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Protein

Ribose-phosphate pyrophosphokinase

Gene

prs

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of ribose 1,5-bisphosphate. Catalyzes the transfer of pyrophosphoryl group from ATP to ribose-5-phosphate (Rib-5-P) to yield phosphoribosyl diphosphate (PRPP) and AMP.UniRule annotation7 Publications

Catalytic activityi

ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate.UniRule annotation4 Publications

Cofactori

Mg2+UniRule annotation5 Publications, Mn2+UniRule annotation5 PublicationsNote: Binds 1 Mg2+ ion per subunit. Mn2+ is also accepted.UniRule annotation5 Publications

Enzyme regulationi

Inhibited by calcium ion, (2',3'-dialdehyde)-ATP (oATP), 1-alpha,2-alpha,3-alpha-trihydroxy-4-beta-cyclopentanemethanol 5-phosphate, alpha,beta-methylene ATP and ADP.5 Publications

Kineticsi

  1. KM=0.094 mM for ATP (at pH 8 and 37 degrees Celsius)1 Publication
  2. KM=0.097 mM for ATP (at pH 8.5 and 37 degrees Celsius)1 Publication
  3. KM=0.138 mM for Rib-5-P (at pH 8 and 37 degrees Celsius)1 Publication
  4. KM=0.23 mM for ATP (at pH 8 and 37 degrees Celsius)1 Publication
  5. KM=0.24 µM for Rib-5-P (at 37 degrees Celsius)1 Publication
  6. KM=0.28 mM for Rib-5-P (at pH 8.5 and 37 degrees Celsius)1 Publication
  7. KM=0.3 mM for Rib-5-P (with 20 mM ATP at pH 8 and 37 degrees Celsius)1 Publication
  8. KM=1 mM for ATP (at 37 degrees Celsius)1 Publication
  1. Vmax=129 µmol/min/mg enzyme toward Rib-5-P (at pH 8.5 and 37 degrees Celsius)1 Publication
  2. Vmax=143 µmol/min/mg enzyme toward ATP (at pH 8.5 and 37 degrees Celsius)1 Publication

pH dependencei

Optimum pH is between 9.7 and 9.8.1 Publication

Pathwayi: 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route I).UniRule annotation1 Publication
Proteins known to be involved in this subpathway in this organism are:
  1. Ribose-phosphate pyrophosphokinase (prs)
This subpathway is part of the pathway 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis, which is itself part of Metabolic intermediate biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route I), the pathway 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis and in Metabolic intermediate biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei105 – 1051Ribose-5-phosphateUniRule annotation
Metal bindingi129 – 1291MagnesiumUniRule annotation
Metal bindingi131 – 1311MagnesiumUniRule annotation
Binding sitei131 – 1311ATPUniRule annotation
Binding sitei136 – 1361ATPUniRule annotation
Metal bindingi140 – 1401MagnesiumUniRule annotation
Metal bindingi144 – 1441MagnesiumUniRule annotation
Binding sitei170 – 1701Ribose-5-phosphateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi37 – 393ATPUniRule annotation
Nucleotide bindingi96 – 994ATPUniRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • kinase activity Source: UniProtKB-KW
  • magnesium ion binding Source: EcoCyc
  • phosphate ion binding Source: EcoCyc
  • ribose phosphate diphosphokinase activity Source: EcoCyc

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Nucleotide biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:PRPPSYN-MONOMER.
ECOL316407:JW1198-MONOMER.
MetaCyc:PRPPSYN-MONOMER.
UniPathwayiUPA00087; UER00172.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribose-phosphate pyrophosphokinase3 PublicationsUniRule annotation (EC:2.7.6.11 PublicationUniRule annotation2 Publications)
Short name:
RPPK3 PublicationsUniRule annotation
Alternative name(s):
5-phospho-D-ribosyl alpha-1-diphosphateUniRule annotation
Phosphoribosyl diphosphate synthaseUniRule annotation
Phosphoribosyl pyrophosphate synthase3 PublicationsUniRule annotation
Short name:
P-Rib-PP synthaseUniRule annotation
Short name:
PRPP synthaseUniRule annotation
Short name:
PRPPaseUniRule annotation
Gene namesi
Name:prs1 PublicationUniRule annotation
Synonyms:prsA
Ordered Locus Names:b1207, JW1198
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10774. prs.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene are unable to grow on nucleosides as purine source.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi220 – 2201D → E: 4-fold decrease in the affinity binding for Rib-5-P in the presence of magnesium ions. In the presence of cobalt ions, it shows a 15-fold decrease in the affinity binding for Rib-5-P. 1 Publication
Mutagenesisi220 – 2201D → F: With magnesium or manganese ions, the affinity binding values for ATP and Rib-5-P are comparable to those of the wild-type. 1 Publication
Mutagenesisi221 – 2211D → A: The affinity binding for ATP is comparable to those of the wild-type, apart from a slight decrease in the presence of manganese ions. The affinity binding for Rib-5-P is greatly decreased in the presence of both manganese and cobalt ions but only about 2-fold in the presence of magnesium ions. 1 Publication
Mutagenesisi224 – 2241D → A: With magnesium or manganese ions, the affinity binding values for ATP and Rib-5-P are comparable to those of the wild-type. 1 Publication
Mutagenesisi224 – 2241D → S: With magnesium or manganese ions, the affinity binding values for ATP and Rib-5-P are comparable to those of the wild-type. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved2 Publications
Chaini2 – 315314Ribose-phosphate pyrophosphokinasePRO_0000141134Add
BLAST

