PYRH_NEIMB
ID PYRH_NEIMB Reviewed; 239 AA.
AC P65932; Q9JQT5;
DT 11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 102.
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=NMB2103;
OS Neisseria meningitidis serogroup B (strain MC58).
OC Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae;
OC Neisseria.
OX NCBI_TaxID=122586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MC58;
RX PubMed=10710307; DOI=10.1126/science.287.5459.1809;
RA Tettelin H., Saunders N.J., Heidelberg J.F., Jeffries A.C., Nelson K.E.,
RA Eisen J.A., Ketchum K.A., Hood D.W., Peden J.F., Dodson R.J., Nelson W.C.,
RA Gwinn M.L., DeBoy R.T., Peterson J.D., Hickey E.K., Haft D.H.,
RA Salzberg S.L., White O., Fleischmann R.D., Dougherty B.A., Mason T.M.,
RA Ciecko A., Parksey D.S., Blair E., Cittone H., Clark E.B., Cotton M.D.,
RA Utterback T.R., Khouri H.M., Qin H., Vamathevan J.J., Gill J., Scarlato V.,
RA Masignani V., Pizza M., Grandi G., Sun L., Smith H.O., Fraser C.M.,
RA Moxon E.R., Rappuoli R., Venter J.C.;
RT "Complete genome sequence of Neisseria meningitidis serogroup B strain
RT MC58.";
RL Science 287:1809-1815(2000).
RN [2]
RP FUNCTION, ACTIVITY REGULATION, KINETIC PARAMETERS, IDENTIFICATION BY MASS
RP SPECTROMETRY, AND SUBUNIT.
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 [3]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
RG New York structural genomics research consortium (NYSGRC);
RT "Crystal structure analysis of uridylate kinase from Neisseria
RT meningitidis.";
RL Submitted (FEB-2005) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the reversible phosphorylation of UMP to UDP.
CC {ECO:0000269|PubMed:17210578}.
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: Allosterically activated by GTP. Inhibited by UTP.
CC {ECO:0000269|PubMed:17210578}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.98 mM for ATP (in the absence of GTP)
CC {ECO:0000269|PubMed:17210578};
CC KM=0.83 mM for ATP (in the presence of GTP)
CC {ECO:0000269|PubMed:17210578};
CC KM=8.7 uM for UMP {ECO:0000269|PubMed:17210578};
CC Vmax=35 umol/min/mg enzyme (in the absence of GTP)
CC {ECO:0000269|PubMed:17210578};
CC Vmax=66 umol/min/mg enzyme (in the presence of GTP)
CC {ECO:0000269|PubMed:17210578};
CC -!- PATHWAY: Pyrimidine metabolism; CTP biosynthesis via de novo pathway;
CC UDP from UMP (UMPK route): step 1/1.
CC -!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:17210578}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the UMP kinase family. {ECO:0000305}.
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DR EMBL; AE002098; AAF42420.1; -; Genomic_DNA.
DR PIR; H81006; H81006.
DR RefSeq; NP_275091.1; NC_003112.2.
DR RefSeq; WP_002215090.1; NC_003112.2.
DR PDB; 1YBD; X-ray; 2.60 A; A/B/C=1-239.
DR PDBsum; 1YBD; -.
DR AlphaFoldDB; P65932; -.
DR SMR; P65932; -.
DR STRING; 122586.NMB2103; -.
DR PaxDb; P65932; -.
DR DNASU; 903933; -.
DR EnsemblBacteria; AAF42420; AAF42420; NMB2103.
DR KEGG; nme:NMB2103; -.
DR PATRIC; fig|122586.8.peg.2685; -.
DR HOGENOM; CLU_033861_0_0_4; -.
DR OMA; PIIVFDM; -.
DR BRENDA; 2.7.4.22; 3593.
DR SABIO-RK; P65932; -.
DR UniPathway; UPA00159; UER00275.
DR EvolutionaryTrace; P65932; -.
DR Proteomes; UP000000425; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0033862; F:UMP kinase activity; IBA:GO_Central.
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: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; Kinase;
KW Nucleotide-binding; Pyrimidine biosynthesis; Reference proteome;
KW Transferase.
FT CHAIN 1..239
FT /note="Uridylate kinase"
FT /id="PRO_0000143866"
FT BINDING 13..16
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 55
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250"
FT BINDING 56
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 60
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 75
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250"
FT BINDING 136..143
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250"
FT BINDING 163
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 164
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 169
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 172
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT STRAND 8..14
FT /evidence="ECO:0007829|PDB:1YBD"
FT HELIX 16..20
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 23..26
FT /evidence="ECO:0007829|PDB:1YBD"
FT HELIX 29..44
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 48..53
FT /evidence="ECO:0007829|PDB:1YBD"
FT HELIX 56..66
FT /evidence="ECO:0007829|PDB:1YBD"
FT HELIX 71..95
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 100..106
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 108..111
FT /evidence="ECO:0007829|PDB:1YBD"
FT HELIX 117..125
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 129..134
FT /evidence="ECO:0007829|PDB:1YBD"
FT HELIX 143..153
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 157..162
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 169..171
FT /evidence="ECO:0007829|PDB:1YBD"
FT HELIX 173..175
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 183..186
FT /evidence="ECO:0007829|PDB:1YBD"
FT HELIX 187..192
FT /evidence="ECO:0007829|PDB:1YBD"
FT HELIX 200..208
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 213..216
FT /evidence="ECO:0007829|PDB:1YBD"
FT HELIX 223..229
FT /evidence="ECO:0007829|PDB:1YBD"
FT STRAND 234..238
FT /evidence="ECO:0007829|PDB:1YBD"
SQ SEQUENCE 239 AA; 25700 MW; CB08FD7E1AFBC5FE CRC64;
MTQQIKYKRV LLKLSGESLM GSDPFGINHD TIVQTVGEIA EVVKMGVQVG IVVGGGNIFR
GVSAQAGSMD RATADYMGMM ATVMNALALK DAFETLGIKA RVQSALSMQQ IAETYARPKA
IQYLEEGKVV IFAAGTGNPF FTTDTAAALR GAEMNCDVML KATNVDGVYT ADPKKDPSAT
RYETITFDEA LLKNLKVMDA TAFALCRERK LNIVVFGIAK EGSLKRVITG EDEGTLVHC
