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753  structures 8923  species 0  interactions 83370  sequences 550  architectures

Clan: Ribokinase (CL0118)


Ribokinase-like superfamily Add an annotation

All of these enzymes are phosphotransferases that have an alcohol group as an acceptor (EC:2.7.1.-). However, 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMPP kinase) catalyses two phosphorylation reactions: one to a hydroxymethyl group of hydroxymethyl pyrimidine (HMP) and the second to the phosphomethyl group of HMPP [1]. The common structural feature for the enzymes in this superfamily is a central eight-stranded sheet that is flanked by eight structurally conserved helices, five on one side and three on the other [1]. The active site is located in a shallow groove along one edge of the sheet, with the phosphate acceptor hydroxyl group and -phosphate of ATP close together in the middle of the groove, and substrate and ATP binding at the ends [1].

This clan contains 5 families and the total number of domains in the clan is 83370. The clan was built by A Bateman.

Literature references

  1. Zhang Y, Dougherty M, Downs DM, Ealick SE; , Structure (Camb) 2004;12:1809-1821.: Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily. PUBMED:15458630 EPMC:15458630


This clan contains the following 5 member families:

ADP_PFK_GK Carb_kinase HK PfkB Phos_pyr_kin

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
PfkB (PF00294) 55298 (66.3%) View
Phos_pyr_kin (PF08543) 13462 (16.1%) View
Carb_kinase (PF01256) 9967 (12.0%) View
HK (PF02110) 3638 (4.4%) View
ADP_PFK_GK (PF04587) 1005 (1.2%) View
Total: 5 Total: 83370 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. More...



For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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