KPRS_METJA
ID KPRS_METJA Reviewed; 284 AA.
AC Q58761;
DT 25-OCT-2002, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2002, sequence version 2.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Ribose-phosphate pyrophosphokinase {ECO:0000255|HAMAP-Rule:MF_00583, ECO:0000303|PubMed:16288921};
DE Short=RPPK {ECO:0000255|HAMAP-Rule:MF_00583, ECO:0000303|PubMed:16288921};
DE EC=2.7.6.1 {ECO:0000255|HAMAP-Rule:MF_00583, ECO:0000269|PubMed:16288921};
DE AltName: Full=5-phospho-D-ribosyl alpha-1-diphosphate {ECO:0000255|HAMAP-Rule:MF_00583};
DE AltName: Full=Phosphoribosyl diphosphate synthase {ECO:0000255|HAMAP-Rule:MF_00583, ECO:0000303|PubMed:16288921};
DE AltName: Full=Phosphoribosyl pyrophosphate synthase {ECO:0000255|HAMAP-Rule:MF_00583, ECO:0000303|PubMed:16288921};
DE Short=P-Rib-PP synthase {ECO:0000255|HAMAP-Rule:MF_00583};
DE Short=PRPP synthase {ECO:0000255|HAMAP-Rule:MF_00583, ECO:0000303|PubMed:16288921};
DE Short=PRPPase {ECO:0000255|HAMAP-Rule:MF_00583};
GN Name=prs {ECO:0000255|HAMAP-Rule:MF_00583, ECO:0000303|PubMed:16288921};
GN OrderedLocusNames=MJ1366;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP REVIEW, AND COFACTOR.
RX PubMed=28031352; DOI=10.1128/mmbr.00040-16;
RA Hove-Jensen B., Andersen K.R., Kilstrup M., Martinussen J., Switzer R.L.,
RA Willemoes M.;
RT "Phosphoribosyl diphosphate (PRPP): biosynthesis, enzymology, utilization,
RT and metabolic significance.";
RL Microbiol. Mol. Biol. Rev. 81:E00040-E00040(2017).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) IN COMPLEX WITH SUBSTRATES,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR,
RP SUBSTRATE SPECIFICITY, ACTIVITY REGULATION, SUBUNIT, AND PATHWAY.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=16288921; DOI=10.1016/j.jmb.2005.10.001;
RA Kadziola A., Jepsen C.H., Johansson E., McGuire J., Larsen S.,
RA Hove-Jensen B.;
RT "Novel class III phosphoribosyl diphosphate synthase: structure and
RT properties of the tetrameric, phosphate-activated, non-allosterically
RT inhibited enzyme from Methanocaldococcus jannaschii.";
RL J. Mol. Biol. 354:815-828(2005).
CC -!- FUNCTION: Involved in the biosynthesis of the central metabolite
CC phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of
CC pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-
CC 5-P). It can also use dATP as diphosphoryl donor. {ECO:0000255|HAMAP-
CC Rule:MF_00583, ECO:0000269|PubMed:16288921}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + D-ribose 5-phosphate = 5-phospho-alpha-D-ribose 1-
CC diphosphate + AMP + H(+); Xref=Rhea:RHEA:15609, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:58017, ChEBI:CHEBI:78346,
CC ChEBI:CHEBI:456215; EC=2.7.6.1; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00583, ECO:0000269|PubMed:16288921};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00583,
CC ECO:0000269|PubMed:16288921};
CC Note=Binds 2 Mg(2+) ions per subunit (PubMed:28031352). Mn(2+) is also
CC accepted, but the activity is less than 15% of that obtained with
CC Mg(2+), when assayed at pH 9.5 (PubMed:16288921). {ECO:0000255|HAMAP-
CC Rule:MF_00583, ECO:0000269|PubMed:16288921,
CC ECO:0000303|PubMed:28031352};
CC -!- ACTIVITY REGULATION: Activated by inorganic phosphate, with a maximal
CC activity at 190 mM. Above this concentration inorganic phosphate
CC progressively inhibits the kinase. Completely inhibited by ADP, and
CC partially inhibited by alpha,beta-methylene ATP (mATP). Lack of
CC allosteric regulation. {ECO:0000269|PubMed:16288921}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.6 mM for ATP (at pH 9 and 85 degrees Celsius)
CC {ECO:0000269|PubMed:16288921};
CC KM=2.8 mM for ribose 5-phosphate (at pH 9 and 85 degrees Celsius)
CC {ECO:0000269|PubMed:16288921};
CC Vmax=2.2 mmol/min/mg enzyme (at pH 9 and 85 degrees Celsius)
CC {ECO:0000269|PubMed:16288921};
CC pH dependence:
CC Optimum pH is 9.5. The activity declines strongly above pH 10.
