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HAMAP rule MF_01987

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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 (); [ 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>
FUNCTIONCatalyzes 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;
SIMILARITYBelongs to the carbohydrate kinase PfkB family. Deoxyribokinase subfamily.
else
FUNCTIONCatalyzes 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 REGULATIONActivated 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.
PATHWAYCarbohydrate metabolism; D-ribose degradation; D-ribose 5- phosphate from beta-D-ribopyranose: step 2/2.
SIMILARITYBelongs to the carbohydrate kinase PfkB family. Ribokinase subfamily.
end case
SUBUNITHomodimer.
SUBCELLULAR LOCATIONCytoplasm.

Keywords [?]


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 To Description Tag Condition FTGroup
SITE 10 10 /note="Important for substrate specificity" deoxyribokinase M
From: RBSK_ECOLI (P0A9J6)
Key From To 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 14 16 /ligand="substrate" x(2)-D
BINDING 42 46 /ligand="substrate" G-[KR]-[GAS]-x-[NR]
ACT_SITE 255 255 /note="Proton acceptor" D
BINDING 249 249 /ligand="K(+)"
/ligand_id="ChEBI:CHEBI:29103"
[DN]
BINDING 251 251 /ligand="K(+)"
/ligand_id="ChEBI:CHEBI:29103"
BINDING 285 285 /ligand="K(+)"
/ligand_id="ChEBI:CHEBI:29103"
BINDING 288 288 /ligand="K(+)"
/ligand_id="ChEBI:CHEBI:29103"
BINDING 290 290 /ligand="K(+)"
/ligand_id="ChEBI:CHEBI:29103"
G
BINDING 294 294 /ligand="K(+)"
/ligand_id="ChEBI:CHEBI:29103"
S
BINDING 143 143 /ligand="substrate" E
BINDING 187 187 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
N
BINDING 255 255 /ligand="substrate" D
BINDING 279 279 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
[HN]

Additional information [?]

Size range 259-382 amino acids
Related rules None
Fusion Nter: None Cter: None
Comments Met-10 in Salmonella deoxyribokinase corresponds to Asn-14 in E.coli ribokinase. It is a key residue differentiating ribose and deoxyribose (PubMed=10648508).



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