Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Bifunctional protein PyrR

Gene

pyrR

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine-dependent manner to specific sites on pyr mRNA. This disrupts an antiterminator hairpin in the RNA and favors formation of a downstream transcription terminator, leading to a reduced expression of downstream genes.
Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.

Catalytic activityi

UMP + diphosphate = uracil + 5-phospho-alpha-D-ribose 1-diphosphate.1 Publication

pH dependencei

Optimum pH is 8.2 for UPRTase activity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei138 – 1381SubstrateBy similarity
Binding sitei162 – 1621SubstrateBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Keywords - Biological processi

Transcription, Transcription regulation, Transcription termination

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciBSUB:BSU15470-MONOMER.
SABIO-RKP39765.

Names & Taxonomyi

Protein namesi
Recommended name:
Bifunctional protein PyrR
Including the following 2 domains:
Pyrimidine operon regulatory protein
Uracil phosphoribosyltransferase (EC:2.4.2.9)
Short name:
UPRTase
Gene namesi
Name:pyrR
Ordered Locus Names:BSU15470
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi15 – 151R → Q: No effect on ability to regulate the pyr operon; no effect on uprtase activity. 1 Publication
Mutagenesisi18 – 181T → A: No effect on ability to regulate the pyr operon only in presence of excess pyrimidines; reduced affinity for RNA; no effect on UPRTase activity. 1 Publication
Mutagenesisi19 – 191R → Q: Loss of ability to regulate the pyr operon; no effect on UPRTase activity. 1 Publication
Mutagenesisi22 – 221H → A: Loss of ability to regulate the pyr operon and to bind to RNA; no effect on UPRTase activity. 1 Publication
Mutagenesisi27 – 271R → Q: No effect on ability to regulate the pyr operon only in presence of excess pyrimidines; reduced affinity for RNA; no effect on UPRTase activity. 1 Publication
Mutagenesisi41 – 411T → I: Reduced ability to regulate the pyr operon; reduced affinity for RNA; loss of UPRTase activity. 1 Publication
Mutagenesisi140 – 1401H → A: Reduced ability to regulate the pyr operon; decreased UPRTase activity. 1 Publication
Mutagenesisi141 – 1411R → Q: Loss of ability to regulate the pyr operon; highly reduced affinity for RNA; no effect on UPRTase activity. 1 Publication
Mutagenesisi146 – 1461R → Q: Reduced ability to regulate the pyr operon, and loss of ability to bind to RNA; no effect on UPRTase activity. 1 Publication
Mutagenesisi152 – 1521K → Q: No effect on ability to regulate the pyr operon only in presence of excess pyrimidines; reduced affinity for RNA; no effect on UPRTase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 181181Bifunctional protein PyrRPRO_0000183030Add
BLAST

Proteomic databases

PaxDbiP39765.

Interactioni

Subunit structurei

Homodimer and homohexamer; in equilibrium.

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100008551.

Structurei

Secondary structure

1
181
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85Combined sources
Helixi10 – 2718Combined sources
Helixi29 – 313Combined sources
Beta strandi34 – 407Combined sources
Helixi41 – 5818Combined sources
Beta strandi64 – 729Combined sources
Beta strandi74 – 763Combined sources
Beta strandi78 – 803Combined sources
Beta strandi84 – 918Combined sources
Beta strandi99 – 11113Combined sources
Helixi112 – 12413Combined sources
Beta strandi128 – 13710Combined sources
Beta strandi142 – 1443Combined sources
Beta strandi148 – 1536Combined sources
Beta strandi160 – 1656Combined sources
Helixi167 – 1704Combined sources
Beta strandi174 – 1796Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1A3CX-ray1.60A1-181[»]
1A4XX-ray2.30A/B1-181[»]
4P82X-ray1.30A2-179[»]
ProteinModelPortaliP39765.
SMRiP39765. Positions 4-180.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39765.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni41 – 422Substrate-bindingBy similarity
Regioni105 – 1139Substrate bindingBy similarity

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi101 – 11313PRPP-bindingBy similarityAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108UK1. Bacteria.
COG2065. LUCA.
HOGENOMiHOG000245770.
InParanoidiP39765.
KOiK02825.
OMAiVPTSRKE.
OrthoDBiEOG61VZD8.
PhylomeDBiP39765.

Family and domain databases

Gene3Di3.40.50.2020. 1 hit.
HAMAPiMF_01219. PyrR.
InterProiIPR000836. PRibTrfase_dom.
IPR029057. PRTase-like.
IPR023050. PyrR.
[Graphical view]
PfamiPF00156. Pribosyltran. 1 hit.
[Graphical view]
SUPFAMiSSF53271. SSF53271. 1 hit.

Sequencei

Sequence statusi: Complete.

