PYRH_ECOLI
ID PYRH_ECOLI Reviewed; 241 AA.
AC P0A7E9; P29464;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Uridylate kinase;
DE Short=UK;
DE EC=2.7.4.22 {ECO:0000269|PubMed:17210578};
DE AltName: Full=Uridine monophosphate kinase;
DE Short=UMP kinase;
DE Short=UMPK;
GN Name=pyrH; Synonyms=smbA; OrderedLocusNames=b0171, JW0166;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CHARACTERIZATION.
RC STRAIN=K12;
RA Smallshaw J.E., Kelln R.A.;
RT "Cloning, nucleotide sequence and expression of the Escherichia coli K-12
RT pyrH gene encoding UMP kinase.";
RL Life Sci. Adv. (Genet.) 11:59-65(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1447125; DOI=10.1128/jb.174.23.7517-7526.1992;
RA Yamanaka K., Ogura T., Niki H., Hiraga S.;
RT "Identification and characterization of the smbA gene, a suppressor of the
RT mukB null mutant of Escherichia coli.";
RL J. Bacteriol. 174:7517-7526(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-8, FUNCTION,
RP BIOPHYSICOCHEMICAL PROPERTIES, CHARACTERIZATION, SUBUNIT, AND MUTAGENESIS
RP OF ASP-201.
RX PubMed=7711027; DOI=10.1021/bi00015a018;
RA Serina L., Blondin C., Krin E., Sismeiro O., Danchin A., Sakamoto H.,
RA Gilles A.-M., Barzu O.;
RT "Escherichia coli UMP-kinase, a member of the aspartokinase family, is a
RT hexamer regulated by guanine nucleotides and UTP.";
RL Biochemistry 34:5066-5074(1995).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T.,
RA Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S.,
RA Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 4.0
RT - 6.0 min (189,987 - 281,416bp) region.";
RL Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
RN [6]
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 [7]
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 [8]
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 [9]
RP CHARACTERIZATION.
RX PubMed=8190075; DOI=10.1007/bf00283870;
RA Yamanaka K., Ogura T., Koonin E.V., Niki H., Hiraga S.;
RT "Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia
RT coli.";
RL Mol. Gen. Genet. 243:9-16(1994).
RN [10]
RP SUBCELLULAR LOCATION.
RX PubMed=9922246; DOI=10.1128/jb.181.3.833-840.1999;
RA Landais S., Gounon P., Laurent-Winter C., Mazie J.-C., Danchin A.,
RA Barzu O., Sakamoto H.;
RT "Immunochemical analysis of UMP kinase from Escherichia coli.";
RL J. Bacteriol. 181:833-840(1999).
RN [11]
RP MUTAGENESIS OF ARG-62; ASP-77; ASP-146; ASP-159; ASP-174 AND ASP-201.
RX PubMed=9457846; DOI=10.1128/jb.180.3.473-477.1998;
RA Bucurenci N., Serina L., Zaharia C., Landais S., Danchin A., Barzu O.;
RT "Mutational analysis of UMP kinase from Escherichia coli.";
RL J. Bacteriol. 180:473-477(1998).
RN [12]
RP ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY, AND
RP PATHWAY.
RX PubMed=17210578; DOI=10.1074/jbc.m606963200;
RA Evrin C., Straut M., Slavova-Azmanova N., Bucurenci N., Onu A., Assairi L.,
RA Ionescu M., Palibroda N., Barzu O., Gilles A.-M.;
RT "Regulatory mechanisms differ in UMP kinases from Gram-negative and Gram-
RT positive bacteria.";
RL J. Biol. Chem. 282:7242-7253(2007).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF MUTANT ASN-159 IN COMPLEX WITH
RP UMP; UDP AND UTP, ACTIVITY REGULATION, AND MUTAGENESIS OF THR-138 AND
RP ASN-140.
RX PubMed=15857829; DOI=10.1074/jbc.m501849200;
RA Briozzo P., Evrin C., Meyer P., Assairi L., Joly N., Barzu O.,
RA Gilles A.-M.;
RT "Structure of Escherichia coli UMP kinase differs from that of other
RT nucleoside monophosphate kinases and sheds new light on enzyme
RT regulation.";
RL J. Biol. Chem. 280:25533-25540(2005).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH GTP, ACTIVITY
RP REGULATION, AND MUTAGENESIS OF ASP-93 AND ASN-140.
