Information on EC 5.3.1.6 - ribose-5-phosphate isomerase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea

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EC NUMBER
COMMENTARY hide
5.3.1.6
-
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RECOMMENDED NAME
GeneOntology No.
ribose-5-phosphate isomerase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-Ribose 5-phosphate = D-ribulose 5-phosphate
show the reaction diagram
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
intramolecular oxidoreduction
-
-
-
-
isomerization
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Bifidobacterium shunt
-
-
Calvin-Benson-Bassham cycle
-
-
formaldehyde assimilation II (assimilatory RuMP Cycle)
-
-
formaldehyde assimilation III (dihydroxyacetone cycle)
-
-
pentose phosphate pathway (non-oxidative branch)
-
-
Rubisco shunt
-
-
pentose phosphate pathway
-
-
photosynthesis
-
-
Pentose phosphate pathway
-
-
Fructose and mannose metabolism
-
-
Carbon fixation in photosynthetic organisms
-
-
Metabolic pathways
-
-
Biosynthesis of secondary metabolites
-
-
Microbial metabolism in diverse environments
-
-
Biosynthesis of antibiotics
-
-
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SYSTEMATIC NAME
IUBMB Comments
D-ribose-5-phosphate aldose-ketose-isomerase
Also acts on D-ribose 5-diphosphate and D-ribose 5-triphosphate.
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CAS REGISTRY NUMBER
COMMENTARY hide
9023-83-0
-
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene RPI2, At2g01290
UniProt
Manually annotated by BRENDA team
Chromatium sp.
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain DSM 2661
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
HB8
-
-
Manually annotated by BRENDA team
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
HB8
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
gene rpiA
UniProt
Manually annotated by BRENDA team
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
deficiency in a cytosolic ribose-5-phosphate isomerase causes chloroplast dysfunction, late flowering and premature cell death in Arabidopsis thaliana
metabolism
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-Allose
D-Psicose
show the reaction diagram
D-allose 6-phosphate
D-allulose 6-phosphate
show the reaction diagram
D-Glucose 6-phosphate
?
show the reaction diagram
-
-
-
-
?
D-gulose
D-sorbose
show the reaction diagram
D-psicose
D-allose
show the reaction diagram
D-Ribose
D-Ribulose
show the reaction diagram
D-ribose 5-diphosphate
D-ribulose 5-diphosphate
show the reaction diagram
D-ribose 5-phosphate
D-ribulose 5-phosphate
show the reaction diagram
D-ribose 5-triphosphate
D-ribulose 5-triphosphate
show the reaction diagram
-
-
?
D-ribose-5-phosphate
D-ribulose-5-phosphate
show the reaction diagram
D-ribulose
D-ribose
show the reaction diagram
D-ribulose 5-diphosphate
D-ribose 5-diphosphate
show the reaction diagram
D-ribulose 5-phosphate
D-ribose 5-phosphate
show the reaction diagram
D-sorbose
D-gulose
show the reaction diagram
D-talose
D-tagatose
show the reaction diagram
L-allose
L-psicose
show the reaction diagram
L-fructose
L-mannose
show the reaction diagram
L-Lyxose
L-Xylulose
show the reaction diagram
L-Mannose
L-Fructose
show the reaction diagram
-
-
-
-
r
L-ribose
L-ribulose
show the reaction diagram
L-tagatose
L-talose
show the reaction diagram
L-talose
L-tagatose
show the reaction diagram
L-xylulose
L-lyxose
show the reaction diagram
additional information
?
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
D-Allose
D-Psicose
show the reaction diagram
-
-
-
-
r
D-Ribose
D-Ribulose
show the reaction diagram
-
-
-
-
r
D-ribose 5-phosphate
D-ribulose 5-phosphate
show the reaction diagram
D-ribose-5-phosphate
D-ribulose-5-phosphate
show the reaction diagram
Q9ZU38
the cytosolic ribose-5-phosphate isomerase catalyzes the reversible interconversion of ribulose-5-phosphate and ribose-5-phosphate in the non-oxidative phase of the oxidative pentose phosphate pathway
-
-
-
D-talose
D-tagatose
show the reaction diagram
-
-
-
-
r
L-allose
L-psicose
show the reaction diagram
-
-
-
-
r
L-ribose
L-ribulose
show the reaction diagram
-
-
-
-
r
L-talose
L-tagatose
show the reaction diagram
-
preferred substrate
-
-
r
additional information
?
