GLND_ECOLI
ID GLND_ECOLI Reviewed; 890 AA.
AC P27249; Q2MCG1;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 2.
DT 03-AUG-2022, entry version 183.
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=b0167, JW0162;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RA Park S.-C., Kim I.H., Rhee S.G.;
RT "Molecular cloning and sequencing of gldD, the gene for uridylyl
RT transferase and uridyl removing enzyme of E. coli.";
RL Submitted (JUL-1992) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8412694; DOI=10.1111/j.1365-2958.1993.tb01706.x;
RA van Heeswijk W.C., Rabenberg M., Westerhoff H.V., Kahn D.D.;
RT "The genes of the glutamine synthetase adenylylation cascade are not
RT regulated by nitrogen in Escherichia coli.";
RL Mol. Microbiol. 9:443-458(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8202364; DOI=10.1093/nar/22.9.1637;
RA Fujita N., Mori H., Yura T., Ishihama A.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-
RT 4.1 min (110,917-193,643 bp) region.";
RL Nucleic Acids Res. 22:1637-1639(1994).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [7]
RP IDENTIFICATION, FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=6130097; DOI=10.1016/s0021-9258(18)32914-4;
RA Garcia E., Rhee S.G.;
RT "Cascade control of Escherichia coli glutamine synthetase. Purification and
RT properties of PII uridylyltransferase and uridylyl-removing enzyme.";
RL J. Biol. Chem. 258:2246-2253(1983).
RN [8]
RP FUNCTION, AND ACTIVITY REGULATION.
RC STRAIN=K12;
RX PubMed=8843440; DOI=10.1046/j.1365-2958.1996.6281349.x;
RA van Heeswijk W.C., Hoving S., Molenaar D., Stegeman B., Kahn D.,
RA Westerhoff H.V.;
RT "An alternative PII protein in the regulation of glutamine synthetase in
RT Escherichia coli.";
RL Mol. Microbiol. 21:133-146(1996).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, KINETIC
RP PARAMETERS, SUBSTRATE SPECIFICITY, AND KINETIC MECHANISM.
RX PubMed=9737855; DOI=10.1021/bi980667m;
RA Jiang P., Peliska J.A., Ninfa A.J.;
RT "Enzymological characterization of the signal-transducing
RT uridylyltransferase/uridylyl-removing enzyme (EC 2.7.7.59) of Escherichia
RT coli and its interaction with the PII protein.";
RL Biochemistry 37:12782-12794(1998).
RN [10]
RP FUNCTION WITH GLNK AS SUBSTRATE, CATALYTIC ACTIVITY, AND ACTIVITY
RP REGULATION.
RX PubMed=10231487; DOI=10.1046/j.1365-2958.1999.01349.x;
RA Atkinson M.R., Ninfa A.J.;
RT "Characterization of the GlnK protein of Escherichia coli.";
RL Mol. Microbiol. 32:301-313(1999).
RN [11]
RP FUNCTION, CATALYTIC ACTIVITY, DOMAIN, ACTIVITY REGULATION, AND MUTAGENESIS
RP OF GLY-93; GLY-94; ASP-107 AND 514-HIS-ASP-515.
RX PubMed=20363937; DOI=10.1128/jb.01674-09;
RA Zhang Y., Pohlmann E.L., Serate J., Conrad M.C., Roberts G.P.;
RT "Mutagenesis and functional characterization of the four domains of GlnD, a
RT bifunctional nitrogen sensor protein.";
RL J. Bacteriol. 192:2711-2721(2010).
CC -!- FUNCTION: Modifies, by uridylylation and deuridylylation, the PII
CC regulatory proteins GlnB and GlnK, in response to the nitrogen status
CC of the cell that GlnD senses through the glutamine level. Under low
CC glutamine levels, catalyzes the conversion of the PII proteins and UTP
CC 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:0000269|PubMed:10231487, ECO:0000269|PubMed:20363937,
CC ECO:0000269|PubMed:6130097, ECO:0000269|PubMed:8843440,
CC ECO:0000269|PubMed:9737855}.
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;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00277,
CC ECO:0000269|PubMed:9737855};
CC Note=Mg(2+) appears to be the physiologically relevant metal ion
CC cofactor for both transferase and uridylyl-removing activities.