RX PubMed=18945668; DOI=10.1074/jbc.m802614200;
RA Meyer P., Evrin C., Briozzo P., Joly N., Barzu O., Gilles A.-M.;
RT "Structural and functional characterization of Escherichia coli UMP kinase
RT in complex with its allosteric regulator GTP.";
RL J. Biol. Chem. 283:36011-36018(2008).
CC -!- FUNCTION: Catalyzes the reversible phosphorylation of UMP to UDP, with
CC ATP as the most efficient phosphate donor.
CC {ECO:0000269|PubMed:7711027}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + UMP = ADP + UDP; Xref=Rhea:RHEA:24400,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:57865, ChEBI:CHEBI:58223,
CC ChEBI:CHEBI:456216; EC=2.7.4.22;
CC Evidence={ECO:0000269|PubMed:17210578};
CC -!- ACTIVITY REGULATION: Allosterically activated by GTP. Competitively
CC inhibited by magnesium-free UTP. Magnesium-bound UTP is unable to
CC inhibit enzyme activity. {ECO:0000269|PubMed:15857829,
CC ECO:0000269|PubMed:17210578, ECO:0000269|PubMed:18945668}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=210 uM for ATP (in the presence of 0.3 mM UMP)
CC {ECO:0000269|PubMed:17210578};
CC KM=50 uM for UMP (in the presence of 0.2 mM ATP)
CC {ECO:0000269|PubMed:17210578};
CC Vmax=62.4 umol/min/mg enzyme with ATP as substrate (in the presence
CC of 0.3 mM UMP) {ECO:0000269|PubMed:17210578};
CC Vmax=46.1 umol/min/mg enzyme with UMP as substrate (in the presence
CC of 0.2 mM ATP) {ECO:0000269|PubMed:17210578};
CC -!- PATHWAY: Pyrimidine metabolism; CTP biosynthesis via de novo pathway;
CC UDP from UMP (UMPK route): step 1/1. {ECO:0000269|PubMed:17210578}.
CC -!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:15857829,
CC ECO:0000269|PubMed:7711027}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:9922246}. Note=Is
CC predominantly localized near the bacterial membranes.
CC -!- MISCELLANEOUS: The peripheral distribution of PyrH is related most
CC probably to its role in the synthesis of membrane sugar components.
CC -!- SIMILARITY: Belongs to the UMP kinase family. {ECO:0000305}.
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DR EMBL; X78809; CAA55388.1; -; Genomic_DNA.
DR EMBL; D13334; BAA02598.1; -; Genomic_DNA.
DR EMBL; U70214; AAB08600.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73282.1; -; Genomic_DNA.
DR EMBL; AP009048; BAB96747.1; -; Genomic_DNA.
DR PIR; B45269; B45269.
DR RefSeq; NP_414713.1; NC_000913.3.
DR RefSeq; WP_000224573.1; NZ_STEB01000032.1.
DR PDB; 2BND; X-ray; 2.60 A; A/B=1-241.
DR PDB; 2BNE; X-ray; 2.30 A; A/B=1-241.
DR PDB; 2BNF; X-ray; 2.45 A; A/B=1-241.
DR PDB; 2V4Y; X-ray; 2.80 A; A/B/C/D/E/F=1-241.
DR PDBsum; 2BND; -.
DR PDBsum; 2BNE; -.
DR PDBsum; 2BNF; -.
DR PDBsum; 2V4Y; -.
DR AlphaFoldDB; P0A7E9; -.
DR SMR; P0A7E9; -.
DR BioGRID; 4262225; 29.
DR BioGRID; 849386; 1.
DR DIP; DIP-31830N; -.
DR IntAct; P0A7E9; 54.
DR STRING; 511145.b0171; -.
DR ChEMBL; CHEMBL4523176; -.
DR MoonProt; P0A7E9; -.
DR jPOST; P0A7E9; -.
DR PaxDb; P0A7E9; -.
DR PRIDE; P0A7E9; -.
DR EnsemblBacteria; AAC73282; AAC73282; b0171.
DR EnsemblBacteria; BAB96747; BAB96747; BAB96747.
DR GeneID; 67416247; -.
DR GeneID; 944989; -.
DR KEGG; ecj:JW0166; -.
DR KEGG; eco:b0171; -.