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
activates
Mg2+
-
activates
additional information
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-phosphoglycerate
-
-
4-deoxy-4-phosphonomethyl-D-erythronate
-
stable and potent competitive inhibitor
4-phospho-D-erythronamide
-
competitive
4-phospho-D-erythronate
4-phospho-D-erythronhydrazide
-
4-phospho-D-erythronohydrazide
-
competitive
4-phospho-D-erythronohydroxamic acid
competitive
4-phosphoerythronate
-
strong competitive
4-phosphono-D-erythronate
-
-
4-phosphono-D-erythronohydroxamate
-
-
4-phosphono-D-erythronohydroxamic acid
-
competitive
5'-AMP
5-deoxy-5-phospho-D-ribonohydroxamate
-
-
5-deoxy-5-phospho-D-ribonohydroxamic acid
5-phospho-D-ribonamide
5-phospho-D-ribonate
5-phospho-D-ribonohydroxamic acid
6-phosphogluconate
arabinose 5-phosphate
citrate
-
10 mM
D-5-Phosphoribonic acid
-
-
D-Allose 6-phosphate
D-allulose 6-phosphate
-
-
D-arabinose 5-phosphate
erythrose 4-phosphate
-
competitive
fructose 6-phosphate
-
-
glyceraldehyde 3-phosphate
-
competitive
iodoacetamide
iodoacetate
iodoacetic acid
suicide inhibitor
Mn2+
-
slight inhibition of enzyme form I and II, strong inhibition of enzyme form III
N-(5-phospho-D-ribonoyl)-gamma-aminobutanoate
N-(5-phospho-D-ribonoyl)-glycine
N-(5-phospho-D-ribonoyl)-hydrazine
N-(5-phospho-D-ribonoyl)-methylamine
Organic mercurials
-
Phenylmercuriacetate
phosphate
ribulose diphosphate
-
1.0 mM, strong
sedoheptulose bisphosphate
-
competitive
Sodium mersalyl
Sodium salt of 2-(ethylmercurimercapto)-benzoxazole-5-carboxylic acid
sulfhydryl reagents
Xylulose 5-phosphate
-
-
additional information
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanol
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
106 - 460
D-Allose
43 - 78
D-psicose
44 - 270
D-ribose
2 - 10
D-Ribose 5-diphosphate
0.017 - 30
D-ribose 5-phosphate
0.52 - 4.41
D-ribose-5-phosphate
34
D-ribulose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
1.4 - 2.5
D-ribulose 5-diphosphate
0.015 - 15
D-ribulose 5-phosphate
232
D-talose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
98
L-allose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
173
L-ribose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
319
L-ribulose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
125
L-tagatose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
5 - 37
L-talose
additional information
additional information
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
200 - 2682
D-Allose
0.116 - 2743
D-psicose
160 - 11880
D-ribose
1 - 97
D-Ribose 5-diphosphate
8.3 - 52000
D-ribose 5-phosphate
0.0421 - 3440
D-ribose-5-phosphate
9193
D-ribulose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
4.7 - 10.7
D-ribulose 5-diphosphate
2 - 39530
D-ribulose 5-phosphate
119
D-talose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
1506
L-allose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
322
L-ribose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
17
L-ribulose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
1822
L-tagatose
-
in 50 mM Tris-HCl buffer (pH 7.5), at 65°C
140 - 13420
L-talose
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.4
D-Allose
-
pH 7.5, 40°C
0.0018 - 64
D-psicose
0.6
D-ribose
-
pH 7.5, 40°C
500 - 3029
D-ribose 5-phosphate
2589
D-ribulose 5-phosphate
-
pH 7.5, 65°C, recombinant enzyme
0.3
L-talose
-
pH 7.5, 40°C
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.074
4-deoxy-4-phosphonomethyl-D-erythronate
-
25°C
2.5
4-phospho-D-erythronamide
-
25°C, pH 7.5
1.7
4-phospho-D-erythronate
-
-
1.8
4-phospho-D-erythronohydrazide
-
25°C, pH 7.5
1.2
4-phospho-D-erythronohydroxamic acid
pH 8.4, 25°C
0.028
4-phosphono-D-erythronate
-
25°C, pH 7.5
0.057
4-phosphono-D-erythronohydroxamate
-
-
0.029
4-phosphono-D-erythronohydroxamic acid
-
25°C, pH 7.5
0.4 - 6.2
5-deoxy-5-phospho-D-ribonohydroxamic acid
0.04 - 0.07
5-phospho-D-ribonamide
0.009
5-phospho-D-ribonate
pH 7.5, 37°C, RpiB, substrate is D-ribose 5-phosphate
0.09 - 0.43
5-phospho-D-ribonohydroxamic acid
0.7
arabinose 5-phosphate
-
pH 8.0, 25°C
15
D-Allose 6-phosphate
in 50 mM Tris-HCl (pH 7.6), 150 mM NaCl and 5 mM MESNA, at 30°C
0.89
D-arabinose 5-phosphate
-
50°C, pH 7.5
0.34
N-(5-phospho-D-ribonoyl)-glycine
pH 7.5, 37°C, RpiB, substrate is D-ribose 5-phosphate
1.9
N-(5-phospho-D-ribonoyl)-hydrazine
-
pH 7.5, 37°C, RpiB, substrate is D-allose 5-phosphate
0.11 - 0.18
N-(5-phospho-D-ribonoyl)-methylamine
