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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 the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P).UniRule annotation7 Publications

Miscellaneous

This enzyme uses a steady state ordered mechanism, where Mg2+ binds first, followed by Mg-ATP and lastly, ribose 5-phosphate.1 Publication

Catalytic activityi

ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate.UniRule annotation3 Publications4 Publications

Cofactori

Mg2+UniRule annotation1 Publication5 PublicationsNote: Binds 2 Mg2+ ions per subunit (Probable). Mn2+, Co2+ and Cd2+ are also accepted (PubMed:3009477, PubMed:2542328, PubMed:8679571, PubMed:9125530, PubMed:10954724).1 Publication5 Publications

Enzyme regulationi

Activated by inorganic phosphate (PubMed:3009477, PubMed:10954724). In addition to form a complex with ATP, Mg2+ also acts as a cofactor (PubMed:9125530). Strongly inhibited by ADP through competitive binding at the activation site and at a specific allosteric site (PubMed:3009477, PubMed:6290219,PubMed:9125530). Competitively inhibited by Ca2+ and ribose 1,5-bisphosphate (Rib-1,5-P2) (PubMed:2542328, PubMed:9125530). Less strongly inhibited by AMP, alpha,beta-methylene ATP (mATP), (2',3'-dialdehyde)-ATP (oATP) and 1-alpha,2-alpha,3-alpha-trihydroxy-4-beta-cyclopentanemethanol 5-phosphate (cRib-5-P) (PubMed:2542328, PubMed:7657655, PubMed:9125530).6 Publications

Kineticsi

  1. KM=138 µM for Rib-5-P (at pH 8 and 37 degrees Celsius)1 Publication
  2. KM=230 µM for ATP (at pH 8 and 37 degrees Celsius)1 Publication
  3. KM=280 µM for Rib-5-P (at pH 8.5 and 37 degrees Celsius)1 Publication
  4. KM=300 µM for Rib-5-P (with 20 mM ATP at pH 8 and 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 9.7-9.8.1 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)DescriptionActionsGraphical viewLength
Metal bindingi131Magnesium 1UniRule annotation1
Metal bindingi170Magnesium 2UniRule annotation1
Active sitei1941 Publication1
Binding sitei196Ribose-5-phosphateUniRule annotation1
Binding sitei220Ribose-5-phosphateUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi37 – 39ATPUniRule annotation3
Nucleotide bindingi96 – 97ATPUniRule annotation2

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

Keywordsi

Molecular functionKinase, Transferase
Biological processNucleotide biosynthesis
LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Ribose-phosphate pyrophosphokinase1 PublicationUniRule annotation (EC:2.7.6.13 Publications4 Publications)
Short name:
RPPK1 PublicationUniRule annotation
Alternative name(s):
5-phospho-D-ribosyl alpha-1-diphosphateUniRule annotation
Phosphoribosyl diphosphate synthaseUniRule annotation
Phosphoribosyl pyrophosphate synthase1 PublicationUniRule 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10774. prs.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cytosol Source: EcoCyc

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)DescriptionActionsGraphical viewLength
Mutagenesisi220D → 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 Publication1
Mutagenesisi220D → 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 Publication1
Mutagenesisi221D → 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 Publication1
Mutagenesisi224D → 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 Publication1
Mutagenesisi224D → 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 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00001411342 – 315Ribose-phosphate pyrophosphokinaseAdd BLAST314

Proteomic databases

PaxDbiP0A717.
PRIDEiP0A717.

Interactioni

Subunit structurei

Homohexamer.UniRule annotation

Binary interactionsi

WithEntry#Exp.IntActNotes
groLP0A6F52EBI-906827,EBI-543750

Protein-protein interaction databases

BioGridi4260813. 13 interactors.
DIPiDIP-35839N.
IntActiP0A717. 155 interactors.
MINTiMINT-1221689.
STRINGi316385.ECDH10B_1260.

Structurei

Secondary structure

1315
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 8Combined sources5
Beta strandi10 – 12Combined sources3
Helixi13 – 22Combined sources10
Beta strandi30 – 34Combined sources5
Beta strandi40 – 44Combined sources5
Beta strandi52 – 56Combined sources5
Helixi63 – 78Combined sources16
Turni79 – 81Combined sources3
Beta strandi82 – 88Combined sources7
Helixi101 – 103Combined sources3
Helixi109 – 120Combined sources12
Beta strandi124 – 129Combined sources6
Helixi135 – 138Combined sources4
Beta strandi143 – 146Combined sources4
Helixi149 – 159Combined sources11
Beta strandi165 – 167Combined sources3
Beta strandi169 – 171Combined sources3
Helixi174 – 183Combined sources10
Beta strandi198 – 200Combined sources3
Beta strandi207 – 209Combined sources3
Beta strandi216 – 226Combined sources11
Helixi227 – 238Combined sources12
Beta strandi245 – 251Combined sources7
Helixi257 – 262Combined sources6
Beta strandi267 – 275Combined sources9
Helixi279 – 282Combined sources4
Beta strandi285 – 290Combined sources6
Helixi293 – 302Combined sources10
Turni303 – 305Combined sources3

3D structure databases

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

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni224 – 228Ribose-5-phosphate bindingUniRule annotation5

Sequence similaritiesi

Belongs to the ribose-phosphate pyrophosphokinase family. Class I subfamily.1 PublicationUniRule annotation

Phylogenomic databases

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

Family and domain databases

CDDicd06223. PRTases_typeI. 1 hit.
HAMAPiMF_00583_B. RibP_PPkinase_B. 1 hit.
InterProiView protein in InterPro
IPR000842. PRib_PP_synth_CS.
IPR029099. Pribosyltran_N.
IPR000836. PRibTrfase_dom.
IPR029057. PRTase-like.
IPR005946. Rib-P_diPkinase.
PfamiView protein in Pfam
PF14572. Pribosyl_synth. 1 hit.
PF13793. Pribosyltran_N. 1 hit.
SUPFAMiSSF53271. SSF53271. 1 hit.
TIGRFAMsiTIGR01251. ribP_PPkin. 1 hit.
PROSITEiView protein in PROSITE
PS00114. PRPP_SYNTHASE. 1 hit.

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)DescriptionActionsGraphical viewLength
Sequence conflicti127T → I in AAA24431 (PubMed:3009477).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti129D → A in mutant PRSA1; alters the binding of divalent cations, especially magnesium. Little alteration in the affinity for ribose 5-phosphate and 27-fold decrease of the affinity for ATP. Absence of inhibition by AMP. 1 Publication1

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.
PATRICifig|511145.12.peg.1255.

Similar proteinsi

Entry informationi

Entry nameiKPRS_ECOLI
AccessioniPrimary (citable) accession number: P0A717
Secondary accession number(s): P08330, P76828, P78058
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: January 23, 2007
Last modified: October 25, 2017
This is version 111 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Although Mg2+ has been found in cristallography study, the positions do not correspond to the correct residues.1 Publication1 Publication

Keywords - Technical termi

3D-structure, Allosteric enzyme, 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