ID   GLND_RHILO              Reviewed;         933 AA.
AC   Q98C27;
DT   13-AUG-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2001, sequence version 1.
DT   27-MAR-2024, entry version 126.
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=mll5321;
OS   Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS   (Mesorhizobium loti (strain MAFF 303099)).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Phyllobacteriaceae; Mesorhizobium.
OX   NCBI_TaxID=266835;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX   PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA   Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA   Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA   Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA   Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA   Tabata S.;
RT   "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT   Mesorhizobium loti.";
RL   DNA Res. 7:331-338(2000).
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; BA000012; BAB51794.1; -; Genomic_DNA.
DR   RefSeq; WP_010913133.1; NC_002678.2.
DR   AlphaFoldDB; Q98C27; -.
DR   SMR; Q98C27; -.
DR   KEGG; mlo:mll5321; -.
DR   PATRIC; fig|266835.9.peg.4220; -.
DR   eggNOG; COG2844; Bacteria.
DR   HOGENOM; CLU_012833_1_0_5; -.
DR   Proteomes; UP000000552; 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: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; 3.30.70.260; -; 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; 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; 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; Nitrogen fixation;
KW   Nucleotidyltransferase; Repeat; Transferase.
FT   CHAIN           1..933
FT                   /note="Bifunctional uridylyltransferase/uridylyl-removing
FT                   enzyme"
FT                   /id="PRO_0000192759"
FT   DOMAIN          496..619
FT                   /note="HD"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT   DOMAIN          737..818
FT                   /note="ACT 1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00277"
FT   DOMAIN          848..922
FT                   /note="ACT 2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00277"
FT   REGION          1..379
FT                   /note="Uridylyltransferase"
FT   REGION          380..736
FT                   /note="Uridylyl-removing"
SQ   SEQUENCE   933 AA;  105280 MW;  79BF065DAC796FF8 CRC64;
     MAKISLKLDE LIDGEALRRE MTALTTATAG DGSGAAARAG VLQLLKARLA EGRKIAEAML
     KEDGGGNACA ERLSHLMDEL IRALYDFAAT HVYRVKNRSS AERMAVVAVG GYGRGTLAPG
     SDIDLLFLLP YKQTPWGEQT VEYMLYMLWD LGLKVGHATR NIDECLRLSR TDITIRTSIL
     EARFLWGERK LYDELMLRFD HEVVRTTGPE YVQAKLAERD ERHAKAGESR YLVEPNVKDG
     KGGLRDLQTL FWIGKYFYRV RTGEELVEKG VFTEAEYREF QKAEDFLWAV RCHMHFLTGK
     AEERLHFDIQ REIAERLGYT THPGLSAVER FMKHYFLVAK DVGDLTRIFC AALEEEQAKH
     VPGFNRIFLT FQRRKRKLAG TSDFIVDNHR INIADDQVFE RDPVNLLRLF WFADKHGLEF
     HPDALKLLTR SLGLVNKSLR RDEEANRLFL DILTSDRNAE LNLRRMNEAG LLGRLIPDFG
     KIVAMMQFSM YHHYTVDEHL IRCIGVLAEI ERGDGEKVHP LSHSLMPGLK KSREALYVAV
     LLHDIAKGRP EDHSEAGARI ARRICPHMGL SAADTETVAW LVENHLAMSM TAQTRDLNDR
     KTIEDFASIV QSVERLKLLL VLTVCDIRGV GPGVWNGWKG QLLRTLYYET ELLLTGGFSE
     VSRAQRTAAA RERLAEALAD WPDKDRKRYV GLHYENYLLT VDLPDQLRHA EFVREADAAG
     KKLATMVKTH QFEAVTEITV LAQDHPRLLS VIAGACVGAG GNIVDAQIFT TADGRALDTI
     LISREFDRDE DERRRAERVG RLIEDVLSGK SWLPEMIEKR TKPKRGAKVF KIPPRAEIRN
     TLSNRFSVIE VEGLDRPGLL SEITGTLSDL SLDIASAHIT TFGEKVIDTF YVTDLTGQKI
     DSPARIATIR NRLMATLEGI APERGGKAKA AAE
//