7.9 - 130
phosphate
4
Xylulose 5-phosphate
-
pH 8.0, 25°C
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5
4-phospho-D-erythronate
Trypanosoma cruzi
Q4CQE2
pH 8.4, 25°C
0.7
4-phospho-D-erythronohydroxamic acid
Trypanosoma cruzi
Q4CQE2
pH 8.4, 25°C
0.2 - 1.33
5-phospho-D-ribonamide
0.031 - 1.31
5-phospho-D-ribonate
0.17 - 0.62
5-phospho-D-ribonohydroxamic acid
2
D-Allose 6-phosphate
Mycobacterium tuberculosis
-
in 50 mM Tris-HCl, pH 7.5, at 37°C
6.3
D-allulose 6-phosphate
Mycobacterium tuberculosis
-
in 50 mM Tris-HCl, pH 7.5, at 37°C
1.42 - 2
N-(5-phospho-D-ribonoyl)-gamma-aminobutanoate
0.57 - 9
N-(5-phospho-D-ribonoyl)-glycine
1
N-(5-phospho-D-ribonoyl)-hydrazine
Mycobacterium tuberculosis
P9WKD7
pH 7.5, 37°C, RpiB, substrate is D-ribose 5-phosphate
0.19 - 0.36
N-(5-phospho-D-ribonoyl)-methylamine
additional information
additional information
Trypanosoma cruzi
Q4CQE2
IC50 values of 5-phospho-D-ribonohydroxamic acid and 4-phospho-D-erythronhydrazide are above 10 mM
-
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0005
-
using D-sorbose as substrate, at 35°C and pH 7.5
0.0011
-
using L-fructose as substrate, at 35°C and pH 7.5
0.0013
-
using L-tagatose as substrate, at 35°C and pH 7.5
0.0019
-
using D-allose as substrate, at 35°C and pH 7.5
0.0021
-
using D-psicose as substrate, at 35°C and pH 7.5
0.0025
-
using D-ribose as substrate, at 35°C and pH 7.5
0.0053
-
using D-gulose as substrate, at 35°C and pH 7.5
0.0096
-
using L-lyxose as substrate, at 35°C and pH 7.5
0.019
-
using L-talose as substrate, at 35°C and pH 7.5
0.027
-
using L-lyxose as substrate, at 35°C and pH 7.5
0.048
-
using D-ribulose as substrate, at 35°C and pH 7.5
0.058
-
using D-glucose 6-phosphate as substrate, at 35°C and pH 7.5
0.121
-
using L-xylulose as substrate, at 35°C and pH 7.5
0.2
-
after 9.1fold purification, at pH 8.0 and 75°C
0.21
-
purified enzyme, using D-tagatose as substrate, at 65°C and pH 7.5
0.259
-
mutant enzyme H98A, using D-psicose as substrate, pH 7.5, 80°C
0.299
-
mutant enzyme H133A, using D-psicose as substrate, pH 7.5, 80°C; mutant enzyme R136A, using D-psicose as substrate, pH 7.5, 80°C
0.388
-
using D-ribose 5-phosphate as substrate, at 35°C and pH 7.5
0.53
-
purified enzyme, using L-allose as substrate, at 65°C and pH 7.5
0.698
-
mutant enzyme N99A, using D-psicose as substrate, pH 7.5, 80°C
0.917
-
mutant enzyme T67A, using D-psicose as substrate, pH 7.5, 80°C
1
-
substrate D-sorbose, pH 7.5, 40°C
1.256
-
mutant enzyme H9A, using D-psicose as substrate, pH 7.5, 80°C
1.815
-
mutant enzyme T135A, using D-psicose as substrate, pH 7.5, 80°C
1.994
-
wild type enzyme, using D-psicose as substrate, pH 7.5, 80°C
2.313
-
mutant enzyme R132A, using D-psicose as substrate, pH 7.5, 80°C
3
-
substrate D-psicose, pH 7.5, 40°C
7
-
substrate L-lyxose, pH 7.5, 40°C
9
-
substrate L-fructose, pH 7.5, 40°C
12
-
purified enzyme, using L-psicose as substrate, at 65°C and pH 7.5
14
-
substrate D-ribulose, pH 7.5, 40°C
15
-
substrate D-allose, pH 7.5, 40°C
28
-
substrate L-talose, pH 7.5, 40°C
45
-
substrate L-talose, pH 7.5, 40°C
50
-
purified enzyme, using D-talose as substrate, at 65°C and pH 7.5
53
-
substrate D-ribose, pH 7.5, 40°C
57
-
substrate L-xylulose, pH 7.5, 40°C
120
-
substrate D-gulose, pH 7.5, 40°C
187
-
cell lysate, at 50°C and pH 7.0
272
-
purified enzyme, using L-ribose as substrate, at 65°C and pH 7.5
290
-
after purification, at 50°C and pH 7.0
600
-
purified enzyme, using L-allose as substrate, at 65°C and pH 7.5
720
-
purified enzyme, using L-ribulose as substrate, at 65°C and pH 7.5
1037
-
purified enzyme, using D-psicose as substrate, at 65°C and pH 7.5; purified recombinant enzyme, substrate D-psicose
1352
-
purified enzyme, using D-allose as substrate, at 65°C and pH 7.5; purified recombinant enzyme, substrate D-allose
1700
-
-
5374
-
purified enzyme, using D-ribulose as substrate, at 65°C and pH 7.5; purified recombinant enzyme, substrate D-ribulose
5800
-
purified enzyme, using D-ribose as substrate, at 65°C and pH 7.5; purified recombinant enzyme, substrate D-ribose
7363
-
purified enzyme, using L-talose as substrate, at 65°C and pH 7.5; purified recombinant enzyme, substrate L-talose
19680
-
purified enzyme, using D-ribulose 5-phosphate as substrate, at 65°C and pH 7.5; purified recombinant enzyme, substrate D-ribulose 5-phosphate
25690
-
