PYRH_UREPA
ID PYRH_UREPA Reviewed; 235 AA.
AC Q9PPX6;
DT 30-AUG-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=Uridylate kinase;
DE Short=UK;
DE EC=2.7.4.22;
DE AltName: Full=Uridine monophosphate kinase;
DE Short=UMP kinase;
DE Short=UMPK;
GN Name=pyrH; OrderedLocusNames=UU513;
OS Ureaplasma parvum serovar 3 (strain ATCC 700970).
OC Bacteria; Tenericutes; Mollicutes; Mycoplasmataceae; Ureaplasma.
OX NCBI_TaxID=273119;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700970;
RX PubMed=11048724; DOI=10.1038/35037619;
RA Glass J.I., Lefkowitz E.J., Glass J.S., Heiner C.R., Chen E.Y.,
RA Cassell G.H.;
RT "The complete sequence of the mucosal pathogen Ureaplasma urealyticum.";
RL Nature 407:757-762(2000).
RN [2]
RP FUNCTION, AND SUBSTRATE SPECIFICITY.
RC STRAIN=ATCC 700970;
RX PubMed=17355283; DOI=10.1111/j.1742-4658.2007.05742.x;
RA Wang L.;
RT "The role of Ureaplasma nucleoside monophosphate kinases in the synthesis
RT of nucleoside triphosphates.";
RL FEBS J. 274:1983-1990(2007).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), FUNCTION, ACTIVITY REGULATION,
RP SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND
RP MUTAGENESIS OF PHE-133.
RC STRAIN=ATCC 700970;
RX PubMed=18021254; DOI=10.1111/j.1742-4658.2007.06157.x;
RA Egeblad-Welin L., Welin M., Wang L., Eriksson S.;
RT "Structural and functional investigations of Ureaplasma parvum UMP kinase
RT - a potential antibacterial drug target.";
RL FEBS J. 274:6403-6414(2007).
CC -!- FUNCTION: Catalyzes the reversible phosphorylation of UMP to UDP, with
CC ATP as the most efficient phosphate donor. Is also able to
CC phosphorylate dUMP. {ECO:0000269|PubMed:17355283,
CC ECO:0000269|PubMed:18021254}.
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 -!- ACTIVITY REGULATION: Unlike other bacteria, is not activated by GTP.
CC UTP is a competitive inhibitor against UMP and a non-competitive
CC inhibitor toward ATP. {ECO:0000269|PubMed:18021254}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=214 uM for UMP {ECO:0000269|PubMed:18021254};
CC Vmax=262 umol/min/mg enzyme {ECO:0000269|PubMed:18021254};
CC Note=Positive cooperativity is observed with ATP as variable
CC substrate, but it is abolished in the presence of UTP.;
CC pH dependence:
CC Optimum pH is 6.8. {ECO:0000269|PubMed:18021254};
CC -!- PATHWAY: Pyrimidine metabolism; CTP biosynthesis via de novo pathway;
CC UDP from UMP (UMPK route): step 1/1.
CC -!- SUBUNIT: Homohexamer; trimer of dimers. {ECO:0000269|PubMed:18021254}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the UMP kinase family. {ECO:0000305}.
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DR EMBL; AF222894; AAF30926.1; -; Genomic_DNA.
DR RefSeq; WP_006688575.1; NC_002162.1.
DR PDB; 2VA1; X-ray; 2.50 A; A/B/C/D/E/F=1-235.
DR PDBsum; 2VA1; -.
DR AlphaFoldDB; Q9PPX6; -.
DR SMR; Q9PPX6; -.
DR STRING; 273119.UU513; -.
DR EnsemblBacteria; AAF30926; AAF30926; UU513.
DR GeneID; 29672214; -.
DR KEGG; uur:UU513; -.
DR eggNOG; COG0528; Bacteria.
DR HOGENOM; CLU_033861_0_1_14; -.
DR OMA; PIIVFDM; -.
DR BRENDA; 2.7.4.22; 9209.
DR UniPathway; UPA00159; UER00275.
DR EvolutionaryTrace; Q9PPX6; -.
DR Proteomes; UP000000423; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0033862; F:UMP kinase activity; IEA:UniProtKB-EC.
DR GO; GO:0044210; P:'de novo' CTP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
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; ATP-binding; Cytoplasm; Kinase; Nucleotide-binding;
KW Pyrimidine biosynthesis; Reference proteome; Transferase.
FT CHAIN 1..235
FT /note="Uridylate kinase"
FT /id="PRO_0000143902"
FT BINDING 9..12
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 50
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250"
FT BINDING 51
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 55
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 70
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250"
FT BINDING 131..138
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250"
FT BINDING 159
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 165
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 168
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MUTAGEN 133
FT /note="F->N,A: Still no activation by GTP. Exhibits
FT negative cooperativity with UMP. Marked decrease in
FT activity."
FT /evidence="ECO:0000269|PubMed:18021254"
FT STRAND 4..10
FT /evidence="ECO:0007829|PDB:2VA1"
FT HELIX 12..15
FT /evidence="ECO:0007829|PDB:2VA1"
FT HELIX 25..38
FT /evidence="ECO:0007829|PDB:2VA1"
FT TURN 39..41
FT /evidence="ECO:0007829|PDB:2VA1"
FT STRAND 42..48
FT /evidence="ECO:0007829|PDB:2VA1"
FT TURN 51..53
FT /evidence="ECO:0007829|PDB:2VA1"
FT HELIX 56..61
FT /evidence="ECO:0007829|PDB:2VA1"
FT HELIX 66..89
FT /evidence="ECO:0007829|PDB:2VA1"
FT TURN 90..92
FT /evidence="ECO:0007829|PDB:2VA1"
FT STRAND 95..101
FT /evidence="ECO:0007829|PDB:2VA1"
FT TURN 104..106
FT /evidence="ECO:0007829|PDB:2VA1"
FT HELIX 112..120
FT /evidence="ECO:0007829|PDB:2VA1"
FT STRAND 124..129
FT /evidence="ECO:0007829|PDB:2VA1"
FT STRAND 132..135
FT /evidence="ECO:0007829|PDB:2VA1"
FT HELIX 138..149
FT /evidence="ECO:0007829|PDB:2VA1"
FT STRAND 152..160
FT /evidence="ECO:0007829|PDB:2VA1"
FT TURN 169..171
FT /evidence="ECO:0007829|PDB:2VA1"
FT STRAND 178..182
FT /evidence="ECO:0007829|PDB:2VA1"
FT HELIX 183..189
FT /evidence="ECO:0007829|PDB:2VA1"
FT HELIX 196..204
FT /evidence="ECO:0007829|PDB:2VA1"
FT STRAND 208..216
FT /evidence="ECO:0007829|PDB:2VA1"
FT HELIX 219..224
FT /evidence="ECO:0007829|PDB:2VA1"
FT STRAND 231..234
FT /evidence="ECO:0007829|PDB:2VA1"
SQ SEQUENCE 235 AA; 25924 MW; CAF39D32C3DFCE2D CRC64;
MRKQRIVIKI SGACLKQNDS SIIDFIKIND LAEQIEKISK KYIVSIVLGG GNIWRGSIAK
ELDMDRNLAD NMGMMATIIN GLALENALNH LNVNTIVLSA IKCDKLVHES SANNIKKAIE
KEQVMIFVAG TGFPYFTTDS CAAIRAAETE SSIILMGKNG VDGVYDSDPK INPNAQFYEH
ITFNMALTQN LKVMDATALA LCQENNINLL VFNIDKPNAI VDVLEKKNKY TIVSK
