IOLO_THEMA
ID IOLO_THEMA Reviewed; 270 AA.
AC Q9WYP7;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=5-keto-L-gluconate epimerase {ECO:0000303|PubMed:23441918};
DE EC=5.1.3.- {ECO:0000269|PubMed:23441918};
DE AltName: Full=Bifunctional nonphosphorylated sugar isomerase {ECO:0000303|PubMed:28258150};
DE AltName: Full=D-erythrose/D-threose isomerase {ECO:0000303|PubMed:28258150};
DE AltName: Full=L-ribulose 3-epimerase {ECO:0000303|PubMed:28258150};
DE Short=R3E {ECO:0000303|PubMed:28258150};
DE AltName: Full=Nonphosphorylated sugar 3-epimerase {ECO:0000305|PubMed:28258150};
DE EC=5.1.3.- {ECO:0000269|PubMed:28258150};
DE AltName: Full=Nonphosphorylated sugar aldose-ketose isomerase {ECO:0000305|PubMed:28258150};
DE EC=5.3.1.- {ECO:0000269|PubMed:28258150};
GN Name=iolO {ECO:0000303|PubMed:23441918}; OrderedLocusNames=TM_0416;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RX PubMed=23441918; DOI=10.1111/1462-2920.12096;
RA Rodionova I.A., Leyn S.A., Burkart M.D., Boucher N., Noll K.M.,
RA Osterman A.L., Rodionov D.A.;
RT "Novel inositol catabolic pathway in Thermotoga maritima.";
RL Environ. Microbiol. 15:2254-2266(2013).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS).
RX PubMed=19255464; DOI=10.1107/s1744309109002115;
RA Sakuraba H., Yoneda K., Satomura T., Kawakami R., Ohshima T.;
RT "Structure of a D-tagatose 3-epimerase-related protein from the
RT hyperthermophilic bacterium Thermotoga maritima.";
RL Acta Crystallogr. F 65:199-203(2009).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.32 ANGSTROMS) IN COMPLEXES WITH COBALT IONS;
RP NICKEL IONS; COPPER IONS; MANGANESE IONS AND L-ERYTHRULOSE, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY,
RP COFACTOR, ACTIVITY REGULATION, SUBUNIT, BIOTECHNOLOGY, ACTIVE SITE, AND
RP REACTION MECHANISM.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=28258150; DOI=10.1128/aem.03291-16;
RA Shin S.M., Cao T.P., Choi J.M., Kim S.B., Lee S.J., Lee S.H., Lee D.W.;
RT "TM0416 is a hyperthermophilic promiscuous non-phosphorylated sugar
RT isomerase that catalyzes various C5 and C6 epimerization reactions.";
RL Appl. Environ. Microbiol. 0:0-0(2017).
CC -!- FUNCTION: Catalyzes the reversible epimerization between 5-keto-L-
CC gluconate (5-dehydro-L-gluconate) and D-tagaturonate, and thus probably
CC functions in a myo-inositol degradation pathway together with IolG,
CC IolM and IolN (PubMed:23441918). Is not active on the enantiomer 5-
CC keto-D-gluconate (PubMed:23441918). Was also shown to be a
CC nonphosphorylated sugar isomerase with broad substrate specificity in
CC vitro (PubMed:28258150). Is able to catalyze the reversible C3-
CC epimerization of L-ribulose to L-xylulose, D-ribulose to D-xylulose, D-
CC psicose to D-fructose, and D-tagatose to D-sorbose, with a substrate
CC preference for ketopentoses rather than ketohexoses (PubMed:28258150).