DR PATRIC; fig|1411691.4.peg.2109; -.
DR EchoBASE; EB1501; -.
DR eggNOG; COG0528; Bacteria.
DR HOGENOM; CLU_033861_0_0_6; -.
DR InParanoid; P0A7E9; -.
DR OMA; PIIVFDM; -.
DR PhylomeDB; P0A7E9; -.
DR BioCyc; EcoCyc:UMPKI-MON; -.
DR BioCyc; MetaCyc:UMPKI-MON; -.
DR BRENDA; 2.7.4.22; 2026.
DR SABIO-RK; P0A7E9; -.
DR UniPathway; UPA00159; UER00275.
DR EvolutionaryTrace; P0A7E9; -.
DR PRO; PR:P0A7E9; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0033862; F:UMP kinase activity; IDA:EcoCyc.
DR GO; GO:0044210; P:'de novo' CTP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0006221; P:pyrimidine nucleotide biosynthetic process; IDA:EcoCyc.
DR GO; GO:0006225; P:UDP biosynthetic process; IBA:GO_Central.
DR CDD; cd04254; AAK_UMPK-PyrH-Ec; 1.
DR Gene3D; 3.40.1160.10; -; 1.
DR HAMAP; MF_01220_B; PyrH_B; 1.
DR InterPro; IPR036393; AceGlu_kinase-like_sf.
DR InterPro; IPR001048; Asp/Glu/Uridylate_kinase.
DR InterPro; IPR011817; Uridylate_kinase.
DR InterPro; IPR015963; Uridylate_kinase_bac.
DR Pfam; PF00696; AA_kinase; 1.
DR PIRSF; PIRSF005650; Uridylate_kin; 1.
DR SUPFAM; SSF53633; SSF53633; 1.
DR TIGRFAMs; TIGR02075; pyrH_bact; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; ATP-binding; Cytoplasm;
KW Direct protein sequencing; Kinase; Nucleotide-binding;
KW Pyrimidine biosynthesis; Reference proteome; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7711027"
FT CHAIN 2..241
FT /note="Uridylate kinase"
FT /id="PRO_0000143842"
FT REGION 23..28
FT /note="Involved in allosteric activation by GTP"
FT /evidence="ECO:0000255"
FT BINDING 15..18
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:15857829,
FT ECO:0000269|PubMed:18945668, ECO:0007744|PDB:2BND,
FT ECO:0007744|PDB:2BNF, ECO:0007744|PDB:2V4Y"
FT BINDING 57
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000269|PubMed:15857829,
FT ECO:0000269|PubMed:18945668, ECO:0007744|PDB:2BND,
FT ECO:0007744|PDB:2BNF, ECO:0007744|PDB:2V4Y"
FT BINDING 58
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:15857829,
FT ECO:0000269|PubMed:18945668, ECO:0007744|PDB:2BND,
FT ECO:0007744|PDB:2BNF, ECO:0007744|PDB:2V4Y"
FT BINDING 62
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:15857829,
FT ECO:0007744|PDB:2BND, ECO:0007744|PDB:2BNE,
FT ECO:0007744|PDB:2BNF"
FT BINDING 77
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000269|PubMed:15857829,
FT ECO:0000269|PubMed:18945668, ECO:0007744|PDB:2BNE,
FT ECO:0007744|PDB:2BNF, ECO:0007744|PDB:2V4Y"
FT BINDING 92..96
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:18945668,
FT ECO:0007744|PDB:2V4Y"
FT BINDING 101..103
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:18945668,
FT ECO:0007744|PDB:2V4Y"
FT BINDING 138..145
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000269|PubMed:15857829,
FT ECO:0000269|PubMed:18945668, ECO:0007744|PDB:2BND,
FT ECO:0007744|PDB:2BNE, ECO:0007744|PDB:2BNF,
FT ECO:0007744|PDB:2V4Y"
FT BINDING 165
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 171
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 174
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT VARIANT 62
FT /note="R -> H (in Smba9)"
FT VARIANT 201
FT /note="D -> N (in Smba2)"
FT MUTAGEN 62
FT /note="R->H: Loss of activation by GTP and decreased
FT affinity for UTP."
FT /evidence="ECO:0000269|PubMed:9457846"
FT MUTAGEN 77
FT /note="D->N: Loss of activation by GTP and decreased
FT affinity for UTP."
