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98  structures 4144  species 3  interactions 14710  sequences 34  architectures

Family: FGGY_C (PF02782)

Summary: FGGY family of carbohydrate kinases, C-terminal domain

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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
PDB 1xup EBI.jpg
enterococcus casseliflavus glycerol kinase complexed with glycerol
Identifiers
Symbol FGGY_N
Pfam PF00370
Pfam clan CL0108
InterPro IPR018484
PROSITE PDOC00408
SCOP 1gla
SUPERFAMILY 1gla
FGGY family of carbohydrate kinases, C-terminal domain
PDB 1bwf EBI.jpg
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
SCOP 1gla
SUPERFAMILY 1gla

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); 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]

References[edit]

  1. ^ 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. 
  2. ^ 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 article incorporates text from the public domain Pfam and InterPro IPR018485

This article incorporates text from the public domain Pfam and InterPro IPR018484

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

  1. 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

  2. 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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018485

It has been shown [PUBMED:1659648] that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase (EC) (gene fucK); gluconokinase (EC) (gene gntK); glycerol kinase (EC) (gene glpK); xylulokinase (EC) (gene xylB); and L-xylulose kinase (EC) (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues.

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.

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 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 29 members:

Acetate_kinase Actin BcrAD_BadFG CmcH_NodU DDR DUF1464 DUF1786 EutA FGGY_C FGGY_N FtsA Fumble GDA1_CD39 Glucokinase Hexokinase_1 Hexokinase_2 HSP70 Hydant_A_N Hydantoinase_A MreB_Mbl MutL Pan_kinase Peptidase_M22 PilM_2 Ppx-GppA ROK StbA T2SL UPF0075

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
(105)
Full
(14710)
Representative proteomes NCBI
(11639)
Meta
(3173)
RP15
(1123)
RP35
(2048)
RP55
(2789)
RP75
(3368)
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Format an alignment

  Seed
(105)
Full
(14710)
Representative proteomes NCBI
(11639)
Meta
(3173)
RP15
(1123)
RP35
(2048)
RP55
(2789)
RP75
(3368)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(105)
Full
(14710)
Representative proteomes NCBI
(11639)
Meta
(3173)
RP15
(1123)
RP35
(2048)
RP55
(2789)
RP75
(3368)
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: Prosite
Previous IDs: none
Type: Domain
Author: Finn RD, Griffiths-Jones SR
Number in seed: 105
Number in full: 14710
Average length of the domain: 190.40 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 38.30 %

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 20.7 20.7
Trusted cut-off 20.7 20.7
Noise cut-off 20.6 20.6
Model length: 198
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

FGGY_C PTS_EIIA_1 FGGY_N

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 98 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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