Proteomic databases

EPDiP0A717.
PaxDbiP0A717.
PRIDEiP0A717.

Interactioni

Protein-protein interaction databases

BioGridi4260813. 13 interactions.
DIPiDIP-35839N.
IntActiP0A717. 109 interactions.
MINTiMINT-1221689.
STRINGi511145.b1207.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4S2UX-ray2.71A2-315[»]
ProteinModelPortaliP0A717.
SMRiP0A717. Positions 4-309.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni194 – 1963Ribose-5-phosphate bindingUniRule annotation
Regioni221 – 2288Ribose-5-phosphate bindingUniRule annotation
Regioni308 – 3103Ribose-5-phosphate bindingUniRule annotation

Sequence similaritiesi

Belongs to the ribose-phosphate pyrophosphokinase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C5T. Bacteria.
COG0462. LUCA.
HOGENOMiHOG000210452.
InParanoidiP0A717.
KOiK00948.
OMAiRENITEW.
OrthoDBiEOG6Z99XQ.
PhylomeDBiP0A717.

Family and domain databases

Gene3Di3.40.50.2020. 2 hits.
HAMAPiMF_00583_B. RibP_PPkinase_B.
InterProiIPR000842. PRib_PP_synth_CS.
IPR029099. Pribosyltran_N.
IPR029057. PRTase-like.
IPR005946. Rib-P_diPkinase.
[Graphical view]
PfamiPF14572. Pribosyl_synth. 1 hit.
PF13793. Pribosyltran_N. 1 hit.
[Graphical view]
SUPFAMiSSF53271. SSF53271. 1 hit.
TIGRFAMsiTIGR01251. ribP_PPkin. 1 hit.
PROSITEiPS00114. PRPP_SYNTHASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A717-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPDMKLFAGN ATPELAQRIA NRLYTSLGDA AVGRFSDGEV SVQINENVRG
60 70 80 90 100
GDIFIIQSTC APTNDNLMEL VVMVDALRRA SAGRITAVIP YFGYARQDRR
110 120 130 140 150
VRSARVPITA KVVADFLSSV GVDRVLTVDL HAEQIQGFFD VPVDNVFGSP
160 170 180 190 200
ILLEDMLQLN LDNPIVVSPD IGGVVRARAI AKLLNDTDMA IIDKRRPRAN
210 220 230 240 250
VSQVMHIIGD VAGRDCVLVD DMIDTGGTLC KAAEALKERG AKRVFAYATH
260 270 280 290 300
PIFSGNAANN LRNSVIDEVV VCDTIPLSDE IKSLPNVRTL TLSGMLAEAI
310
RRISNEESIS AMFEH
Length:315
Mass (Da):34,218
Last modified:January 23, 2007 - v2
Checksum:i4D69B7D118F93720
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti127 – 1271T → I in AAA24431 (PubMed:3009477).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti129 – 1291D → A in mutant PRSA1; defective in the binding of divalent cations, especially magnesium. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M13174 Genomic DNA. Translation: AAA24431.1.
U00096 Genomic DNA. Translation: AAC74291.1.
AP009048 Genomic DNA. Translation: BAA36065.1.
PIRiD64867. KIECRY.
RefSeqiNP_415725.1. NC_000913.3.
WP_001298109.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74291; AAC74291; b1207.
BAA36065; BAA36065; BAA36065.
GeneIDi945772.
KEGGiecj:JW1198.
eco:b1207.
PATRICi32117666. VBIEscCol129921_1255.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M13174 Genomic DNA. Translation: AAA24431.1.
U00096 Genomic DNA. Translation: AAC74291.1.
AP009048 Genomic DNA. Translation: BAA36065.1.
PIRiD64867. KIECRY.
RefSeqiNP_415725.1. NC_000913.3.
WP_001298109.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4S2UX-ray2.71A2-315[»]
ProteinModelPortaliP0A717.
SMRiP0A717. Positions 4-309.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260813. 13 interactions.
DIPiDIP-35839N.
IntActiP0A717. 109 interactions.
MINTiMINT-1221689.
STRINGi511145.b1207.

