HAMAP rule MF_01987
General rule information
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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
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Identifier, protein and gene names
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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
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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
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ATP-binding |
Carbohydrate metabolism |
Cytoplasm |
Kinase |
Magnesium |
Metal-binding |
Nucleotide-binding |
Transferase |
Potassium |
Gene Ontology
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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
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PROSITE | PS00584; PFKB_KINASES_2; 1; |
Pfam | PF00294; PfkB; 1; |
PRINTS | PR00990; RIBOKINASE; 1; |
NCBIfam | TIGR02152; D_ribokin_bact; 1; |
Features
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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
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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). |