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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)DescriptionActionsGraphical viewLength
Binding sitei138SubstrateBy similarity1
Binding sitei162SubstrateBy similarity1

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)DescriptionActionsGraphical viewLength
Mutagenesisi15R → Q: No effect on ability to regulate the pyr operon; no effect on uprtase activity. 1 Publication1
Mutagenesisi18T → 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 Publication1
Mutagenesisi19R → Q: Loss of ability to regulate the pyr operon; no effect on UPRTase activity. 1 Publication1
Mutagenesisi22H → A: Loss of ability to regulate the pyr operon and to bind to RNA; no effect on UPRTase activity. 1 Publication1
Mutagenesisi27R → 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 Publication1
Mutagenesisi41T → I: Reduced ability to regulate the pyr operon; reduced affinity for RNA; loss of UPRTase activity. 1 Publication1
Mutagenesisi140H → A: Reduced ability to regulate the pyr operon; decreased UPRTase activity. 1 Publication1
Mutagenesisi141R → Q: Loss of ability to regulate the pyr operon; highly reduced affinity for RNA; no effect on UPRTase activity. 1 Publication1
Mutagenesisi146R → Q: Reduced ability to regulate the pyr operon, and loss of ability to bind to RNA; no effect on UPRTase activity. 1 Publication1
Mutagenesisi152K → 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 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001830301 – 181Bifunctional protein PyrRAdd BLAST181

Proteomic databases

PaxDbiP39765.

Interactioni

Subunit structurei

Homodimer and homohexamer; in equilibrium.

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100008551.

Structurei

Secondary structure

1181
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 8Combined sources5
Helixi10 – 27Combined sources18
Helixi29 – 31Combined sources3
Beta strandi34 – 40Combined sources7
Helixi41 – 58Combined sources18
Beta strandi64 – 72Combined sources9
Beta strandi74 – 76Combined sources3
Beta strandi78 – 80Combined sources3
Beta strandi84 – 91Combined sources8
Beta strandi99 – 111Combined sources13
Helixi112 – 124Combined sources13
Beta strandi128 – 137Combined sources10
Beta strandi142 – 144Combined sources3
Beta strandi148 – 153Combined sources6
Beta strandi160 – 165Combined sources6
Helixi167 – 170Combined sources4
Beta strandi174 – 179Combined sources6

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP39765.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni41 – 42Substrate-bindingBy similarity2
Regioni105 – 113Substrate bindingBy similarity9

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi101 – 113PRPP-bindingBy similarityAdd BLAST13

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108UK1. Bacteria.
COG2065. LUCA.
HOGENOMiHOG000245770.
InParanoidiP39765.
KOiK02825.
OMAiLMDMGRP.
PhylomeDBiP39765.

Family and domain databases

CDDicd06223. PRTases_typeI. 1 hit.
Gene3Di3.40.50.2020. 1 hit.
HAMAPiMF_01219. PyrR. 1 hit.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1A3CX-ray1.60A1-181[»]
1A4XX-ray2.30A/B1-181[»]
4P82X-ray1.30A2-179[»]
ProteinModelPortaliP39765.
SMRiP39765.
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.
OMAiLMDMGRP.
PhylomeDBiP39765.

Enzyme and pathway databases

BioCyciBSUB:BSU15470-MONOMER.
SABIO-RKP39765.

Miscellaneous databases

EvolutionaryTraceiP39765.

Family and domain databases

CDDicd06223. PRTases_typeI. 1 hit.
Gene3Di3.40.50.2020. 1 hit.
HAMAPiMF_01219. PyrR. 1 hit.
InterProiIPR000836. PRibTrfase_dom.
IPR029057. PRTase-like.
IPR023050. PyrR.
[Graphical view]
PfamiPF00156. Pribosyltran. 1 hit.
[Graphical view]
SUPFAMiSSF53271. SSF53271. 1 hit.
ProtoNetiSearch...

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: November 2, 2016
This is version 124 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.