CC Also catalyzes the aldose-ketose isomerization reaction from either D-
CC erythrose or D-threose to D-erythrulose (PubMed:28258150). Exhibits no
CC activity for C4-epimerization of D-tagatose to D-fructose
CC (PubMed:28258150). {ECO:0000269|PubMed:23441918,
CC ECO:0000269|PubMed:28258150}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-dehydro-L-gluconate = keto-D-tagaturonate;
CC Xref=Rhea:RHEA:53272, ChEBI:CHEBI:17886, ChEBI:CHEBI:137108;
CC Evidence={ECO:0000269|PubMed:23441918};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-ribulose = L-xylulose; Xref=Rhea:RHEA:53268,
CC ChEBI:CHEBI:16880, ChEBI:CHEBI:17399;
CC Evidence={ECO:0000269|PubMed:28258150};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribulose = D-xylulose; Xref=Rhea:RHEA:51544,
CC ChEBI:CHEBI:17140, ChEBI:CHEBI:17173;
CC Evidence={ECO:0000269|PubMed:28258150};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=keto-D-tagatose = keto-D-sorbose; Xref=Rhea:RHEA:43048,
CC ChEBI:CHEBI:13022, ChEBI:CHEBI:47693;
CC Evidence={ECO:0000269|PubMed:28258150};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-allulose = keto-D-fructose; Xref=Rhea:RHEA:42360,
CC ChEBI:CHEBI:27605, ChEBI:CHEBI:48095;
CC Evidence={ECO:0000269|PubMed:28258150};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-erythrose = D-erythrulose; Xref=Rhea:RHEA:53180,
CC ChEBI:CHEBI:16023, ChEBI:CHEBI:27904;
CC Evidence={ECO:0000269|PubMed:28258150};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-threose = D-erythrulose; Xref=Rhea:RHEA:53280,
CC ChEBI:CHEBI:16023, ChEBI:CHEBI:28587;
CC Evidence={ECO:0000269|PubMed:28258150};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:28258150};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:28258150};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:28258150};
CC Note=Binds 1 divalent metal cation per subunit. Mn(2+) is the most
CC efficient metal cofactor, but can also use other divalent metal cations
CC such as Ni(2+), Mg(2+), and, to a lesser extent, Co(2+) and Zn(2+), but
CC not Ca(2+), Cu(2+), and Fe(2+). {ECO:0000269|PubMed:28258150};
CC -!- ACTIVITY REGULATION: Is completely inhibited by EDTA in vitro.
CC {ECO:0000269|PubMed:28258150}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=452 mM for D-erythrose (at pH 7 and 70 degrees Celsius)
CC {ECO:0000269|PubMed:28258150};
CC KM=232 mM for D-threose (at pH 7 and 70 degrees Celsius)
CC {ECO:0000269|PubMed:28258150};
CC KM=78 mM for D-erythrulose (at pH 7 and 70 degrees Celsius)
CC {ECO:0000269|PubMed:28258150};
CC KM=46 mM for L-ribulose (at pH 7 and 70 degrees Celsius)
CC {ECO:0000269|PubMed:28258150};
CC KM=348 mM for D-ribulose (at pH 7 and 70 degrees Celsius)
CC {ECO:0000269|PubMed:28258150};
CC KM=459 mM for L-xylulose (at pH 7 and 70 degrees Celsius)
CC {ECO:0000269|PubMed:28258150};
CC KM=2332 mM for D-xylulose (at pH 7 and 70 degrees Celsius)
CC {ECO:0000269|PubMed:28258150};
CC Vmax=1.23 umol/min/mg enzyme with D-erythrose as substrate (at pH 7
CC and 70 degrees Celsius) {ECO:0000269|PubMed:28258150};
CC Vmax=0.64 umol/min/mg enzyme with D-threose as substrate (at pH 7 and
CC 70 degrees Celsius) {ECO:0000269|PubMed:28258150};
CC Vmax=0.08 umol/min/mg enzyme with D-erythrulose as substrate (at pH 7
CC and 70 degrees Celsius) {ECO:0000269|PubMed:28258150};
CC Vmax=0.23 umol/min/mg enzyme with L-ribulose as substrate (at pH 7
CC and 70 degrees Celsius) {ECO:0000269|PubMed:28258150};
CC Vmax=0.62 umol/min/mg enzyme with D-ribulose as substrate (at pH 7
CC and 70 degrees Celsius) {ECO:0000269|PubMed:28258150};
CC Vmax=1.4 umol/min/mg enzyme with L-xylulose as substrate (at pH 7 and
CC 70 degrees Celsius) {ECO:0000269|PubMed:28258150};
CC Vmax=0.26 umol/min/mg enzyme with D-xylulose as substrate (at pH 7
CC and 70 degrees Celsius) {ECO:0000269|PubMed:28258150};
CC pH dependence:
CC Optimum pH is 6.5-7.0 with L-ribulose as substrate.
CC {ECO:0000269|PubMed:28258150};
CC Temperature dependence:
CC Optimum temperature is about 80 degrees Celsius with L-ribulose as
CC substrate. Is hyperthermostable, with an apparent melting temperature
CC (Tm) of 102.4 degrees Celsius. {ECO:0000269|PubMed:28258150};
CC -!- PATHWAY: Polyol metabolism; myo-inositol metabolism.
CC {ECO:0000305|PubMed:23441918}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:28258150}.
CC -!- BIOTECHNOLOGY: High thermostability and very broad substrate
CC specificity of this enzyme make it a potential candidate for the
CC production of rare sugars for the food and pharmaceutical industries.
CC {ECO:0000305|PubMed:28258150}.
CC -!- SIMILARITY: Belongs to the hyi family. {ECO:0000305}.
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DR EMBL; AE000512; AAD35501.1; -; Genomic_DNA.
DR PIR; F72381; F72381.
DR RefSeq; NP_228226.1; NC_000853.1.