P39765-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNQKAVILDE QAIRRALTRI AHEMIERNKG MNNCILVGIK TRGIYLAKRL
60 70 80 90 100
AERIEQIEGN PVTVGEIDIT LYRDDLSKKT SNDEPLVKGA DIPVDITDQK
110 120 130 140 150
VILVDDVLYT GRTVRAGMDA LVDVGRPSSI QLAVLVDRGH RELPIRADYI
160 170 180
GKNIPTSKSE KVMVQLDEVD QNDLVAIYEN E
Length:181
Mass (Da):20,263
Last modified:January 31, 2002 - v2
Checksum:i3926D7F1E87E5D6C
GO

Mass spectrometryi

Molecular mass is 20263±2 Da from positions 1 - 181. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M59757 Genomic DNA. Translation: AAA21265.2.
AL009126 Genomic DNA. Translation: CAB13421.1.
U48870 Genomic DNA. Translation: AAB57770.1.
PIRiA69687. B57986.
RefSeqiNP_389430.1. NC_000964.3.
WP_003232127.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB13421; CAB13421; BSU15470.
GeneIDi938030.
KEGGibsu:BSU15470.
PATRICi18974901. VBIBacSub10457_1642.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M59757 Genomic DNA. Translation: AAA21265.2.
AL009126 Genomic DNA. Translation: CAB13421.1.
U48870 Genomic DNA. Translation: AAB57770.1.
PIRiA69687. B57986.
RefSeqiNP_389430.1. NC_000964.3.
WP_003232127.1. NZ_JNCM01000035.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1A3CX-ray1.60A1-181[»]
1A4XX-ray2.30A/B1-181[»]
4P82X-ray1.30A2-179[»]
ProteinModelPortaliP39765.
SMRiP39765. Positions 4-180.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100008551.

Proteomic databases

PaxDbiP39765.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13421; CAB13421; BSU15470.
GeneIDi938030.
KEGGibsu:BSU15470.
PATRICi18974901. VBIBacSub10457_1642.

Phylogenomic databases

eggNOGiENOG4108UK1. Bacteria.
COG2065. LUCA.
HOGENOMiHOG000245770.
InParanoidiP39765.
KOiK02825.
OMAiVPTSRKE.
OrthoDBiEOG61VZD8.
PhylomeDBiP39765.

Enzyme and pathway databases

BioCyciBSUB:BSU15470-MONOMER.
SABIO-RKP39765.

Miscellaneous databases

EvolutionaryTraceiP39765.

Family and domain databases

Gene3Di3.40.50.2020. 1 hit.
HAMAPiMF_01219. PyrR.
InterProiIPR000836. PRibTrfase_dom.
IPR029057. PRTase-like.
IPR023050. PyrR.
[Graphical view]
PfamiPF00156. Pribosyltran. 1 hit.
[Graphical view]
SUPFAMiSSF53271. SSF53271. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Functional organization and nucleotide sequence of the Bacillus subtilis pyrimidine biosynthetic operon."
    Quinn C.L., Stephenson B.T., Switzer R.L.
    J. Biol. Chem. 266:9113-9127(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 1A610 and JH861.
  2. "Regulation of the Bacillus subtilis pyrimidine biosynthetic (pyr) gene cluster by an autogenous transcriptional attenuation mechanism."
    Turner R.J., Lu Y., Switzer R.L.
    J. Bacteriol. 176:3708-3722(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION, CHARACTERIZATION.
  3. Switzer R.L.
    Submitted (MAY-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 34 AND 53.
  4. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  5. "The signal peptidase II (lsp) gene of Bacillus subtilis."
    Pragai Z., Tjalsma H., Bolhuis A., van Dijl J.M., Venema G., Bron S.
    Microbiology 143:1327-1333(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-173.
    Strain: 168.
  6. "Two genes encoding uracil phosphoribosyltransferase are present in Bacillus subtilis."
    Martinussen J., Glaser P., Andersen P.S., Saxild H.H.
    J. Bacteriol. 177:271-274(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME ACTIVITY.
  7. "Purification and characterization of Bacillus subtilis PyrR, a bifunctional pyr mRNA-binding attenuation protein/uracil phosphoribosyltransferase."
    Turner R.J., Bonner E.R., Grabner G.K., Switzer R.L.
    J. Biol. Chem. 273:5932-5938(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, MASS SPECTROMETRY.
  8. "Characterization of the interaction of Bacillus subtilis PyrR with pyr mRNA by site-directed mutagenesis of the protein."
    Savacool H.K., Switzer R.L.
    J. Bacteriol. 184:2521-2528(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ARG-15; THR-18; ARG-19; HIS-22; ARG-27; THR-41; HIS-140; ARG-141; ARG-146 AND LYS-152.
  9. "Adaptation of an enzyme to regulatory function: structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase."
    Tomchick D.R., Turner R.J., Switzer R.L., Smith J.L.
    Structure 6:337-350(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).

Entry informationi

Entry nameiPYRR_BACSU
AccessioniPrimary (citable) accession number: P39765
Secondary accession number(s): P25982, Q45483
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: January 31, 2002
Last modified: February 17, 2016
This is version 121 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Mutagenesis studies identified four amino acid residues that seem to be involved directly in binding of the protein to pyr mRNA: Thr-18, His-22, Arg-141 and Arg-146. Arg-27 and Lys-152 were also likely to be involved in RNA-binding, but mutations may have altered their subunit-subunit interactions. Arg-19 was implicated in pyr regulation, but a specific role in RNA-binding could not be demonstrated.
UMP and UTP incresase the affinity of PyrR for RNA.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.