HAMAP rule MF_01987

General rule information [?]

Accession	MF_01987
Dates	29-FEB-2016 (Created) 7-NOV-2023 (Last updated, Version 11)
Name	Ribokinase
Scope(s)	Bacteria Archaea
Template(s)	P0A9J6 (RBSK_ECOLI); A0A0H2WZY4 (RBSK_STAAC); P0DX97 (DEOK_SALTI); [ Recover all ]
Triggered by	case c? <OC:Bacteria> or <OC:Archaea> HAMAP; MF_01987 (Get profile general information and statistics) end case

Propagated annotation [?]

Identifier, protein and gene names [?]

case <FTTag:deoxyribokinase>
Identifier	DEOK
Protein name	RecName: Full=Deoxyribokinase; Short=dRK; EC=2.7.1.229; AltName: Full=ATP:2-deoxy-D-ribose 5-phosphotransferase;
Gene name	Name=deoK;
else
Identifier	RBSK
Protein name	RecName: Full=Ribokinase; Short=RK; EC=2.7.1.15;
Gene name	Name=rbsK;
end case

Comments [?]

case <FTTag:deoxyribokinase>
FUNCTION	Catalyzes the ATP-dependent phosphorylation of 2-deoxy-D- ribose to 2-deoxy-D-ribose 5-phosphate (dRib-5P), allowing the use of deoxyribose as the sole carbon source.
CATALYTIC ACTIVITY	Reaction=2-deoxy-D-ribose + ATP = 2-deoxy-D-ribose 5-phosphate + ADP + H(+); Xref=Rhea:RHEA:30871, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:62877, ChEBI:CHEBI:90761, ChEBI:CHEBI:456216; EC=2.7.1.229;
COFACTOR	Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
SIMILARITY	Belongs to the carbohydrate kinase PfkB family. Deoxyribokinase subfamily.
else
FUNCTION	Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.
CATALYTIC ACTIVITY	Reaction=ATP + D-ribose = ADP + D-ribose 5-phosphate + H(+); Xref=Rhea:RHEA:13697, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:47013, ChEBI:CHEBI:78346, ChEBI:CHEBI:456216; EC=2.7.1.15;
COFACTOR	Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Note=Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate.;
ACTIVITY REGULATION	Activated by a monovalent cation that binds near, but not in, the active site. The most likely occupant of the site in vivo is potassium. Ion binding induces a conformational change that may alter substrate affinity.
PATHWAY	Carbohydrate metabolism; D-ribose degradation; D-ribose 5- phosphate from beta-D-ribopyranose: step 2/2.
SIMILARITY	Belongs to the carbohydrate kinase PfkB family. Ribokinase subfamily.
end case
SUBUNIT	Homodimer.
SUBCELLULAR LOCATION	Cytoplasm.

Keywords [?]

ATP-binding

Carbohydrate metabolism

Gene Ontology [?]

GO:0005737; Cellular component:cytoplasm
GO:0005524; Molecular function:ATP binding
case not <FTTag:deoxyribokinase>
GO:0004747; Molecular function:ribokinase activity
end case
GO:0046835; Biological process:carbohydrate phosphorylation
case not <FTTag:deoxyribokinase>
GO:0019303; Biological process:D-ribose catabolic process
end case

Cross-references [?]

PROSITE	PS00584; PFKB_KINASES_2; 1;
Pfam	PF00294; PfkB; 1;
PRINTS	PR00990; RIBOKINASE; 1;
NCBIfam	TIGR02152; D_ribokin_bact; 1;

Features [?]

From: DEOK_SALTI (P0DX97)

Key

From

Description

Tag

Condition

FTGroup

SITE

/note="Important for substrate specificity"

deoxyribokinase

From: RBSK_ECOLI (P0A9J6)

Key

From

Description

Tag

Condition

FTGroup

BINDING

223

228

/ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"

x(2)-G-x(2)-G

BINDING

254

255

/ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"

G-D

BINDING

/ligand="substrate"

x(2)-D

BINDING

/ligand="substrate"

G-[KR]-[GAS]-x-[NR]

ACT_SITE

255

/note="Proton acceptor"

BINDING

249