CC {ECO:0000255|HAMAP-Rule:MF_00277, ECO:0000269|PubMed:9737855};
CC -!- ACTIVITY REGULATION: Uridylyltransferase (UTase) activity is inhibited
CC by glutamine, while glutamine activates uridylyl-removing (UR)
CC activity. Both reactions are activated by ATP and 2-ketoglutarate, via
CC the binding of these effector molecules to the substrates PII and PII-
CC UMP. {ECO:0000255|HAMAP-Rule:MF_00277, ECO:0000269|PubMed:10231487,
CC ECO:0000269|PubMed:20363937, ECO:0000269|PubMed:8843440,
CC ECO:0000269|PubMed:9737855}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.0 uM for GlnB protein {ECO:0000269|PubMed:9737855};
CC KM=40 uM for UTP {ECO:0000269|PubMed:9737855};
CC KM=2.3 uM for uridylyl-[protein-PII] (in the absence of glutamine)
CC {ECO:0000269|PubMed:9737855};
CC KM=0.82 uM for uridylyl-[protein-PII] (in the presence of 2.5 mM
CC glutamine) {ECO:0000269|PubMed:9737855};
CC Note=kcat is 137 min(-1) for the UTase reaction. kcat is 2.7 min(-1)
CC for the UR reaction in the absence of glutamine, and 6.5 min(-1) in
CC the presence of 2.5 mM glutamine.;
CC -!- SUBUNIT: Monomer. Can also form homooligomers that are much less
CC active. {ECO:0000269|PubMed:6130097}.
CC -!- INTERACTION:
CC P27249; P0A9Z1: glnB; NbExp=3; IntAct=EBI-552032, EBI-551053;
CC P27249; P0AC55: glnK; NbExp=3; IntAct=EBI-552032, EBI-559503;
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 ECO:0000269|PubMed:20363937}.
CC -!- MISCELLANEOUS: The transferase reaction proceeds by an ordered bi-bi
CC kinetic mechanism, with PII binding before UTP and pyrophosphate (PPi)
CC released before PII-UMP. The uridylyl-removing reaction proceeds with
CC rapid equilibrium binding of substrate and random release of products
CC (PubMed:9737855). {ECO:0000305|PubMed:9737855}.
CC -!- SIMILARITY: Belongs to the GlnD family. {ECO:0000255|HAMAP-
CC Rule:MF_00277}.
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DR EMBL; M96431; AAA23878.1; -; Genomic_DNA.
DR EMBL; Z21842; CAA79887.1; -; Genomic_DNA.
DR EMBL; U70214; AAB08596.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73278.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76045.1; -; Genomic_DNA.
DR PIR; G64740; G64740.
DR RefSeq; NP_414709.1; NC_000913.3.
DR RefSeq; WP_001094586.1; NZ_SSZK01000004.1.
DR AlphaFoldDB; P27249; -.
DR SMR; P27249; -.
DR BioGRID; 4259747; 20.
DR BioGRID; 849263; 3.
DR DIP; DIP-9779N; -.
DR IntAct; P27249; 24.
DR STRING; 511145.b0167; -.
DR jPOST; P27249; -.
DR PaxDb; P27249; -.
DR PRIDE; P27249; -.
DR EnsemblBacteria; AAC73278; AAC73278; b0167.
DR EnsemblBacteria; BAE76045; BAE76045; BAE76045.
DR GeneID; 944863; -.
DR KEGG; ecj:JW0162; -.
DR KEGG; eco:b0167; -.
DR PATRIC; fig|1411691.4.peg.2114; -.
DR EchoBASE; EB1383; -.
DR eggNOG; COG2844; Bacteria.
DR HOGENOM; CLU_012833_0_0_6; -.
DR InParanoid; P27249; -.
DR OMA; WIAKYVY; -.
DR PhylomeDB; P27249; -.
DR BioCyc; EcoCyc:GLND-MON; -.
DR BRENDA; 2.7.7.59; 2026.
DR SABIO-RK; P27249; -.
DR PRO; PR:P27249; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008773; F:[protein-PII] uridylyltransferase activity; IDA:EcoCyc.
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; cd00077; HDc; 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 PANTHER; PTHR47320; PTHR47320; 1.
DR Pfam; PF01842; ACT; 2.
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; SSF55021; 2.
DR SUPFAM; SSF81301; SSF81301; 1.
DR TIGRFAMs; TIGR01693; UTase_glnD; 1.
