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7  structures 153  species 0  interactions 234  sequences 6  architectures

Family: ADP_PFK_GK (PF04587)

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

  1. 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

  2. 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

  3. 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

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.

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 6 members:

ADP_PFK_GK Aldolase_2 Carb_kinase HK PfkB Phos_pyr_kin

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(9)
Full
(234)
Representative proteomes NCBI
(223)
Meta
(1)
RP15
(42)
RP35
(64)
RP55
(112)
RP75
(154)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(9)
Full
(234)
Representative proteomes NCBI
(223)
Meta
(1)
RP15
(42)
RP35
(64)
RP55
(112)
RP75
(154)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(9)
Full
(234)
Representative proteomes NCBI
(223)
Meta
(1)
RP15
(42)
RP35
(64)
RP55
(112)
RP75
(154)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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.

Note: You can also download the data file for the tree.

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 View help on the curation process

Seed source: Pfam-B_4731 (release 7.5)
Previous IDs: none
Type: Family
Author: Waterfield DI, Finn RD
Number in seed: 9
Number in full: 234
Average length of the domain: 386.20 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 87.69 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 20.9
Trusted cut-off 24.5 23.8
Noise cut-off 20.3 18.3
Model length: 445
Family (HMM) version: 10
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 7 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 seqence.

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