M-CSA Mechanism and Catalytic Site Atlas

Ribokinase

Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. The reaction is the first step in ribose metabolism and acts partly to trap ribose within the cell after uptake. Phosphorylation also prepares the sugar for use in the synthesis of nucleotides, histidine and for entry into the pentose phosphate pathway. Ribokinase is apart of the Ribokinase superfamily (also known as the PfkB family) alongside fructokinase and adenosine kinase which share two conserved motifs at the N and C terminus.

Reference Protein and Structure

Sequence: P0A9J6 (2.7.1.15) (Sequence Homologues) (PDB Homologues)
Biological species: Escherichia coli K-12 (Bacteria)
PDB: 1rk2 - E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121 (2.25 Å)
Catalytic CATH Domains: 3.40.1190.20 (see all for 1rk2)
Cofactors: Magnesium(2+) (2), Water (7)

Click To Show Structure

Enzyme Reaction (EC:2.7.1.15)

ATP(4-)

CHEBI:30616

D-ribofuranose

CHEBI:47013

→

ADP(3-)

CHEBI:456216

hydron

CHEBI:15378

D-ribofuranose 5-phosphate(2-)

CHEBI:78346

Enzyme reaction links: IntEnz ENZYME ExplorEnz

Alternative enzyme names: D-ribokinase, Deoxyribokinase, Ribokinase (phosphorylating),

Enzyme Mechanism

Mechanism Proposal 1 ☆☆☆

Summary
Step 1
Step 2
Products
All Steps

Introduction

Asp255 acts as a base to deprotonate the O5'-hydroxyl group of ribose. The negatively charged O5' atom then makes a direct nucleophilic attack on the gamma-phosphate group of ATP in an in-line mechanism. An anion hole formed by backbone amide group of residues 252-255 (Ala252, Ala253, Gly254, Asp255) stabilise the transition state. Ribokinase has two Mg2+ ions present in its active site. Mg2+A coordinating to the alpha and beta phosphates is thought to promote ADP as a leaving group white Mg2+B coordinates to the beta and gamma phosphate, stabilising the developing negative charges in the reaction transition state. It is also thought to be activated by a monovalent cation such as K+ and interact with a phosphate ion.

Catalytic Residues Roles

UniProt	PDB* (1rk2)
Ala252 (main-N), Ala253 (main-N), Gly254 (main-N)	Ala252A (main-N), Ala253A (main-N), Gly254A (main-N)	It forms an oxyanion hole to stabilise the transition state.	electrostatic stabiliser, polar interaction
Asp255	Asp255A	Its side chain acts as a base to deprotonate the O5'-hydroxyl group of ribose to promote its nucleophilic attack on the gamma-phosphate group of ATP. Its backbone amide forms an oxyanion hole to stabilise the transition state.	proton acceptor, electrostatic stabiliser, proton donor

*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

bimolecular nucleophilic substitution, proton transfer, overall product formed, overall reactant used, inferred reaction step, native state of enzyme regenerated

References

Sigrell JA et al. (1998), Structure, 6, 183-193. Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 å resolution: insights into a new family of kinase structures. DOI:10.1016/s0969-2126(98)00020-3. PMID:9519409.
Merino F et al. (2012), Biochimie, 94, 516-524. Catalytic and regulatory roles of divalent metal cations on the phosphoryl-transfer mechanism of ADP-dependent sugar kinases from hyperthermophilic archaea. DOI:10.1016/j.biochi.2011.08.021. PMID:21906652.
Park J et al. (2008), Cell Mol Life Sci, 65, 2875-2896. Adenosine kinase and ribokinase--the RK family of proteins. DOI:10.1007/s00018-008-8123-1. PMID:18560757.
Miallau L et al. (2007), J Biol Chem, 282, 19948-19957. Structures of Staphylococcus aureus D-tagatose-6-phosphate kinase implicate domain motions in specificity and mechanism. DOI:10.1074/jbc.M701480200. PMID:17459874.
Andersson CE et al. (2002), J Mol Biol, 315, 409-419. Activation of ribokinase by monovalent cations. DOI:10.1006/jmbi.2001.5248. PMID:11786021.
Maj MC et al. (2002), Biochemistry, 41, 4059-4069. Pentavalent Ions Dependency Is a Conserved Property of Adenosine Kinase from Diverse Sources: Identification of a Novel Motif Implicated in Phosphate and Magnesium Ion Binding and Substrate Inhibition†. DOI:10.1021/bi0119161.

Step 1. Asp255 deprotonates the 5' OH on ribose. This increases the group's nucleophilicity to then attack the gamma phosphate on ATP.

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Catalytic Residues Roles

Residue	Roles
Gly254A (main-N)	electrostatic stabiliser
Asp255A	electrostatic stabiliser
Ala253A (main-N)	electrostatic stabiliser
Ala252A (main-N)	electrostatic stabiliser
Ala252A (main-N)	polar interaction
Ala253A (main-N)	polar interaction
Gly254A (main-N)	polar interaction
Asp255A	proton acceptor