Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
114  structures 4900  species 3  interactions 15529  sequences 62  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
Symbol GHMP_kinases_N
Pfam PF00288
Pfam clan CL0329
InterPro IPR006204
PROSITE PDOC00545
SCOP 1fwl
SUPERFAMILY 1fwl
GHMP kinases C terminal
PDB 1s4e EBI.jpg
pyrococcus furiosus galactokinase in complex with galactose, adp and magnesium
Identifiers
Symbol GHMP_kinases_C
Pfam PF08544
InterPro IPR013750
PROSITE PDOC00545
SCOP 1fwl
SUPERFAMILY 1fwl

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[edit]

  1. ^ Bork P, Sander C, Valencia A (January 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. 
  2. ^ Tsay YH, Robinson GW (February 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. 
  3. ^ Lee M, Leustek T (December 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. 
  4. ^ Zhou T, Daugherty M, Grishin NV, Osterman AL, Zhang H (December 2000). "Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily". Structure 8 (12): 1247–57. PMID 11188689. 

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...

Loading domain graphics...

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 14 members:

ChlI DNA_mis_repair EFG_IV Fae GHMP_kinases_N IGPD Lon_C LpxC Ribonuclease_P Ribosomal_S5_C 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(455)
Full
(15529)
Representative proteomes NCBI
(10927)
Meta
(3091)
RP15
(1260)
RP35
(2384)
RP55
(3266)
RP75
(3877)
Jalview View  View  View  View  View  View  View  View 
HTML View    View  View  View  View     
PP/heatmap 1   View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(455)
Full
(15529)
Representative proteomes NCBI
(10927)
Meta
(3091)
RP15
(1260)
RP35
(2384)
RP55
(3266)
RP75
(3877)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(455)
Full
(15529)
Representative proteomes NCBI
(10927)
Meta
(3091)
RP15
(1260)
RP35
(2384)
RP55
(3266)
RP75
(3877)
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: GHMP_kinases;
Type: Family
Author: Finn RD, Mistry J
Number in seed: 455
Number in full: 15529
Average length of the domain: 64.70 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 18.95 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 67
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

The 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

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

GHMP_kinases_N GalKase_gal_bdg GHMP_kinases_C

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 114 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.

Loading structure mapping...