FT /evidence="ECO:0000269|PubMed:9457846"
FT MUTAGEN 93
FT /note="D->A: Loss of activation by GTP and of inhibition by
FT UTP."
FT /evidence="ECO:0000269|PubMed:18945668"
FT MUTAGEN 138
FT /note="T->A: Loss of activation by GTP. Moderate loss of
FT sensitivity to UTP inhibition. 4-fold and 2-fold decrease
FT in affinity for UMP and ATP, respectively."
FT /evidence="ECO:0000269|PubMed:15857829"
FT MUTAGEN 140
FT /note="N->A: Loss of activation by GTP. Moderate loss of
FT sensitivity to UTP inhibition."
FT /evidence="ECO:0000269|PubMed:15857829,
FT ECO:0000269|PubMed:18945668"
FT MUTAGEN 146
FT /note="D->N: Drastically reduced activity."
FT /evidence="ECO:0000269|PubMed:9457846"
FT MUTAGEN 159
FT /note="D->N: Increased solubility at neutral pH. Nearly no
FT change in kinetic properties and stability."
FT /evidence="ECO:0000269|PubMed:9457846"
FT MUTAGEN 174
FT /note="D->N: Reduced UMP-binding affinity."
FT /evidence="ECO:0000269|PubMed:9457846"
FT MUTAGEN 201
FT /note="D->N: Loss of activation by GTP."
FT /evidence="ECO:0000269|PubMed:7711027,
FT ECO:0000269|PubMed:9457846"
FT CONFLICT 64..69
FT /note="AGLAKA -> RWSGET (in Ref. 1; CAA55388)"
FT /evidence="ECO:0000305"
FT STRAND 10..16
FT /evidence="ECO:0007829|PDB:2BNE"
FT HELIX 18..21
FT /evidence="ECO:0007829|PDB:2BNE"
FT STRAND 26..28
FT /evidence="ECO:0007829|PDB:2BNE"
FT HELIX 31..46
FT /evidence="ECO:0007829|PDB:2BNE"
FT STRAND 50..55
FT /evidence="ECO:0007829|PDB:2BNE"
FT TURN 58..60
FT /evidence="ECO:0007829|PDB:2BNE"
FT HELIX 63..68
FT /evidence="ECO:0007829|PDB:2BNE"
FT HELIX 73..97
FT /evidence="ECO:0007829|PDB:2BNE"
FT STRAND 102..108
FT /evidence="ECO:0007829|PDB:2BNE"
FT TURN 111..113
FT /evidence="ECO:0007829|PDB:2BNE"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:2BNE"
FT HELIX 119..127
FT /evidence="ECO:0007829|PDB:2BNE"
FT STRAND 131..136
FT /evidence="ECO:0007829|PDB:2BNE"
FT STRAND 139..142
FT /evidence="ECO:0007829|PDB:2BNF"
FT HELIX 145..155
FT /evidence="ECO:0007829|PDB:2BNE"
FT STRAND 159..169
FT /evidence="ECO:0007829|PDB:2BNE"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:2BNE"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:2BND"
FT STRAND 185..188
FT /evidence="ECO:0007829|PDB:2BNE"
FT HELIX 189..194
FT /evidence="ECO:0007829|PDB:2BNE"
FT HELIX 202..210
FT /evidence="ECO:0007829|PDB:2BNE"
FT STRAND 215..219
FT /evidence="ECO:0007829|PDB:2BNE"
FT HELIX 225..230
FT /evidence="ECO:0007829|PDB:2BNE"
FT STRAND 236..240
FT /evidence="ECO:0007829|PDB:2BNE"
SQ SEQUENCE 241 AA; 25970 MW; 82EFA75F7226E201 CRC64;
MATNAKPVYK RILLKLSGEA LQGTEGFGID ASILDRMAQE IKELVELGIQ VGVVIGGGNL
FRGAGLAKAG MNRVVGDHMG MLATVMNGLA MRDALHRAYV NARLMSAIPL NGVCDSYSWA
EAISLLRNNR VVILSAGTGN PFFTTDSAAC LRGIEIEADV VLKATKVDGV FTADPAKDPT
ATMYEQLTYS EVLEKELKVM DLAAFTLARD HKLPIRVFNM NKPGALRRVV MGEKEGTLIT
E
