Summary: FGGY family of carbohydrate kinases, C-terminal domain
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "FGGY carbohydrate kinase family". More...
FGGY carbohydrate kinase family Edit Wikipedia article
FGGY family of carbohydrate kinases, N-terminal domain | |||||||||
---|---|---|---|---|---|---|---|---|---|
![]() enterococcus casseliflavus glycerol kinase complexed with glycerol | |||||||||
Identifiers | |||||||||
Symbol | FGGY_N | ||||||||
Pfam | PF00370 | ||||||||
Pfam clan | CL0108 | ||||||||
InterPro | IPR018484 | ||||||||
PROSITE | PDOC00408 | ||||||||
SCOPe | 1gla / SUPFAM | ||||||||
CDD | cd00366 | ||||||||
|
FGGY family of carbohydrate kinases, C-terminal domain | |||||||||
---|---|---|---|---|---|---|---|---|---|
![]() escherichia coli glycerol kinase mutant with bound atp analog showing substantial domain motion | |||||||||
Identifiers | |||||||||
Symbol | FGGY_C | ||||||||
Pfam | PF02782 | ||||||||
Pfam clan | CL0108 | ||||||||
InterPro | IPR018485 | ||||||||
PROSITE | PDOC00408 | ||||||||
SCOPe | 1gla / SUPFAM | ||||||||
CDD | cd00366 | ||||||||
|
In molecular biology the FGGY carbohydrate kinase family is a family of evolutionary related carbohydrate kinase enzymes. These enzymes include L-fucolokinase EC 2.7.1.51 (gene fucK); gluconokinase EC 2.7.1.12 (gene gntK); glycerol kinase EC 2.7.1.30 (gene glpK); xylulokinase EC 2.7.1.17 (gene xylB); D-ribulose kinase EC 2.7.1.47 (gene FGGY/YDR109c);[1] and L-xylulose kinase EC 2.7.1.53 (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues.
These enzymes consist of two domains. The N-terminal and C-terminal domains both adopt a ribonuclease H-like fold and are structurally related to each other.[1][2][3]
References
- ^ a b Singh C, Glaab E, Linster C. "Molecular Identification of D-Ribulokinase in Budding Yeast and Mammals". J. Biol. Chem. in press. doi:10.1074/jbc.M116.760744. PMC 5247636.
- ^ Hurley JH, Faber HR, Worthylake D, Meadow ND, Roseman S, Pettigrew DW, Remington SJ (January 1993). "Structure of the regulatory complex of Escherichia coli IIIGlc with glycerol kinase". Science. 259 (5095): 673–7. doi:10.1126/science.8430315. PMID 8430315.
- ^ Ormo M, Bystrom CE, Remington SJ (November 1998). "Crystal structure of a complex of Escherichia coli glycerol kinase and an allosteric effector fructose 1,6-bisphosphate". Biochemistry. 37 (47): 16565–72. doi:10.1021/bi981616s. PMID 9843423.
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
FGGY family of carbohydrate kinases, C-terminal domain Provide feedback
This domain adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain.
Literature references
-
Hurley JH, Faber HR, Worthylake D, Meadow ND, Roseman S, Pettigrew DW, Remington SJ; , Science. 1993;259:673-677.: Structure of the regulatory complex of Escherichia coli IIIGlc with glycerol kinase. PUBMED:8430315 EPMC:8430315
-
Ormo M, Bystrom CE, Remington SJ; , Biochemistry 1998;37:16565-16572.: Crystal structure of a complex of Escherichia coli glycerol kinase and an allosteric effector fructose 1,6-bisphosphate. PUBMED:9843423 EPMC:9843423
Internal database links
SCOOP: | AnmK BcrAD_BadFG FtsA HSP70 MreB_Mbl Peptidase_M22 |
External database links
PROSITE: | PDOC00408 |
SCOP: | 1gla |
This tab holds annotation information from the InterPro database.
InterPro entry IPR018485
FGGY carbohydrate kinases carry out ATP-dependent phosphorylation on one out of at least nine distinct sugar substrates [PUBMED:22215998]. These enzymes include L-ribulokinase (EC) (gene araB); Erythriol kinase (EC) (gene eryA); L-fucolokinase (EC) (gene fucK); gluconokinase (EC) (gene gntK); glycerol kinase (EC) (gene glpK); xylulokinase (EC) (gene xylB); L-xylulose kinase (EC) (gene lyxK), D-ribulokinase (EC) (gene rbtK); and rhamnulokinase (EC) (gene rhaB). This family also contains a divergent subfamily functioning in quorum sensing, which phosphorylates AI-2, a bacterial signaling molecule derived from 4,5-dihydroxy-2,3-pentanedione (DPD) [PUBMED:17274596]. All described members of this enzyme family are composed of two homologous actin-like ATPase domains. A catalytic cleft is formed by the interface between these two domains, where the sugar substrate and ATP co-substrate bind.This entry represents the C-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain [PUBMED:8430315, PUBMED:9843423].
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...
Loading domain graphics...
Pfam Clan
This family is a member of clan Actin_ATPase (CL0108), which has the following description:
The actin-like ATPase domain forms an alpha/beta canonical fold. The domain can be subdivided into 1A, 1B, 2A and 2B subdomains. Subdomains 1A and 1B share the same RNAseH-like fold (a five-stranded beta-sheet decorated by a number of alpha-helices). Domains 1A and 2A are conserved in all members of this superfamily, whereas domain 1B and 2B have a variable structure and are even missing from some homologues [1]. Within the actin-like ATPase domain the ATP-binding site is highly conserved. The phosphate part of the ATP is bound in a cleft between subdomains 1A and 2A, whereas the adenosine moiety is bound to residues from domains 2A and 2B[1].
The clan contains the following 34 members:
Acetate_kinase Actin Actin_micro ALP_N AnmK BcrAD_BadFG Carbam_trans_N DDR DUF1464 DUF2229 EutA FGGY_C FGGY_N FtsA Fumble GDA1_CD39 Glucokinase Hexokinase_1 Hexokinase_2 HGD-D HSP70 Hydant_A_N Hydantoinase_A HypF_C MreB_Mbl MutL Pan_kinase Peptidase_M22 PilM_2 Ppx-GppA RACo_C_ter ROK StbA T2SSLAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
View options
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 (64) |
Full (24861) |
Representative proteomes | UniProt (66409) |
NCBI (114265) |
Meta (3178) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (5243) |
RP35 (14707) |
RP55 (22775) |
RP75 (32990) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
Download options
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 (64) |
Full (24861) |
Representative proteomes | UniProt (66409) |
NCBI (114265) |
Meta (3178) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (5243) |
RP35 (14707) |
RP55 (22775) |
RP75 (32990) |
||||||
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
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
Seed source: | Prosite |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 64 |
Number in full: | 24861 |
Average length of the domain: | 189.60 aa |
Average identity of full alignment: | 25 % |
Average coverage of the sequence by the domain: | 37.71 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 198 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Interactions
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 FGGY_C domain has been found. There are 156 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.
Loading structure mapping...