Information on EC 5.4.99.62 - D-ribose pyranase

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

EC NUMBER
COMMENTARY hide
5.4.99.62
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RECOMMENDED NAME
GeneOntology No.
D-ribose pyranase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
beta-D-ribopyranose = beta-D-ribofuranose
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
ribose degradation
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degradation of pentoses
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SYSTEMATIC NAME
IUBMB Comments
D-ribopyranose furanomutase
The enzyme also catalyses the conversion between beta-allopyranose and beta-allofuranose.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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UniProt
Manually annotated by BRENDA team
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SwissProt
Manually annotated by BRENDA team
bifunctional L-fucose mutarotase, EC 5.1.3.29, and L-rhamnose mutarotase
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
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the level of pyranase rbsD transcription increases markedly in a LacI-type transcription factor RbsR knockout mutant. In the presence of D-ribose, the level of rbsD mRNA in wild-type significantly increases but it does not show any change in the rbsR mutant
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
beta-allopyranose
beta-allofuranose
show the reaction diagram
beta-D-ribopyranose
beta-D-ribofuranose
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
beta-D-ribopyranose
beta-D-ribofuranose
show the reaction diagram
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Staphylococcus aureus (strain NCTC 8325)
Staphylococcus aureus (strain NCTC 8325)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
14000
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10 * 14000, SDS-PAGE, main form plus apparently larger oligomeric forms
150000
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PAGE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decamer
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10 * 14000, SDS-PAGE, main form plus apparently larger oligomeric forms
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
to 2.3 A resolution. Protein shows a decameric toroidal assembly. The intersubunit cleft of the protein binds specific forms of D-ribose, but it does not have an enzyme activity toward the sugar
to 1.9 A resolution. Protein forms a decameric toroid with each active site formed by two adjacent subunits. While one subunit provides most of the fucose-interacting residues including a catalytic tyrosine residue, the other subunit provides a catalytic His-Asp dyad. This active-site feature is critical both for the mutarotase activity toward L-fucose and for the pyranase activity toward D-ribose
to 1.9 A resolution. Protein assembles into four different oligomeric forms, among which the smallest homodimeric form is most abundant and would be the predominant species under physiological conditions. This homodimer has two fucose-binding sites that are devoid of the His-Asp dyad and catalytically inactive, indicating that the mutarotase and the pyranase activities appear dispensable in vertebrates
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the level of pyranase rbsD transcription increases markedly in a LacI-type transcription factor RbsR knockout mutant. In the presence of D-ribose, the level of rbsD mRNA in wild-type significantly increases but it does not show any change in the rbsR mutant
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D64N
mutant exhibits significantly reduced catalytic activity toward D-ribose
H106A
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the mutant enzyme retains one-third of the original pyranase activity, the mutant proteins are able to form an oligomer as is the case for the wild type, mutant binds to ribose as much as the wild type does,
H20A
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mutation completely abolishes the pyranase activity, the mutant proteins are able to form an oligomer as is the case for the wild type, mutant binds to ribose as much as the wild type does,
H22A
mutant exhibits significantly reduced catalytic activity toward D-ribose
Y111F
mutant exhibits significantly reduced catalytic activity toward D-ribose
H106A
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the mutant enzyme retains one-third of the original pyranase activity, the mutant proteins are able to form an oligomer as is the case for the wild type, mutant binds to ribose as much as the wild type does,
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H20A
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mutation completely abolishes the pyranase activity, the mutant proteins are able to form an oligomer as is the case for the wild type, mutant binds to ribose as much as the wild type does,
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Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
after being completely denatured in the presence of 8 M urea, isoform RbsD is able to refold and reassemble spontaneously. The oligomeric size of the protein appears to be fully recovered. Urea-induced disassembly occurs in a stepwise manner. The disassembly intermediates lose almost all their secondary structures. Reassembly of RbsD is a fast and apparently nonstepwise process
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