CC {ECO:0000269|PubMed:16288921};
CC Temperature dependence:
CC Optimum temperature is 85 degrees Celsius. 70% of maximal activity at
CC 72 and 95 degrees Celsius. {ECO:0000269|PubMed:16288921};
CC -!- PATHWAY: Metabolic intermediate biosynthesis; 5-phospho-alpha-D-ribose
CC 1-diphosphate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate from
CC D-ribose 5-phosphate (route I): step 1/1. {ECO:0000255|HAMAP-
CC Rule:MF_00583, ECO:0000305|PubMed:16288921}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:16288921}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00583}.
CC -!- MISCELLANEOUS: M.jannaschii PRPP synthase is more compact than the PRPP
CC synthase in the B. subtilis subunit. This is mainly due to truncations
CC of eight residues at the N terminus, 14 residues at the C terminus and
CC to a seven-residue shorter loop. {ECO:0000305|PubMed:16288921}.
CC -!- SIMILARITY: Belongs to the ribose-phosphate pyrophosphokinase family.
CC Class III (archaeal) subfamily. {ECO:0000255|HAMAP-Rule:MF_00583,
CC ECO:0000303|PubMed:28031352, ECO:0000305|PubMed:16288921}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB99374.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; L77117; AAB99374.1; ALT_INIT; Genomic_DNA.
DR PIR; E64470; E64470.
DR PDB; 1U9Y; X-ray; 2.65 A; A/B/C/D=1-284.
DR PDB; 1U9Z; X-ray; 2.80 A; A/B/C/D=1-284.
DR PDBsum; 1U9Y; -.
DR PDBsum; 1U9Z; -.
DR AlphaFoldDB; Q58761; -.
DR SMR; Q58761; -.
DR STRING; 243232.MJ_1366; -.
DR EnsemblBacteria; AAB99374; AAB99374; MJ_1366.
DR KEGG; mja:MJ_1366; -.
DR eggNOG; arCOG00067; Archaea.
DR HOGENOM; CLU_033546_2_2_2; -.
DR InParanoid; Q58761; -.
DR OMA; FGWARQD; -.
DR PhylomeDB; Q58761; -.
DR BRENDA; 2.7.6.1; 3260.
DR UniPathway; UPA00087; UER00172.
DR EvolutionaryTrace; Q58761; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0002189; C:ribose phosphate diphosphokinase complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004749; F:ribose phosphate diphosphokinase activity; IBA:GO_Central.
DR GO; GO:0006015; P:5-phosphoribose 1-diphosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0006164; P:purine nucleotide biosynthetic process; IBA:GO_Central.
DR GO; GO:0009156; P:ribonucleoside monophosphate biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd06223; PRTases_typeI; 1.
DR Gene3D; 3.40.50.2020; -; 2.
DR HAMAP; MF_00583_A; RibP_PPkinase_A; 1.
DR InterPro; IPR029099; Pribosyltran_N.
DR InterPro; IPR000836; PRibTrfase_dom.
