0000313|EMBL:EEZ79673.1, ECO:0000313|Proteomes:UP000009383}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=19900896; DOI=10.1126/science.1175309;
RA Walsh D.A., Zaikova E., Howes C.L., Song Y.C., Wright J.J., Tringe S.G.,
RA Tortell P.D., Hallam S.J.;
RT "Metagenome of a versatile chemolithoautotroph from expanding oceanic dead
RT zones.";
RL Science 326:578-582(2009).
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 metabolism.
CC {ECO:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_00277};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=guanosine 3',5'-bis(diphosphate) + H2O = diphosphate + GDP +
CC H(+); Xref=Rhea:RHEA:14253, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:58189, ChEBI:CHEBI:77828; EC=3.1.7.2;
CC Evidence={ECO:0000256|ARBA:ARBA00024273};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00277};
CC -!- ACTIVITY REGULATION: Uridylyltransferase (UTase) activity is inhibited
CC by glutamine, while glutamine activates uridylyl-removing (UR)
CC activity. {ECO:0000256|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:0000256|HAMAP-Rule:MF_00277}.
CC -!- SIMILARITY: Belongs to the GlnD family. {ECO:0000256|HAMAP-
CC Rule:MF_00277}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00277}.
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DR EMBL; GG730026; EEZ79673.1; -; Genomic_DNA.
DR AlphaFoldDB; D1KDX5; -.
DR STRING; 655186.Sup05_0972; -.
DR PATRIC; fig|655186.3.peg.165; -.
DR Proteomes; UP000009383; Unassembled WGS sequence.
DR GO; GO:0008773; F:[protein-PII] uridylyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008893; F:guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity; IEA:RHEA.
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; 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; 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 {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_00277};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00277};
KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268, ECO:0000256|HAMAP-
KW Rule:MF_00277};
KW Nucleotidyltransferase {ECO:0000256|HAMAP-Rule:MF_00277,
KW ECO:0000313|EMBL:EEZ79673.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000009383};
KW Repeat {ECO:0000256|ARBA:ARBA00022737};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00277}.
FT DOMAIN 429..538
FT /note="HD"
FT /evidence="ECO:0000259|PROSITE:PS51831"
FT DOMAIN 669..748
FT /note="ACT"
FT /evidence="ECO:0000259|PROSITE:PS51671"
FT DOMAIN 770..838
FT /note="ACT"
FT /evidence="ECO:0000259|PROSITE:PS51671"
FT REGION 1..311
FT /note="Uridylyltransferase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00277"
SQ SEQUENCE 838 AA; 96939 MW; 766A67F43AD8335D CRC64;
MNLEDFKKQY QKIQSSIQQG FLKDPDSVEA LVLGRSDAID TLLSDIWHSF KMGDELCLVA
VGGYGRSELH LYSDIDLLVL IPNESHNVHQ QSISNFLTFL WDVGLEVGHA TRDIQDCIHV
IDDLSVVTNL LESRLLIGNN LLFLKMRSMI KASDWSSQSF FVEKQKEQHN RHLNFSNTAY
NLEPNVKESP GGLRDIQTIA WVAKWYFDVN LLSDLIDKKY LTKNEYDLLR QGQLFLWKTR
LALHIIAKHR EDRLAFQYQK QVATMLGYID GDSMAVESLM KDYYQTVTKV SRLNDILLQL
LEDRVLHTQD LNERFIISYG YIKASDDQVF IKNPSAFLEI FLLITRHNYV RGISAGTLRL
MQFSLNIIDE NYHKKRNNNR LFIELLQQKQ GINKALKLMN RYGILEHYIP SFGKIIGLMQ
YDLFHAYTVD QHTLFVIRNL RRFFVPEFAK EFSLCSEIAQ TIKKPELLLL AGLFHDIAKG
RGGDHAQLGG EDARGFCKHH QLKTQETNLV ANLVEKHLLM SQTAQKKNID DIEVVDEFAQ
AVGSVEFLEF LYLLTVADIR STKADLWNDW KDSLLKKLFY KTKDHLQSGK TELPNINQQI
ETIKQSVAIE VQRQGYEVNE IENLFATLPK DYFLRYEIDE ILWHLGVVIK CQDQEVVVAS
KISEYNVVDV FVCSKDSKGL FFRLVSIIEK LGLDIVDAKI LTTKDHKVYN TISILQDRMF
EQININQEIE DELSQSSSGV KEVGVKLSHR YFDYKMRINF SVNKKWNLTQ VEISVIDKQG
LLSNIAYVFY QLNISIINAR IATLGERVED VFFVSSAQNK PLSKDEERAL QRALEERL
//