purified enzyme, using D-ribose 5-phosphate as substrate, at 65°C and pH 7.5; purified recombinant enzyme, substrate D-ribose 5-phosphate
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 9
-
-
7.7 - 7.8
-
D-ribulose 5-phosphate, D-ribose 5-phosphate
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 9.9
-
pH 6: about 40% of maximal activity, pH 9.9: about 65% of maximal activity
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 80
-
30°C: about 50% of maximal activity, 80°C: about 45% of maximal activity
40 - 99
-
enzyme activity increases significantly when the temperature increases until 80°C. The optimum temperature is 80°C. The activity at 30°C is 25% of that at 80°C. The enzyme activity decreases after 80°C. It is still highly active when the temperature reaches 99°C, 90% activity of that of 80°C. This enzyme shows relatively high activity (above 50% of its maximum activity) over a large temperature range of 40-99°C
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.77
isoelectric focusing
5.1
-
isoelectric focusing
6.4
-
isoelectric focusing
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
one electrophorectic form
Manually annotated by BRENDA team
-
two electrophorectic forms
Manually annotated by BRENDA team
-
two electrophorectic forms
Manually annotated by BRENDA team
-
one electrophorectic form
Manually annotated by BRENDA team
-
one electrophorectic form
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
-
two electrophorectic forms
Manually annotated by BRENDA team
-
two electrophorectic forms
Manually annotated by BRENDA team
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Anaplasma phagocytophilum (strain HZ)
Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1)
Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)
Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Francisella tularensis subsp. tularensis (strain WY96-3418)
Giardia intestinalis (strain ATCC 50803 / WB clone C6)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Lactobacillus salivarius (strain UCC118)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Neisseria gonorrhoeae (strain NCCP11945)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Toxoplasma gondii (strain ATCC 50611 / Me49)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Trypanosoma cruzi (strain CL Brener)
Vibrio vulnificus (strain YJ016)
Vibrio vulnificus (strain YJ016)
Vibrio vulnificus (strain YJ016)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
15867
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x * 15867, calculated from amino acid sequence
16000
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x * 16000, SDS-PAGE
16015
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2 * 16015, calculated from amino acid sequence
16800
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2 * 16800, SDS-PAGE
17200
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2 * 17217, calculated, 2 * 17200, SD-PAGE
17217
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2 * 17217, calculated, 2 * 17200, SD-PAGE
17300
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2 * 17300, calculation from nucleotide sequence
17400
2 * 17400, calculated, 2 * 18000, SDS-PAGE
18000
2 * 17400, calculated, 2 * 18000, SDS-PAGE
23400
x * 23400, isoform RpiB, calculated from amino acid sequence
23724
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4 * 23724, calculated from amino acid sequence
24000
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4 * 24000, SDS-PAGE
24570
x * 24570, isoform RpiA, calculated from amino acid sequence
25000
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2 * 25000, SDS-PAGE
25066
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2 * 25066, calculation from nucleotide sequence
25163
4 * 25163, calculation from nucleotide sequence
25300
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x * 25300, SDS-PAGE
26400
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x * 26400, SDS-PAGE
30000 - 35000
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gel filtration
32000 - 34000
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ribosephosphate isomerase B, gel filtration
32000
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dynamic light scattering
35000
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about, native PAGE, recombinant enzyme
35200
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gel filtration
39600
gel filtration
49000
