Summary: ADP-specific Phosphofructokinase/Glucokinase conserved region
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ADP-specific Phosphofructokinase/Glucokinase conserved region Provide feedback
In archaea a novel type of glycolytic pathway exists that is deviant from the classical Embden-Meyerhof pathway. This pathway utilises two novel proteins: an ADP-dependent Glucokinase and an ADP-dependent Phosphofructokinase. This conserved region is present at the C-terminal of both these proteins. Interestingly this family contains sequences from higher eukaryotes. [1,2,3].
Literature references
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Tuininga JE, Verhees CH, van der Oost J, Kengen SW, Stams AJ, de Vos WM; , J Biol Chem 1999;274:21023-21028.: Molecular and biochemical characterization of the ADP-dependent phosphofructokinase from the hyperthermophilic archaeon Pyrococcus furiosus. PUBMED:10409652 EPMC:10409652
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Verhees CH, Tuininga JE, Kengen SW, Stams AJ, van der Oost J, de Vos WM; , J Bacteriol 2001;183:7145-7153.: ADP-dependent phosphofructokinases in mesophilic and thermophilic methanogenic archaea. PUBMED:11717273 EPMC:11717273
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Ronimus RS, de Heus E, Morgan HW; , Biochim Biophys Acta 2001;1517:384-391.: Sequencing, expression, characterisation and phylogeny of the ADP-dependent phosphofructokinase from the hyperthermophilic, euryarchaeal Thermococcus zilligii. PUBMED:11342216 EPMC:11342216
External database links
SCOP: | 1l2l |
This tab holds annotation information from the InterPro database.
InterPro entry IPR007666
Although ATP is the most common phosphoryl group donor for kinases, certain hyperthermophilic archaea, such as Thermococcus litoralis and Pyrococcus furiosus, utilise unusual ADP-dependent glucokinases (ADPGKs) and phosphofructokinases (ADPPKKs) in their glycolytic pathways [ PUBMED:11286887 , PUBMED:12237466 , PUBMED:12909015 ]. ADPGKs and ADPPFKs exhibit significant similarity, and form an ADP-dependent kinase (ADPK) family, which was tentatively named the PFKC family [ PUBMED:11778837 ]. A ~460-residue ADPK domain is also found in a bifunctional ADP-dependent gluco/phosphofructo- kinase (ADP-GK/PFK) from Methanocaldococcus jannaschii (Methanococcus jannaschii) as well as in homologous hypothetical proteins present in several eukaryotes [ PUBMED:11717273 ].
The whole structure of the ADPK domain can be divided into large and small alpha/beta subdomains. The larger subdomain, which carries the ADP binding site, consists of a twisted 12-stranded beta sheet flanked on both faces by 13 alpha helices and three 3(10) helices, forming an alpha/beta 3-layer sandwich. The smaller subdomain, which covers the active site, forms an alpha/beta two-layer structure containing 5 beta strands and four alpha helices. The ADP molecule is buried in a shallow pocket in the large subdomain. The binding of substrate sugar induces a structural change, the small domain closing to form a complete substrate sugar binding site [ PUBMED:11286887 , PUBMED:12237466 , PUBMED:12909015 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | phosphotransferase activity, alcohol group as acceptor (GO:0016773) |
Biological process | carbohydrate metabolic process (GO:0005975) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Ribokinase (CL0118), which has the following description:
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].
The clan contains the following 5 members:
ADP_PFK_GK Carb_kinase HK PfkB Phos_pyr_kinAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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Seed (67) |
Full (840) |
Representative proteomes | UniProt (2142) |
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RP15 (215) |
RP35 (428) |
RP55 (798) |
RP75 (1146) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (67) |
Full (840) |
Representative proteomes | UniProt (2142) |
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RP15 (215) |
RP35 (428) |
RP55 (798) |
RP75 (1146) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_4731 (release 7.5) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Waterfield DI |
Number in seed: | 67 |
Number in full: | 840 |
Average length of the domain: | 372.50 aa |
Average identity of full alignment: | 32 % |
Average coverage of the sequence by the domain: | 83.78 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 426 | ||||||||||||
Family (HMM) version: | 17 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the ADP_PFK_GK domain has been found. There are 22 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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