R15PI_THEKO
ID R15PI_THEKO Reviewed; 322 AA.
AC Q5JFM9;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Ribose 1,5-bisphosphate isomerase {ECO:0000255|HAMAP-Rule:MF_02230};
DE Short=R15P isomerase {ECO:0000255|HAMAP-Rule:MF_02230};
DE Short=R15Pi {ECO:0000255|HAMAP-Rule:MF_02230};
DE EC=5.3.1.29 {ECO:0000255|HAMAP-Rule:MF_02230, ECO:0000269|PubMed:17303759, ECO:0000269|PubMed:22511789, ECO:0000269|PubMed:23065974};
DE AltName: Full=Ribulose 1,5-bisphosphate synthase {ECO:0000255|HAMAP-Rule:MF_02230};
DE Short=RuBP synthase {ECO:0000255|HAMAP-Rule:MF_02230};
GN OrderedLocusNames=TK0185;
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=17303759; DOI=10.1126/science.1135999;
RA Sato T., Atomi H., Imanaka T.;
RT "Archaeal type III RuBisCOs function in a pathway for AMP metabolism.";
RL Science 315:1003-1006(2007).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION,
RP KINETIC PARAMETERS, INDUCTION, AND PATHWAY.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=23065974; DOI=10.1128/jb.01335-12;
RA Aono R., Sato T., Yano A., Yoshida S., Nishitani Y., Miki K., Imanaka T.,
RA Atomi H.;
RT "Enzymatic characterization of AMP phosphorylase and ribose-1,5-
RT bisphosphate isomerase functioning in an archaeal AMP metabolic pathway.";
RL J. Bacteriol. 194:6847-6855(2012).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF APOENZYME AND WILD-TYPE IN
RP COMPLEX WITH PRODUCT AND MUTANT SER-133 IN COMPLEX WITH SUBSTRATE,
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBUNIT, REACTION
RP MECHANISM, ACTIVE SITES, AND MUTAGENESIS OF CYS-133; ASP-202 AND ARG-227.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=22511789; DOI=10.1074/jbc.m112.349423;
RA Nakamura A., Fujihashi M., Aono R., Sato T., Nishiba Y., Yoshida S.,
RA Yano A., Atomi H., Imanaka T., Miki K.;
RT "Dynamic, ligand-dependent conformational change triggers reaction of
RT ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1.";
RL J. Biol. Chem. 287:20784-20796(2012).
CC -!- FUNCTION: Catalyzes the isomerization of ribose 1,5-bisphosphate (R15P)
CC to ribulose 1,5-bisphosphate (RuBP), the CO(2) acceptor and substrate
CC for RubisCO. Only accepts the alpha-anomer of D-ribose 1,5-bisphosphate
CC as substrate, being inactive on the beta-anomer. Displays a strict
CC substrate specificity, since other phosphorylated sugars such as R5P,
CC ribose, G16P, G6P, G1P, FBP, F6P, and PRPP, are not substrates.
CC Functions in an archaeal AMP degradation pathway, together with AMP
CC phosphorylase and RubisCO. {ECO:0000269|PubMed:17303759,
CC ECO:0000269|PubMed:22511789, ECO:0000269|PubMed:23065974}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=alpha-D-ribose 1,5-bisphosphate = D-ribulose 1,5-bisphosphate;
CC Xref=Rhea:RHEA:32243, ChEBI:CHEBI:57870, ChEBI:CHEBI:68688;
CC EC=5.3.1.29; Evidence={ECO:0000255|HAMAP-Rule:MF_02230,
CC ECO:0000269|PubMed:17303759, ECO:0000269|PubMed:22511789,
CC ECO:0000269|PubMed:23065974};
CC -!- ACTIVITY REGULATION: Is highly activated in the presence of AMP, with
CC an increase of >40-fold in activity levels. Among other nucleotides,
CC isomerase activity is slightly increased in the presence of GMP, but
CC CMP, UMP, TMP, and NAD(+) have no effect; therefore, AMP is likely the
CC major activator of R15P isomerase in vivo. To a lesser extent, various
CC compounds with an adenosyl moiety, such as dAMP, adenosine, or
CC methylthioadenosine, can also act as activators. The regulation of this
CC enzyme by AMP prevents excess degradation of intracellular AMP by the
CC archaeal AMP degradation pathway. {ECO:0000269|PubMed:23065974}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.6 mM for D-ribose 1,5-bisphosphate (in the presence of AMP, at
CC 85 degrees Celsius) {ECO:0000269|PubMed:23065974};
CC Note=kcat is 29.2 sec(-1) (in the presence of AMP, at 85 degrees
CC Celsius).;
CC -!- SUBUNIT: Homohexamer; trimer of dimers. {ECO:0000269|PubMed:22511789}.
CC -!- INDUCTION: Up-regulated by nucleosides (at protein level).
CC {ECO:0000269|PubMed:23065974}.
CC -!- MISCELLANEOUS: Reaction proceeds via a cis-phosphoenolate intermediate.
CC {ECO:0000255|HAMAP-Rule:MF_02230}.
CC -!- SIMILARITY: Belongs to the eIF-2B alpha/beta/delta subunits family.
CC R15P isomerase subfamily. {ECO:0000255|HAMAP-Rule:MF_02230,
CC ECO:0000305}.
