PYRR_BACSU
ID PYRR_BACSU Reviewed; 181 AA.
AC P39765; P25982; Q45483;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 31-JAN-2002, sequence version 2.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=Bifunctional protein PyrR;
DE Includes:
DE RecName: Full=Pyrimidine operon regulatory protein;
DE Includes:
DE RecName: Full=Uracil phosphoribosyltransferase;
DE Short=UPRTase;
DE EC=2.4.2.9;
GN Name=pyrR; OrderedLocusNames=BSU15470;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=1A610, and JH861;
RX PubMed=1709162; DOI=10.1016/s0021-9258(18)31559-x;
RA Quinn C.L., Stephenson B.T., Switzer R.L.;
RT "Functional organization and nucleotide sequence of the Bacillus subtilis
RT pyrimidine biosynthetic operon.";
RL J. Biol. Chem. 266:9113-9127(1991).
RN [2]
RP SEQUENCE REVISION, AND CHARACTERIZATION.
RX PubMed=8206849; DOI=10.1128/jb.176.12.3708-3722.1994;
RA Turner R.J., Lu Y., Switzer R.L.;
RT "Regulation of the Bacillus subtilis pyrimidine biosynthetic (pyr) gene
RT cluster by an autogenous transcriptional attenuation mechanism.";
RL J. Bacteriol. 176:3708-3722(1994).
RN [3]
RP SEQUENCE REVISION TO 34 AND 53.
RA Switzer R.L.;
RL Submitted (MAY-1999) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-173.
RC STRAIN=168;
RX PubMed=9141696; DOI=10.1099/00221287-143-4-1327;
RA Pragai Z., Tjalsma H., Bolhuis A., van Dijl J.M., Venema G., Bron S.;
RT "The signal peptidase II (lsp) gene of Bacillus subtilis.";
RL Microbiology 143:1327-1333(1997).
RN [6]
RP ENZYME ACTIVITY.
RX PubMed=7798145; DOI=10.1128/jb.177.1.271-274.1995;
RA Martinussen J., Glaser P., Andersen P.S., Saxild H.H.;
RT "Two genes encoding uracil phosphoribosyltransferase are present in
RT Bacillus subtilis.";
RL J. Bacteriol. 177:271-274(1995).
RN [7]
RP CHARACTERIZATION, AND MASS SPECTROMETRY.
RX PubMed=9488732; DOI=10.1074/jbc.273.10.5932;
RA Turner R.J., Bonner E.R., Grabner G.K., Switzer R.L.;
RT "Purification and characterization of Bacillus subtilis PyrR, a
RT bifunctional pyr mRNA-binding attenuation protein/uracil
RT phosphoribosyltransferase.";
RL J. Biol. Chem. 273:5932-5938(1998).
RN [8]
RP MUTAGENESIS OF ARG-15; THR-18; ARG-19; HIS-22; ARG-27; THR-41; HIS-140;
RP ARG-141; ARG-146 AND LYS-152.
RX PubMed=11948166; DOI=10.1128/jb.184.9.2521-2528.2002;
RA Savacool H.K., Switzer R.L.;
RT "Characterization of the interaction of Bacillus subtilis PyrR with pyr
RT mRNA by site-directed mutagenesis of the protein.";
RL J. Bacteriol. 184:2521-2528(2002).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
RX PubMed=9551555; DOI=10.1016/s0969-2126(98)00036-7;
RA Tomchick D.R., Turner R.J., Switzer R.L., Smith J.L.;
RT "Adaptation of an enzyme to regulatory function: structure of Bacillus
RT subtilis PyrR, a pyr RNA-binding attenuation protein and uracil
RT phosphoribosyltransferase.";
RL Structure 6:337-350(1998).
CC -!- FUNCTION: Regulates transcriptional attenuation of the pyrimidine
CC nucleotide (pyr) operon by binding in a uridine-dependent manner to
CC specific sites on pyr mRNA. This disrupts an antiterminator hairpin in
CC the RNA and favors formation of a downstream transcription terminator,
CC leading to a reduced expression of downstream genes.
CC -!- FUNCTION: Also displays a weak uracil phosphoribosyltransferase
CC activity which is not physiologically significant.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate +
CC uracil; Xref=Rhea:RHEA:13017, ChEBI:CHEBI:17568, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:57865, ChEBI:CHEBI:58017; EC=2.4.2.9;
CC Evidence={ECO:0000269|PubMed:7798145};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8.2 for UPRTase activity.;
CC -!- SUBUNIT: Homodimer and homohexamer; in equilibrium.
CC -!- MASS SPECTROMETRY: Mass=20263; Mass_error=2; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:9488732};
CC -!- MISCELLANEOUS: Mutagenesis studies identified four amino acid residues
CC that seem to be involved directly in binding of the protein to pyr
CC mRNA: Thr-18, His-22, Arg-141 and Arg-146. Arg-27 and Lys-152 were also
CC likely to be involved in RNA-binding, but mutations may have altered
CC their subunit-subunit interactions. Arg-19 was implicated in pyr
CC regulation, but a specific role in RNA-binding could not be
CC demonstrated.
CC -!- MISCELLANEOUS: UMP and UTP increase the affinity of PyrR for RNA.
CC -!- SIMILARITY: Belongs to the purine/pyrimidine phosphoribosyltransferase
CC family. PyrR subfamily. {ECO:0000305}.
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DR EMBL; M59757; AAA21265.2; -; Genomic_DNA.
DR EMBL; AL009126; CAB13421.1; -; Genomic_DNA.
DR EMBL; U48870; AAB57770.1; -; Genomic_DNA.
DR PIR; A69687; B57986.
DR RefSeq; NP_389430.1; NC_000964.3.