DR PROSITE; PS51671; ACT; 2.
DR PROSITE; PS51831; HD; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Magnesium; Multifunctional enzyme; Nucleotidyltransferase;
KW Reference proteome; Repeat; Transferase.
FT CHAIN 1..890
FT /note="Bifunctional uridylyltransferase/uridylyl-removing
FT enzyme"
FT /id="PRO_0000192732"
FT DOMAIN 468..590
FT /note="HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT DOMAIN 709..789
FT /note="ACT 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00277"
FT DOMAIN 816..890
FT /note="ACT 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00277"
FT REGION 1..349
FT /note="Uridylyltransferase"
FT REGION 350..708
FT /note="Uridylyl-removing"
FT MUTAGEN 93
FT /note="G->L,V: Loss of UTase activity, while no significant
FT effect on UR activity."
FT /evidence="ECO:0000269|PubMed:20363937"
FT MUTAGEN 94
FT /note="G->D: Loss of UTase activity, while no significant
FT effect on UR activity."
FT /evidence="ECO:0000269|PubMed:20363937"
FT MUTAGEN 107
FT /note="D->A,V,Y: Loss of UTase activity, while no
FT significant effect on UR activity."
FT /evidence="ECO:0000269|PubMed:20363937"
FT MUTAGEN 514..515
FT /note="HD->AA,QN: Loss of UR activity, while no significant
FT effect on UTase activity."
FT /evidence="ECO:0000269|PubMed:20363937"
FT CONFLICT 47
FT /note="L -> S (in Ref. 1; AAA23878)"
FT /evidence="ECO:0000305"
FT CONFLICT 225
FT /note="G -> A (in Ref. 3)"
FT /evidence="ECO:0000305"
FT CONFLICT 357..358
FT /note="RG -> TR (in Ref. 1; AAA23878)"
FT /evidence="ECO:0000305"
FT CONFLICT 523
FT /note="D -> H (in Ref. 1; AAA23878)"
FT /evidence="ECO:0000305"
FT CONFLICT 703
FT /note="A -> R (in Ref. 2; CAA79887)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 890 AA; 102390 MW; 6FF0006341A71D34 CRC64;
MNTLPEQYAN TALPTLPGQP QNPCVWPRDE LTVGGIKAHI DTFQRWLGDA FDNGISAEQL
IEARTEFIDQ LLQRLWIEAG FSQIADLALV AVGGYGRGEL HPLSDVDLLI LSRKKLPDDQ
AQKVGELLTL LWDVKLEVGH SVRTLEECML EGLSDLTVAT NLIESRLLIG DVALFLELQK
HIFSEGFWPS DKFYAAKVEE QNQRHQRYHG TSYNLEPDIK SSPGGLRDIH TLQWVARRHF
GATSLDEMVG FGFLTSAERA ELNECLHILW RIRFALHLVV SRYDNRLLFD RQLSVAQRLN
YSGEGNEPVE RMMKDYFRVT RRVSELNQML LQLFDEAILA LPADEKPRPI DDEFQLRGTL
IDLRDETLFM RQPEAILRMF YTMVHNSAIT GIYSTTLRQL RHARRHLQQP LCNIPEARKL
FLSILRHPGA VRRGLLPMHR HSVLGAYMPQ WSHIVGQMQF DLFHAYTVDE HTIRVMLKLE
SFASEETRQR HPLCVDVWPR LPSTELIFIA ALFHDIAKGR GGDHSILGAQ DVVHFAELHG
LNSRETQLVA WLVRQHLLMS VTAQRRDIQD PEVIKQFAEE VQTENRLRYL VCLTVADICA
TNETLWNSWK QSLLRELYFA TEKQLRRGMQ NTPDMRERVR HHQLQALALL RMDNIDEEAL
HQIWSRCRAN YFVRHSPNQL AWHARHLLQH DLSKPLVLLS PQATRGGTEI FIWSPDRPYL
FAAVCAELDR RNLSVHDAQI FTTRDGMAMD TFIVLEPDGN PLSADRHEVI RFGLEQVLTQ
SSWQPPQPRR QPAKLRHFTV ETEVTFLPTH TDRKSFLELI ALDQPGLLAR VGKIFADLGI
SLHGARITTI GERVEDLFII ATADRRALNN ELQQEVHQRL TEALNPNDKG