DR RefSeq; WP_004083268.1; NZ_CP011107.1.
DR PDB; 2ZVR; X-ray; 2.20 A; A/B=1-270.
DR PDB; 5B7Y; X-ray; 1.32 A; A/B=1-270.
DR PDB; 5B7Z; X-ray; 1.50 A; A/B=1-270.
DR PDB; 5B80; X-ray; 1.70 A; A/B=1-270.
DR PDB; 5H1W; X-ray; 1.63 A; A/B=1-270.
DR PDB; 5H6H; X-ray; 1.45 A; A/B=1-270.
DR PDBsum; 2ZVR; -.
DR PDBsum; 5B7Y; -.
DR PDBsum; 5B7Z; -.
DR PDBsum; 5B80; -.
DR PDBsum; 5H1W; -.
DR PDBsum; 5H6H; -.
DR AlphaFoldDB; Q9WYP7; -.
DR SMR; Q9WYP7; -.
DR STRING; 243274.THEMA_02645; -.
DR EnsemblBacteria; AAD35501; AAD35501; TM_0416.
DR KEGG; tma:TM0416; -.
DR eggNOG; COG1082; Bacteria.
DR InParanoid; Q9WYP7; -.
DR OMA; AMFDTHH; -.
DR OrthoDB; 1007505at2; -.
DR BioCyc; MetaCyc:MON-17951; -.
DR UniPathway; UPA00914; -.
DR EvolutionaryTrace; Q9WYP7; -.
DR Proteomes; UP000008183; Chromosome.
DR GO; GO:0016853; F:isomerase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006020; P:inositol metabolic process; IEA:UniProtKB-UniPathway.
DR InterPro; IPR036237; Xyl_isomerase-like_sf.
DR InterPro; IPR013022; Xyl_isomerase-like_TIM-brl.
DR Pfam; PF01261; AP_endonuc_2; 1.
DR SUPFAM; SSF51658; SSF51658; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Isomerase; Manganese; Metal-binding;
KW Reference proteome.
FT CHAIN 1..270
FT /note="5-keto-L-gluconate epimerase"
FT /id="PRO_0000209114"
FT ACT_SITE 149
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:28258150"
FT ACT_SITE 243
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:28258150"
FT BINDING 149
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:28258150,
FT ECO:0007744|PDB:5H1W"
FT BINDING 155
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28258150,
FT ECO:0007744|PDB:5H1W"
FT BINDING 182
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:28258150,
FT ECO:0007744|PDB:5H1W"
FT BINDING 185
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28258150,
FT ECO:0007744|PDB:5H1W"
FT BINDING 208
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:28258150,
FT ECO:0007744|PDB:5H1W"
FT BINDING 214
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28258150,
FT ECO:0007744|PDB:5H1W"
FT BINDING 243
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:28258150,
FT ECO:0007744|PDB:5H1W"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:5B7Y"
FT STRAND 12..14
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 16..33
FT /evidence="ECO:0007829|PDB:5B7Y"
FT STRAND 36..41
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 50..60
FT /evidence="ECO:0007829|PDB:5B7Y"
FT STRAND 64..68
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 71..74
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 85..105
FT /evidence="ECO:0007829|PDB:5B7Y"
FT STRAND 108..112
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 123..140
FT /evidence="ECO:0007829|PDB:5B7Y"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:5B7Y"
FT TURN 153..155
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 162..172
FT /evidence="ECO:0007829|PDB:5B7Y"
FT STRAND 177..182
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 183..189
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 193..200
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 201..203
FT /evidence="ECO:0007829|PDB:5B7Y"
FT STRAND 204..209
FT /evidence="ECO:0007829|PDB:5B7Y"
FT STRAND 214..216
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 224..233
FT /evidence="ECO:0007829|PDB:5B7Y"
FT STRAND 238..242
FT /evidence="ECO:0007829|PDB:5B7Y"
FT TURN 247..249
FT /evidence="ECO:0007829|PDB:5B7Y"
FT HELIX 251..267
FT /evidence="ECO:0007829|PDB:5B7Y"
SQ SEQUENCE 270 AA; 30464 MW; 10948413A7624158 CRC64;
MKLSLVISTS DAAFDALAFK GDLRKGMELA KRVGYQAVEI AVRDPSIVDW NEVKILSEEL
NLPICAIGTG QAYLADGLSL THPNDEIRKK AIERVVKHTE VAGMFGALVI IGLVRGRREG
RSYEETEELF IESMKRLLEL TEHAKFVIEP LNRYETDFIN TIDDALRILR KINSNRVGIL
ADTFHMNIEE VNIPESLKRA GEKLYHFHVA DSNRWAPGCG HFDFRSVFNT LKEIGYNRYV
SVECLPLPGG MEEAAEIAFK TLKELIIKLT