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DR EMBL; AP006878; BAD84374.1; -; Genomic_DNA.
DR RefSeq; WP_011249140.1; NC_006624.1.
DR PDB; 3A11; X-ray; 2.50 A; A/B/C/D/E/F=1-322.
DR PDB; 3A9C; X-ray; 2.60 A; A/B/C/D/E/F=1-322.
DR PDB; 3VM6; X-ray; 2.85 A; A/B/C=1-322.
DR PDBsum; 3A11; -.
DR PDBsum; 3A9C; -.
DR PDBsum; 3VM6; -.
DR AlphaFoldDB; Q5JFM9; -.
DR SMR; Q5JFM9; -.
DR STRING; 69014.TK0185; -.
DR EnsemblBacteria; BAD84374; BAD84374; TK0185.
DR GeneID; 3235541; -.
DR KEGG; tko:TK0185; -.
DR PATRIC; fig|69014.16.peg.185; -.
DR eggNOG; arCOG01124; Archaea.
DR HOGENOM; CLU_016218_2_1_2; -.
DR InParanoid; Q5JFM9; -.
DR OMA; GDVIMTH; -.
DR OrthoDB; 36100at2157; -.
DR PhylomeDB; Q5JFM9; -.
DR BRENDA; 5.3.1.29; 5246.
DR EvolutionaryTrace; Q5JFM9; -.
DR Proteomes; UP000000536; Chromosome.
DR GO; GO:0043917; F:ribose 1,5-bisphosphate isomerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046523; F:S-methyl-5-thioribose-1-phosphate isomerase activity; IBA:GO_Central.
DR GO; GO:0019509; P:L-methionine salvage from methylthioadenosine; IBA:GO_Central.
DR GO; GO:0019323; P:pentose catabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 1.20.120.420; -; 1.
DR Gene3D; 3.40.50.10470; -; 1.
DR HAMAP; MF_02230; R15P_isomerase; 1.
DR InterPro; IPR000649; IF-2B-related.
DR InterPro; IPR042529; IF_2B-like_C.
DR InterPro; IPR011559; Initiation_fac_2B_a/b/d.
DR InterPro; IPR027363; M1Pi_N.
DR InterPro; IPR037171; NagB/RpiA_transferase-like.
DR InterPro; IPR005250; Ribulose_e2b2.
DR Pfam; PF01008; IF-2B; 1.
DR SUPFAM; SSF100950; SSF100950; 1.
DR TIGRFAMs; TIGR00524; eIF-2B_rel; 1.
DR TIGRFAMs; TIGR00511; ribulose_e2b2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Isomerase; Reference proteome.
FT CHAIN 1..322
FT /note="Ribose 1,5-bisphosphate isomerase"
FT /id="PRO_0000422826"
FT ACT_SITE 133
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02230,
FT ECO:0000269|PubMed:22511789"
FT ACT_SITE 202
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02230,
FT ECO:0000269|PubMed:22511789"
FT BINDING 20..23
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02230"
FT BINDING 63
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02230,
FT ECO:0000269|PubMed:22511789"
FT BINDING 135..137
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02230"
FT BINDING 212..213
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02230"
FT BINDING 238
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02230,
FT ECO:0000269|PubMed:22511789"
FT SITE 227
FT /note="Plays a key role in hexamerization"
FT MUTAGEN 133
FT /note="C->A,S: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:22511789"
FT MUTAGEN 202
FT /note="D->N: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:22511789"
FT MUTAGEN 227
FT /note="R->E: Impairs molecular assembly. 60-fold decrease
FT in catalytic activity."
FT /evidence="ECO:0000269|PubMed:22511789"
FT HELIX 6..15
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 22..39
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 45..60
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 68..85
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 90..120
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 128..131
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 136..147
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 153..157
FT /evidence="ECO:0007829|PDB:3A11"
FT TURN 160..163
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 164..174
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 179..182
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:3A11"
FT TURN 187..190
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 191..193
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 195..199
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 202..204
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 210..213
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 216..225
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 229..233
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 236..238
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 244..247
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 256..258
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 262..265
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 272..274
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 277..282
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 284..286
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 288..292
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 299..301
FT /evidence="ECO:0007829|PDB:3A11"
FT HELIX 302..310
FT /evidence="ECO:0007829|PDB:3A11"
FT STRAND 314..316
FT /evidence="ECO:0007829|PDB:3A11"
SQ SEQUENCE 322 AA; 36302 MW; 44A19FD24E140250 CRC64;
MAVVKEVLEI AEKIKNMEIR GAGKIARSAA YALQLQAEKS KATNVDEFWK EMKQAAKILF
ETRPTAVSLP NALRYVMHRG KIAYSSGADL EQLRFVIINA AKEFIHNSEK ALERIGEFGA
KRIEDGDVIM THCHSKAAIS VMKTAWEQGK DIKVIVTETR PKWQGKITAK ELASYGIPVI
YVVDSAARHY MKMTDKVVMG ADSITVNGAV INKIGTALIA LTAKEHRVWT MIAAETYKFH
PETMLGQLVE IEMRDPTEVI PEDELKTWPK NIEVWNPAFD VTPPEYVDVI ITERGIIPPY
AAIDILREEF GWALKYTEPW ED