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gel filtration
50000
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dynamic light scattering
53000
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high-speed equilibrium centrifugation
58000
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4 * 58000, SDS-PAGE
75000
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1 * 75000, alpha, + 2 * 54000, beta, SDS-PAGE
96000
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gel filtration
98000
gel filtration
105000
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gel filtration
183000
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gel filtration
228000
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analytical ultracentrifugation
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
homotetramer
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4 * 23724, calculated from amino acid sequence; 4 * 24000, SDS-PAGE
tetramer
trimer
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1 * 75000, alpha, + 2 * 54000, beta, SDS-PAGE
additional information
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homology modeling of RpiB, substrate binding structure, overview
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
molecular dockng using L-xylose and D-ribose as the substrate. Residue M95 seems to be a determinant residue for the specificity on free sugars
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co-crystallization in the presence of 20 mM ribose-5-phosphate or 20 mM ribose-5-phosphate with 12 mM MnCl2, sitting drop vapor diffusion method, using 0.1 M Na citrate pH 5.0, 20% (w/v) PEG 6000
hanging drop vapor diffusion method, enzyme form RpiA
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hanging drop vapor diffusion method, structure of a complex with arabinose 5-phosphate at 1.25 A resolution
purified recombinant MJ1603, microbatch-under-oil method, 0.0005 ml of 8.1 mg/ml protein in 20 mM Tris-HCl buffer, pH 8.0, containing 200 mM NaCl are mixed with 0.0005 ml of crystallization reagent, consisting of 0.1 M acetate, pH 4.5 containing 40% v/v 1,2-propanediol and 0.05 M calcium acetate, 18°C. The mixture is covered with 0.015 ml silicone and paraffin oil, X-ray diffraction structure determination and analysis at 1.78 A resolution, molecular replacement and modeling
hanging drop vapour diffusion method, X-ray structure of ribose-5-phosphate isomerase B in complex with the inhibitors 4-phosphono-D-erythronohydroxamate and 4-phospho-D-erythronate refined to resolutions of 2.1 and 2.2 A
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in complex with 5-deoxy-5-phospho-D-ribonohydroxamate, hanging drop vapour diffusion method, with 15% PEG 8000, 0.1 M MES buffer, pH 6, 5% PEG 1000, and 0.2 M Li2SO4, or in complex with D-ribose 5-phosphate, sitting drop vapour diffusion method, with 20% PEG 3K, 0.1 M Tris, pH 7, and 0.2 M Ca acetate
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sitting drop vapour diffusion method
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molecular replacement at 2.9 A resolution
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hanging drop vapor diffusion method, crystal structure of the free enzyme and the complex with D-4-phosphoerythronic acid
in complex with ribose 5-phosphate, ribose or allose, sitting drop vapor diffusion method, using 0.05 M Tris pH 7.0, 10% (w/v) PEG 8000, 0.15 M magnesium chloride, and 0.2 M potassium chloride
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purified recombinant RpiB, sitting drop vapour diffusion method, 0.001 ml of 7 mg/ml protein in mM Tris-HCl buffer pH 7.5 is mixed with 0.001 ml of reservoir solution, containing 0.05 M Tris, pH 7.0, 10% PEG 8000, 0.15 M MgCl2 and 0.2 M KCl, and equilibrated against 1 ml of reservoir solution, 3 weeks, flash-cooling in liquid nitrogen with a cryoprotectant solution containing 65 mM Tris pH 7.0, 13% PEG 8000, 195 mM MgCl2, 260 mM KCl and 20% glycerol, X-ray diffraction structure determination and analysis at 1.9 A resolution, modeling
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2.1 A resolution crystal structure. Crystals are cryo-protected by transfering through crystallization solution with progressively higher ethylene glycol concentration up to 30% v/v and then flash cooled in liquid nitrogen. The protein crystallizes in space group F432 with cell dimensions a = b = c = 209A, corresponding to one molecule per asymmetric unit and a solvent content of 47%
