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501  structures 19844  species 9  interactions 186466  sequences 240  architectures

Clan: Ribokinase (CL0118)

Summary

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 186466. 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

Members

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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Alignments

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

Pfam family Num. domains Alignment
PfkB (PF00294) 118351 (63.5%) View
Phos_pyr_kin (PF08543) 36287 (19.5%) View
Carb_kinase (PF01256) 18769 (10.1%) View
HK (PF02110) 12653 (6.8%) View
ADP_PFK_GK (PF04587) 406 (0.2%) View
Total: 5 Total: 186466 Clan alignment
 

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Family relationships

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

Species distribution

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

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Interactions

There are 9 interactions for this clan. More...

Interacting families
A B
ADP_PFK_GK ADP_PFK_GK
Carb_kinase Carb_kinase
HK HK
PfkB PfkB
Phos_pyr_kin Phos_pyr_kin
ThiP_synth
ThiP_synth Phos_pyr_kin
TMP-TENI HK
YjeF_N Carb_kinase

Structures

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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