PYRH_PYRFU
ID PYRH_PYRFU Reviewed; 225 AA.
AC Q8U122;
DT 30-AUG-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 108.
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=PF1407;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [2]
RP FUNCTION, SUBSTRATE SPECIFICITY, AND CRYSTALLIZATION.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=15698963; DOI=10.1016/j.bbapap.2004.11.010;
RA Marco-Marin C., Escamilla-Honrubia J.M., Rubio V.;
RT "First-time crystallization and preliminary X-ray crystallographic analysis
RT of a bacterial-archaeal type UMP kinase, a key enzyme in microbial
RT pyrimidine biosynthesis.";
RL Biochim. Biophys. Acta 1747:271-275(2005).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH UMP;
RP ATP ANALOG AND MAGNESIUM, AND SUBUNIT.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=16095620; DOI=10.1016/j.jmb.2005.07.045;
RA Marco-Marin C., Gil-Ortiz F., Rubio V.;
RT "The crystal structure of Pyrococcus furiosus UMP kinase provides insight
RT into catalysis and regulation in microbial pyrimidine nucleotide
RT biosynthesis.";
RL J. Mol. Biol. 352:438-454(2005).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) IN COMPLEX WITH UTP.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RA Marco-Marin C., Rubio V.;
RT "Structure of UMP kinase from Pyrococcus furiosus complexed with UTP.";
RL Submitted (OCT-2007) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the reversible phosphorylation of UMP to UDP, with
CC ATP as the most efficient phosphate donor.
CC {ECO:0000269|PubMed:15698963}.
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: Inhibited by UTP. {ECO:0000250}.
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:16095620,
CC ECO:0000269|Ref.4}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the UMP kinase family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AE009950; AAL81531.1; -; Genomic_DNA.
DR RefSeq; WP_011012554.1; NC_003413.1.
DR PDB; 2BMU; X-ray; 2.55 A; A/B=1-225.
DR PDB; 2BRI; X-ray; 3.00 A; A/B=1-225.
DR PDB; 2BRX; X-ray; 2.40 A; A/B=1-225.
DR PDB; 2JI5; X-ray; 2.45 A; A/B=1-225.
DR PDBsum; 2BMU; -.
DR PDBsum; 2BRI; -.
DR PDBsum; 2BRX; -.
DR PDBsum; 2JI5; -.
DR AlphaFoldDB; Q8U122; -.
DR SMR; Q8U122; -.
DR STRING; 186497.PF1407; -.
DR PRIDE; Q8U122; -.
DR DNASU; 1469283; -.
DR EnsemblBacteria; AAL81531; AAL81531; PF1407.
DR GeneID; 1469283; -.
DR KEGG; pfu:PF1407; -.
DR PATRIC; fig|186497.12.peg.1470; -.
DR eggNOG; arCOG00858; Archaea.
DR HOGENOM; CLU_079546_0_0_2; -.
DR OMA; MGGTHPG; -.
DR OrthoDB; 48934at2157; -.
DR PhylomeDB; Q8U122; -.
DR BRENDA; 2.7.4.22; 5243.
DR UniPathway; UPA00159; UER00275.
DR EvolutionaryTrace; Q8U122; -.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion 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; cd04253; AAK_UMPK-PyrH-Pf; 1.
DR Gene3D; 3.40.1160.10; -; 1.
DR HAMAP; MF_01220_A; PyrH_A; 1.
DR InterPro; IPR036393; AceGlu_kinase-like_sf.
DR InterPro; IPR001048; Asp/Glu/Uridylate_kinase.
DR InterPro; IPR011817; Uridylate_kinase.
DR InterPro; IPR011818; Uridylate_kinase_arch/spir.
DR Pfam; PF00696; AA_kinase; 1.
DR PIRSF; PIRSF005650; Uridylate_kin; 1.
DR SUPFAM; SSF53633; SSF53633; 1.
DR TIGRFAMs; TIGR02076; pyrH_arch; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Kinase; Magnesium; Metal-binding;
KW Nucleotide-binding; Pyrimidine biosynthesis; Reference proteome;
KW Transferase.
FT CHAIN 1..225
FT /note="Uridylate kinase"
FT /id="PRO_0000143923"
FT BINDING 6
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16095620"
FT BINDING 9..10
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 44
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000269|PubMed:16095620"
FT BINDING 45
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 49
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 66
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000269|PubMed:16095620"
FT BINDING 114..120
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000269|PubMed:16095620"
FT BINDING 120
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16095620"
FT BINDING 121
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16095620"
FT BINDING 121
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:16095620"
FT BINDING 140
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 141
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 146
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 149
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 179
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000269|PubMed:16095620"
FT BINDING 182
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 182
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:16095620"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:2BRX"
FT HELIX 9..12
FT /evidence="ECO:0007829|PDB:2BRX"
FT STRAND 14..16
FT /evidence="ECO:0007829|PDB:2BRX"
FT HELIX 19..35
FT /evidence="ECO:0007829|PDB:2BRX"
FT STRAND 36..42
FT /evidence="ECO:0007829|PDB:2BRX"
FT HELIX 45..56
FT /evidence="ECO:0007829|PDB:2BRX"
FT TURN 57..59
FT /evidence="ECO:0007829|PDB:2BRX"
FT HELIX 62..84
FT /evidence="ECO:0007829|PDB:2BRX"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:2BRX"
FT HELIX 96..104
FT /evidence="ECO:0007829|PDB:2BRX"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:2BMU"
FT HELIX 120..130
FT /evidence="ECO:0007829|PDB:2BRX"
FT STRAND 134..139
FT /evidence="ECO:0007829|PDB:2BRX"
FT STRAND 141..144
FT /evidence="ECO:0007829|PDB:2BRX"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:2BRX"
FT TURN 150..152
FT /evidence="ECO:0007829|PDB:2BRX"
FT STRAND 160..162
FT /evidence="ECO:0007829|PDB:2BRX"
FT HELIX 164..172
FT /evidence="ECO:0007829|PDB:2BRX"
FT STRAND 182..184
FT /evidence="ECO:0007829|PDB:2BRI"
FT HELIX 186..195
FT /evidence="ECO:0007829|PDB:2BRX"
FT STRAND 199..202
FT /evidence="ECO:0007829|PDB:2BRX"
FT HELIX 204..207
FT /evidence="ECO:0007829|PDB:2BRX"
FT HELIX 210..214
FT /evidence="ECO:0007829|PDB:2BRX"
FT STRAND 218..223
FT /evidence="ECO:0007829|PDB:2BRX"
SQ SEQUENCE 225 AA; 24491 MW; 510D151A02F8D534 CRC64;
MRIVFDIGGS VLVPENPDID FIKEIAYQLT KVSEDHEVAV VVGGGKLARK YIEVAEKFNS
SETFKDFIGI QITRANAMLL IAALREKAYP VVVEDFWEAW KAVQLKKIPV MGGTHPGHTT
DAVAALLAEF LKADLLVVIT NVDGVYTADP KKDPTAKKIK KMKPEELLEI VGKGIEKAGS
SSVIDPLAAK IIARSGIKTI VIGKEDAKDL FRVIKGDHNG TTIEP