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sitting drop vapor diffusion method, using 20% (w/v) PEG 3350, 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 0.1 M NaCl, 2.0 M ammonium sulfate; sitting drop vapor diffusion method, using 20% (w/v) PEG 3350, 0.2 M ammonium acetate, 0.1 M Tris-HCl pH 8.5 and 25% (w/v) PEG 3350, 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.5
crystal structure of enzyme complexed with the open chain form of the ribose 5-phosphate and the open chain form of the C2 epimeric inhibitor arabinose 5-phosphate as well as the apo form at high resolution
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RpiB (wild type or C69A mutant enzyme), sitting drop vapor diffusion method, using 0.5% (v/v) Jeffamine ED-2001, 0.1 M HEPES, 1.1 M Na-malonate (pH 7.0) for the wild type enzyme in complex with phosphate, or 0.8 M Na?K phosphate (pH 8.2) for the mutant enzyme C69A in complex with phosphate, or 20% (w/v) poly(ethyleneglycol) 550 monomethyl ether, 0.1 M NaCl, 0.1 M bicine (pH 9.0) for the wild type enzyme in complex with D-ribose 5-phosphate, or 20% (w/v) poly(ethylene glycol) 6000, 0.2 M ammonium chloride, 0.1 M Tris-HCl (pH 8.0) for wild type enzyme in complex with 4-phospho-D-erythronohydroxamic acid, or 20% (w/v) poly(ethylene glycol) 3350, 0.2 M sodium acetate, 0.1 M bis-Tris propane (pH 8.5) for mutant enzyme C69A in complex with allose 6-phosphate
open form RpiA in complex with substrate ribose 5-phosphate, the closed form complexed with arabinose-5-phosphate, and the apo-RpiA, hanging drop vapor diffusion method, 0.002 ml of 30 mg/ml protein in 20 mM HEPES, pH 7.5, and 150 mM KCl are mixed with 0.002 ml of a reservoir solution containing 50 mM succinate, pH 4.1, 180 mM ammonium sulfate, and 8% PEG 4000, 3 days, 20°C, for complexed enzyme addition of 20 mM ligand, X-ray diffraction structure determination and analysis at 1.49-2.07 A resolution, molecular replacement
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 10
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35 - 50
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enzyme activity is stable for 48 h at 35°C, and shows half-lives of 15 h at 40°C, and 6 h at 50°C
55
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half-life 53 min
57
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1 h, 50% loss of activity
60
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ribosephosphate isomerase A: complex dependence on protein concentration, at 1.0 mg/ml protein and greater, all activity is lost. At 0.05-0.75 mg/ml protein, 20-30% of the original activity is left after 30 min; ribosephosphate isomerase B: half-life 2.2 min, independent of enzyme and protein concentration
60 - 75
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the half-lives of the wild type enzyme at 60°C, 65°C, 70°C, 75°C, and 80°C are 11, 7.0, 4.2, 1.5, and 0.6 h, respectively
60 - 80
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the purified enzyme at 0.1 mg/ml is very stable at 60 and 70°C but is deactivated at 80°C. The enzyme shows half lifetimes of 70.8, 53.1, 6.4, and 1.2 h at 60, 70, 80, and 90°C, respectively
75
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the half-life at 75°C is 3.3 h
91
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1 h, 50% loss of activity
100
stability and integrity up to, needs at least 250 mM NaCl to maintain its hyperthermostability
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
(NH4)2SO4, NaCl, KCl and LiCl increase thermal stability. LiBr, CaCl2, methanol, ethanol, and 1-propanol decrease thermal stability. Alcohols decrease the stability in the following order: methanol, ethanol, propanol
ethylene glycol has little effect on the mesophilic enzyme
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ethylene glycol increases stability
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freeze-labile
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freezing and thawing destroys activity
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maximum activities in sodium dihydrogen phosphate-ciitric acid buffer at pH 6.5-8.0 and in 50 mM Tris-HCl buffer pH 7.0-9.0. This enzyme retains about 65% activity from pH 8.8-11.0 in glycine-NaOH buffer
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 2 months, stable