Proteomic databases

EPDiP0A717.
PaxDbiP0A717.
PRIDEiP0A717.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74291; AAC74291; b1207.
BAA36065; BAA36065; BAA36065.
GeneIDi945772.
KEGGiecj:JW1198.
eco:b1207.
PATRICi32117666. VBIEscCol129921_1255.

Organism-specific databases

EchoBASEiEB0767.
EcoGeneiEG10774. prs.

Phylogenomic databases

eggNOGiENOG4105C5T. Bacteria.
COG0462. LUCA.
HOGENOMiHOG000210452.
InParanoidiP0A717.
KOiK00948.
OMAiRENITEW.
OrthoDBiEOG6Z99XQ.
PhylomeDBiP0A717.

Enzyme and pathway databases

UniPathwayiUPA00087; UER00172.
BioCyciEcoCyc:PRPPSYN-MONOMER.
ECOL316407:JW1198-MONOMER.
MetaCyc:PRPPSYN-MONOMER.

Miscellaneous databases

PROiP0A717.

Family and domain databases

Gene3Di3.40.50.2020. 2 hits.
HAMAPiMF_00583_B. RibP_PPkinase_B.
InterProiIPR000842. PRib_PP_synth_CS.
IPR029099. Pribosyltran_N.
IPR029057. PRTase-like.
IPR005946. Rib-P_diPkinase.
[Graphical view]
PfamiPF14572. Pribosyl_synth. 1 hit.
PF13793. Pribosyltran_N. 1 hit.
[Graphical view]
SUPFAMiSSF53271. SSF53271. 1 hit.
TIGRFAMsiTIGR01251. ribP_PPkin. 1 hit.
PROSITEiPS00114. PRPP_SYNTHASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Phosphoribosylpyrophosphate synthetase of Escherichia coli. Properties of the purified enzyme and primary structure of the prs gene."
    Hove-Jensen B., Harlow K.W., King C.J., Switzer R.L.
    J. Biol. Chem. 261:6765-6771(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, COFACTOR.
  2. "Characterization of the Escherichia coli prsA1-encoded mutant phosphoribosylpyrophosphate synthetase identifies a divalent cation-nucleotide binding site."
    Bower S.G., Harlow K.W., Switzer R.L., Hove-Jensen B.
    J. Biol. Chem. 264:10287-10291(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION TO 127, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, ENZYME REGULATION, MUTANT PRSA1.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
    Link A.J., Robison K., Church G.M.
    Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-12.
    Strain: K12 / EMG2.
  7. "Phosphoribosylpyrophosphate synthetase of Escherichia coli, Identification of a mutant enzyme."
    Hove-Jensen B., Nygaard P.
    Eur. J. Biochem. 126:327-332(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, BIOPHYSICOCHEMICAL PROPERTIES, NOMENCLATURE.
  8. "Inactivation of Escherichia coli phosphoribosylpyrophosphate synthetase by the 2',3'-dialdehyde derivative of ATP. Identification of active site lysines."
    Hilden I., Hove-Jensen B., Harlow K.W.
    J. Biol. Chem. 270:20730-20736(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION.
  9. "Effects of mutagenesis of aspartic acid residues in the putative phosphoribosyl diphosphate binding site of Escherichia coli phosphoribosyl diphosphate synthetase on metal ion specificity and ribose 5-phosphate binding."
    Willemoes M., Nilsson D., Hove-Jensen B.
    Biochemistry 35:8181-8186(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-220; ASP-221 AND ASP-224, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
  10. "Binding of divalent magnesium by Escherichia coli phosphoribosyl diphosphate synthetase."
    Willemoes M., Hove-Jensen B.
    Biochemistry 36:5078-5083(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION, COFACTOR.
  11. "Steady state kinetic model for the binding of substrates and allosteric effectors to Escherichia coli phosphoribosyl-diphosphate synthase."
    Willemoes M., Hove-Jensen B., Larsen S.
    J. Biol. Chem. 275:35408-35412(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION, COFACTOR.

Entry informationi

Entry nameiKPRS_ECOLI
AccessioniPrimary (citable) accession number: P0A717
Secondary accession number(s): P08330, P76828, P78058
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.