DR InterPro; IPR029057; PRTase-like.
DR InterPro; IPR005946; Rib-P_diPkinase.
DR InterPro; IPR037514; Rib-P_diPkinase_arc.
DR PANTHER; PTHR10210; PTHR10210; 1.
DR Pfam; PF00156; Pribosyltran; 1.
DR Pfam; PF13793; Pribosyltran_N; 1.
DR SUPFAM; SSF53271; SSF53271; 2.
DR TIGRFAMs; TIGR01251; ribP_PPkin; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Kinase; Magnesium; Manganese;
KW Metal-binding; Nucleotide biosynthesis; Nucleotide-binding;
KW Reference proteome; Transferase.
FT CHAIN 1..284
FT /note="Ribose-phosphate pyrophosphokinase"
FT /id="PRO_0000141238"
FT ACT_SITE 186
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00583"
FT BINDING 34..36
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00583,
FT ECO:0000269|PubMed:16288921, ECO:0007744|PDB:1U9Z"
FT BINDING 92..93
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00583,
FT ECO:0000305|PubMed:16288921, ECO:0007744|PDB:1U9Z"
FT BINDING 125
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00583"
FT BINDING 163
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00583"
FT BINDING 188
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00583"
FT BINDING 212
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00583,
FT ECO:0000269|PubMed:16288921, ECO:0007744|PDB:1U9Z"
FT BINDING 216..220
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00583,
FT ECO:0000269|PubMed:16288921, ECO:0007744|PDB:1U9Z"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:1U9Y"
FT HELIX 7..9
FT /evidence="ECO:0007829|PDB:1U9Z"
FT HELIX 10..19
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 27..31
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 37..41
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 47..53
FT /evidence="ECO:0007829|PDB:1U9Y"
FT HELIX 59..74
FT /evidence="ECO:0007829|PDB:1U9Y"
FT TURN 75..77
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 80..84
FT /evidence="ECO:0007829|PDB:1U9Y"
FT TURN 89..92
FT /evidence="ECO:0007829|PDB:1U9Z"
FT HELIX 104..115
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 117..123
FT /evidence="ECO:0007829|PDB:1U9Y"
FT HELIX 127..132
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 137..140
FT /evidence="ECO:0007829|PDB:1U9Y"
FT HELIX 143..150
FT /evidence="ECO:0007829|PDB:1U9Y"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 158..163
FT /evidence="ECO:0007829|PDB:1U9Y"
FT HELIX 164..166
FT /evidence="ECO:0007829|PDB:1U9Y"
FT HELIX 167..177
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 181..184
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 198..200
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 208..214
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 216..218
FT /evidence="ECO:0007829|PDB:1U9Y"
FT HELIX 219..230
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 235..242
FT /evidence="ECO:0007829|PDB:1U9Y"
FT HELIX 249..256
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 259..264
FT /evidence="ECO:0007829|PDB:1U9Y"
FT STRAND 272..274
FT /evidence="ECO:0007829|PDB:1U9Y"
FT HELIX 277..281
FT /evidence="ECO:0007829|PDB:1U9Y"
SQ SEQUENCE 284 AA; 31395 MW; 9EAE9805785B1127 CRC64;
MIVVSGSQSQ NLAFKVAKLL NTKLTRVEYK RFPDNEIYVR IVDEINDDEA VIINTQKNQN
DAIVETILLC DALRDEGVKK ITLVAPYLAY ARQDKKFNPG EAISIRALAK IYSNIVDKLI
TINPHETHIK DFFTIPFIYG DAVPKLAEYV KDKLNDPIVL APDKGALEFA KTASKILNAE
YDYLEKTRLS PTEIQIAPKT LDAKDRDVFI VDDIISTGGT MATAVKLLKE QGAKKIIAAC
VHPVLIGDAL NKLYSAGVEE VVGTDTYLSE VSKVSVAEVI VDLL