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-20°C, stable for several months
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-20°C, stable for several weeks
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2°C, stable for several months
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4°C, stable for 2 weeks
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4°C, stable for 6-8 weeks
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4°C, stable for several months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
3 forms: I, I, III
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affinity chromatographic method
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heat precipitation
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HisTrap HP column chromatography
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HisTrap HP column chromatography; recombinant RpiB from Escherichia coli strain ER2566 by His affinity chromatography
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HiTrap Q anion exchange column chromatography and Sephacryl S-300 gel filtration
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Ni-affinity column chromatography
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Ni-NTA column chromatography and Superdex 75 gel filtration
Ni2+-chelating column chromatography and Superdex S75 gel filtration; Ni2+-chelating column chromatography and Superdex S75 gel filtration
ox muscle, calf spleen and liver, partial
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recombinant enzyme
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recombinant His-tagged RpiA from Escherichia coli strain BL21(DE3) by nickel affinity chromatography. The His-tag is cleaved off and removed, folowed by anion exchange chromatography and gel filtration
recombinant MJ1603 from Escherichia coli strain Rosetta (DE3) by anion exchange and hydroxyapatite chromatography, and gel filtration
recombinant RpiB from Escherichia coli strain ER2566 by His affinity chromatography
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Superdex 75 gel filtration
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 (DE3) R3 Rosetta cells
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli BL21(DE3) cells; expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli ER2566 cells
expressed in Escherichia coli ER2566 cells; gene rpiB, expression in Escherichia coli strain ER2566
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expressed in Escherichia coli Top10 cells
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expression in Escherichia coli
expression of MJ1603 in Escherichia coli strain Rosetta (DE3)
gene RPI2, phylogenetic analysis
gene rpiA, expression of the His-tagged enzyme in Escherichia coli strain BL21(DE3)
gene rpiB, expression in Escherichia coli strain ER2566
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overexpression as a His-tagged Se-Met-labeled protein
overexpression in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C65A
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the mutant shows no activity for D-psicose
D8A
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the mutant shows no activity for D-psicose
H133A
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the mutant shows 15% activity compared to the wild type enzyme
H98A
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the mutant shows 13% activity compared to the wild type enzyme
H9A
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the mutant shows 63% activity compared to the wild type enzyme
N99A
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the mutant shows 35% activity compared to the wild type enzyme
R132A
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the mutant exhibits an increase in D-psicose isomerization activity (116% activity compared to the wild type enzyme)
R132D
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the mutant shows increased catalytic efficiency toward D-psicose compared to the wild type enzyme
R132E
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the mutant shows increased catalytic efficiency toward D-psicose compared to the wild type enzyme; the specific activity and catalytic efficiency (kcat/Km) of the R132E mutant for D-psicose are 1.4 and 1.5fold higher than those of the wild type enzyme, respectively
R132I
