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277  structures 8516  species 0  interactions 29307  sequences 242  architectures

Family: GHMP_kinases_N (PF00288)

Summary: GHMP kinases N 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 "GHMP kinase family". More...

GHMP kinase family Edit Wikipedia article

GHMP kinases N terminal domain
PDB 1k47 EBI.jpg
crystal structure of the streptococcus pneumoniae phosphomevalonate kinase (pmk)
Identifiers
SymbolGHMP_kinases_N
PfamPF00288
Pfam clanCL0329
InterProIPR006204
PROSITEPDOC00545
SCOP21fwl / SCOPe / SUPFAM
GHMP kinases C terminal
PDB 1s4e EBI.jpg
pyrococcus furiosus galactokinase in complex with galactose, adp and magnesium
Identifiers
SymbolGHMP_kinases_C
PfamPF08544
InterProIPR013750
PROSITEPDOC00545
SCOP21fwl / SCOPe / SUPFAM

In molecular biology, the GHMP kinase family is a family of kinase enzymes. Members of this family include homoserine kinases EC 2.7.1.39, galactokinases EC 2.7.1.6, and mevalonate kinasesEC 2.7.1.36. These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes.[1] These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. These enzymes contain, in their N-terminal section, a conserved Gly/Ser-rich region which is probably involved in the binding of ATP.[2][3] The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, creates a novel nucleotide binding fold.[4]


References

  1. ^ Bork P, Sander C, Valencia A (1993). "Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases". Protein Sci. 2 (1): 31–40. doi:10.1002/pro.5560020104. PMC 2142297. PMID 8382990. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Tsay YH, Robinson GW (1991). "Cloning and characterization of ERG8, an essential gene of Saccharomyces cerevisiae that encodes phosphomevalonate kinase". Mol. Cell. Biol. 11 (2): 620–31. PMC 359713. PMID 1846667. {{cite journal}}: Unknown parameter |month= ignored (help)
  3. ^ Lee M, Leustek T (1999). "Identification of the gene encoding homoserine kinase from Arabidopsis thaliana and characterization of the recombinant enzyme derived from the gene". Arch. Biochem. Biophys. 372 (1): 135–42. doi:10.1006/abbi.1999.1481. PMID 10562426. {{cite journal}}: Unknown parameter |month= ignored (help)
  4. ^ Zhou T, Daugherty M, Grishin NV, Osterman AL, Zhang H (2000). "Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily". Structure. 8 (12): 1247–57. PMID 11188689. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR013750
This article incorporates text from the public domain Pfam and InterPro: IPR006204

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.

GHMP kinases N terminal domain Provide feedback

This family includes homoserine kinases, galactokinases and mevalonate kinases.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006204

The galacto- ( EC ), homoserine ( EC ), mevalonate ( EC ) and phosphomevalonate ( EC ) kinases contain, in their N-terminal section, a conserved domain with a Gly/Ser-rich region which is probably involved in the binding of ATP [ PUBMED:1846667 , PUBMED:10562426 ]. This group of kinases has been called 'GHMP' (from the first letter of their substrates).

This domain is also found in diphosphomevalonate decarboxylases, which are structurally related members of the GHMP superfamily [ PUBMED:17583736 ], but do not possess kinase activity.

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 S5 (CL0329), which has the following description:

This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.

The clan contains the following 18 members:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_N

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(447)
Full
(29307)
Representative proteomes UniProt
(122122)
RP15
(4403)
RP35
(14101)
RP55
(27938)
RP75
(45676)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(447)
Full
(29307)
Representative proteomes UniProt
(122122)
RP15
(4403)
RP35
(14101)
RP55
(27938)
RP75
(45676)
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
(447)
Full
(29307)
Representative proteomes UniProt
(122122)
RP15
(4403)
RP35
(14101)
RP55
(27938)
RP75
(45676)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: GHMP_kinases;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Mistry J
Number in seed: 447
Number in full: 29307
Average length of the domain: 65.8 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 16.96 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.3 22.3
Trusted cut-off 22.3 22.3
Noise cut-off 22.2 22.2
Model length: 66
Family (HMM) version: 29
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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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...

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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 GHMP_kinases_N domain has been found. There are 277 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044V168 View 3D Structure Click here
A0A044VJ56 View 3D Structure Click here
A0A077ZCE8 View 3D Structure Click here
A0A077ZCS3 View 3D Structure Click here
A0A077ZHD2 View 3D Structure Click here
A0A0A2V6L9 View 3D Structure Click here
A0A0D2FFY6 View 3D Structure Click here
A0A0D2G4C7 View 3D Structure Click here
A0A0D2GW63 View 3D Structure Click here
A0A0D2GZY0 View 3D Structure Click here
A0A0D2HBU3 View 3D Structure Click here
A0A0G2JVI4 View 3D Structure Click here
A0A0H3GMA8 View 3D Structure Click here
A0A0H3GQD1 View 3D Structure Click here
A0A0H3GZM1 View 3D Structure Click here
A0A0H3H2A4 View 3D Structure Click here
A0A0J9XY66 View 3D Structure Click here
A0A0K0DVE7 View 3D Structure Click here
A0A0K0DX29 View 3D Structure Click here
A0A0K0EQ95 View 3D Structure Click here
A0A0N4U218 View 3D Structure Click here
A0A0N4UMG5 View 3D Structure Click here
A0A0R0FP88 View 3D Structure Click here
A0A158Q108 View 3D Structure Click here
A0A158Q5X6 View 3D Structure Click here
A0A175VP82 View 3D Structure Click here
A0A175VQZ9 View 3D Structure Click here
A0A175VRM1 View 3D Structure Click here
A0A175VSK8 View 3D Structure Click here
A0A175WAF1 View 3D Structure Click here
A0A1C1C8S9 View 3D Structure Click here
A0A1C1CBV9 View 3D Structure Click here
A0A1C1CF86 View 3D Structure Click here
A0A1C1CT87 View 3D Structure Click here
A0A1C1D1X2 View 3D Structure Click here
A0A1D6E029 View 3D Structure Click here
A0A1D6GVC9 View 3D Structure Click here
A0A1D6JL91 View 3D Structure Click here
A0A1D6KB09 View 3D Structure Click here
A0A1D6LAE7 View 3D Structure Click here