DR RefSeq; WP_003232127.1; NZ_JNCM01000035.1.
DR PDB; 1A3C; X-ray; 1.60 A; A=1-181.
DR PDB; 1A4X; X-ray; 2.30 A; A/B=1-181.
DR PDB; 4P82; X-ray; 1.30 A; A=2-179.
DR PDBsum; 1A3C; -.
DR PDBsum; 1A4X; -.
DR PDBsum; 4P82; -.
DR AlphaFoldDB; P39765; -.
DR SMR; P39765; -.
DR STRING; 224308.BSU15470; -.
DR PaxDb; P39765; -.
DR PRIDE; P39765; -.
DR EnsemblBacteria; CAB13421; CAB13421; BSU_15470.
DR GeneID; 938030; -.
DR KEGG; bsu:BSU15470; -.
DR PATRIC; fig|224308.179.peg.1686; -.
DR eggNOG; COG2065; Bacteria.
DR InParanoid; P39765; -.
DR OMA; PIQPDFC; -.
DR PhylomeDB; P39765; -.
DR BioCyc; BSUB:BSU15470-MON; -.
DR SABIO-RK; P39765; -.
DR EvolutionaryTrace; P39765; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004845; F:uracil phosphoribosyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006353; P:DNA-templated transcription, termination; IEA:UniProtKB-UniRule.
DR CDD; cd06223; PRTases_typeI; 1.
DR Gene3D; 3.40.50.2020; -; 1.
DR HAMAP; MF_01219; PyrR; 1.
DR InterPro; IPR000836; PRibTrfase_dom.
DR InterPro; IPR029057; PRTase-like.
DR InterPro; IPR023050; PyrR.
DR Pfam; PF00156; Pribosyltran; 1.
DR SUPFAM; SSF53271; SSF53271; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Glycosyltransferase; Reference proteome; RNA-binding;
KW Transcription; Transcription regulation; Transcription termination;
KW Transferase.
FT CHAIN 1..181
FT /note="Bifunctional protein PyrR"
FT /id="PRO_0000183030"
FT MOTIF 101..113
FT /note="PRPP-binding"
FT /evidence="ECO:0000250"
FT BINDING 41..42
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 105..113
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 138
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 162
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MUTAGEN 15
FT /note="R->Q: No effect on ability to regulate the pyr
FT operon; no effect on uprtase activity."
FT /evidence="ECO:0000269|PubMed:11948166"
FT MUTAGEN 18
FT /note="T->A: No effect on ability to regulate the pyr
FT operon only in presence of excess pyrimidines; reduced
FT affinity for RNA; no effect on UPRTase activity."
FT /evidence="ECO:0000269|PubMed:11948166"
FT MUTAGEN 19
FT /note="R->Q: Loss of ability to regulate the pyr operon; no
FT effect on UPRTase activity."
FT /evidence="ECO:0000269|PubMed:11948166"
FT MUTAGEN 22
FT /note="H->A: Loss of ability to regulate the pyr operon and
FT to bind to RNA; no effect on UPRTase activity."
FT /evidence="ECO:0000269|PubMed:11948166"
FT MUTAGEN 27
FT /note="R->Q: No effect on ability to regulate the pyr
FT operon only in presence of excess pyrimidines; reduced
FT affinity for RNA; no effect on UPRTase activity."
FT /evidence="ECO:0000269|PubMed:11948166"
FT MUTAGEN 41
FT /note="T->I: Reduced ability to regulate the pyr operon;
FT reduced affinity for RNA; loss of UPRTase activity."
FT /evidence="ECO:0000269|PubMed:11948166"
FT MUTAGEN 140
FT /note="H->A: Reduced ability to regulate the pyr operon;
FT decreased UPRTase activity."
FT /evidence="ECO:0000269|PubMed:11948166"
FT MUTAGEN 141
FT /note="R->Q: Loss of ability to regulate the pyr operon;
FT highly reduced affinity for RNA; no effect on UPRTase
FT activity."
FT /evidence="ECO:0000269|PubMed:11948166"
FT MUTAGEN 146
FT /note="R->Q: Reduced ability to regulate the pyr operon,
FT and loss of ability to bind to RNA; no effect on UPRTase
FT activity."
FT /evidence="ECO:0000269|PubMed:11948166"
FT MUTAGEN 152
FT /note="K->Q: No effect on ability to regulate the pyr
FT operon only in presence of excess pyrimidines; reduced
FT affinity for RNA; no effect on UPRTase activity."
FT /evidence="ECO:0000269|PubMed:11948166"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:4P82"
FT HELIX 10..27
FT /evidence="ECO:0007829|PDB:4P82"
FT HELIX 29..31
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 34..40
FT /evidence="ECO:0007829|PDB:4P82"
FT HELIX 41..58
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 64..72
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 74..76
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 84..91
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 99..111
FT /evidence="ECO:0007829|PDB:4P82"
FT HELIX 112..124
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 128..137
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 142..144
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 148..153
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 160..165
FT /evidence="ECO:0007829|PDB:4P82"
FT HELIX 167..170
FT /evidence="ECO:0007829|PDB:4P82"
FT STRAND 174..179
FT /evidence="ECO:0007829|PDB:4P82"
SQ SEQUENCE 181 AA; 20263 MW; 3926D7F1E87E5D6C CRC64;
MNQKAVILDE QAIRRALTRI AHEMIERNKG MNNCILVGIK TRGIYLAKRL AERIEQIEGN
PVTVGEIDIT LYRDDLSKKT SNDEPLVKGA DIPVDITDQK VILVDDVLYT GRTVRAGMDA
LVDVGRPSSI QLAVLVDRGH RELPIRADYI GKNIPTSKSE KVMVQLDEVD QNDLVAIYEN
E