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the mutant shows decreased catalytic efficiency toward D-psicose compared to the wild type enzyme
R132K
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the mutant shows decreased catalytic efficiency toward D-psicose compared to the wild type enzyme
R132Q
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the mutant shows decreased catalytic efficiency toward D-psicose compared to the wild type enzyme
R136A
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the mutant shows 15% activity compared to the wild type enzyme
T135A
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the mutant shows 91% activity compared to the wild type enzyme
T67A
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the mutant shows 46% activity compared to the wild type enzyme
Y42A
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the mutant shows no activity for D-psicose
C65A
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the mutant shows no activity for D-psicose
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H9A
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the mutant shows 63% activity compared to the wild type enzyme
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N99A
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the mutant shows 35% activity compared to the wild type enzyme
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R136A
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the mutant shows 15% activity compared to the wild type enzyme
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T135A
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the mutant shows 91% activity compared to the wild type enzyme
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R189K
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6% of the wild-type activity. Loss of the structural integrity of the protein seems to be responsible for the greatly diminished activity
D87A
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turnover number with D-ribose-5-phosphate is 0.0012% of value for the the wild-type enzyme, moderate change in Km-value
D90A
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turnover number with D-ribose-5-phosphate is 0.38% of value for the the wild-type enzyme, moderate change in Km-value
E91A
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turnover number with D-ribose-5-phosphate is 27.5% of value for the the wild-type enzyme, moderate change in Km-value
K100A
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turnover number with D-ribose-5-phosphate is 0.074% of value for the the wild-type enzyme, moderate change in Km-value
H102A
kinetics severeyl impaired with substrate ribose 5-phosphate, but not affected with substrate ribulose 5-phosphate
H11A
6fold increase in Km value, 8fold increase in kcat value, decrease in stability to freezing and thawing
H138A
little variations in kinetics compared to wild-type
C69A
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inactive; no catalytic activity
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H102A
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kinetics severeyl impaired with substrate ribose 5-phosphate, but not affected with substrate ribulose 5-phosphate
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H11A
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6fold increase in Km value, 8fold increase in kcat value, decrease in stability to freezing and thawing
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H138A
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little variations in kinetics compared to wild-type
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additional information
construction of T-DNA knockout mutants of the RPI2 gene, which encodes the cytosolic ribose-5-phosphate isomerase. Knockout of the RPI2 gene does not significantly change the total RPI activity in the mutant plants, but knockout of RPI2 interferes with chloroplast structure and decreases chloroplast photosynthetic capacity. Rpi2 mutants accumulate less starch in the leaves and flower significantly later than wild-type when grown under short-day conditions, and rpi2 mutants display premature cell death in the leaves when grown at an above-normal temperature of 26°C, phenotypes, detailed overview
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
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