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174  structures 8356  species 0  interactions 23661  sequences 177  architectures

Family: GHMP_kinases_C (PF08544)

Summary: GHMP kinases C terminal

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

  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 2142297Freely accessible. 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 359713Freely accessible. 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. doi:10.1016/s0969-2126(00)00533-5. 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 C terminal 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 IPR013750

This domain is found in homoserine kinases ( EC ), galactokinases ( EC ) and mevalonate kinases ( EC ). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes [ PUBMED:8382990 ]. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. 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, create a novel nucleotide binding fold [ PUBMED:11188689 ].

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

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 GHMP_C (CL0677), which has the following description:

The GHMP kinases are a group of structurally related small kinases which are mostly involved in intermediary metabolism. The group is named after four members - galactokinase, homserine kinase, mevalonate kinase and phosphomevalonate kinase. It also includes 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase, isopentenyl monophosphate kinase, mevalonate diphosphate decarboxylase, archaeal shikimate kinases, N-acetyl galactosamine kinase, L-threonine kinase, glucuronokinase and galacturonic acid kinase. In addition to these enzymes, two proteins without catalytic activity - the Saccharomyces cerevisiae transcriptional regulator, Gal3p and the Caenorhabditis elegans sex fate determining protein XOL-1 have similar folds [1]. Of the seven enzymes, six kinases and one decarboxylase, two have been linked to human disease, two are involved in the biosynthesis of aromatic and nonaromatic amino acids, folates, and ubiquinones, one is needed to deliver galactose to the glycolytic pathway, and four are essential for either the mevalonate- or non-mevalonate-dependent synthesis of isoprenoids. The structural scaffold of the family has been evolutionary maintained, while the residues have been allowed to drift, however there are highly conserved solvent-accessible residues that are characteristic of the GHMP kinase family [2]. This clan represents the structurally conserved C-terminal domain which has a central alpha-beta plait fold and an insertion of four helices. Together with the N-terminal fold it creates a nucleotide binding fold with the active site located at the domain interface [3].

The clan contains the following 3 members:

GHMP_kinases_C MDD_C Xol-1_GHMP-like

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...

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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
(111)
Full
(23661)
Representative proteomes UniProt
(98633)
RP15
(3333)
RP35
(11173)
RP55
(22752)
RP75
(37664)
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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
(111)
Full
(23661)
Representative proteomes UniProt
(98633)
RP15
(3333)
RP35
(11173)
RP55
(22752)
RP75
(37664)
Alignment:
Format:
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Sequence:
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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
(111)
Full
(23661)
Representative proteomes UniProt
(98633)
RP15
(3333)
RP35
(11173)
RP55
(22752)
RP75
(37664)
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: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 111
Number in full: 23661
Average length of the domain: 82.10 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 21.30 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 85
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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_C domain has been found. There are 174 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
A0A0G2JVI4 View 3D Structure Click here
A0A0R0J3A5 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
A0A1D6QT52 View 3D Structure Click here
A0A1D8PEL1 View 3D Structure Click here
A0A1D8PLH0 View 3D Structure Click here
A0A1I9LRU1 View 3D Structure Click here
A0A368UI64 View 3D Structure Click here
A2BGN1 View 3D Structure Click here
A4HWN3 View 3D Structure Click here
A4I5Y9 View 3D Structure Click here
A4I6L2 View 3D Structure Click here
A4IBE2 View 3D Structure Click here
B4FKF4 View 3D Structure Click here
B6TB55 View 3D Structure Click here
B6UAN3 View 3D Structure Click here
C0PBZ4 View 3D Structure Click here
D2DKF1 View 3D Structure Click here
E7FDP4 View 3D Structure Click here
F1R3T4 View 3D Structure Click here
F1RC65 View 3D Structure Click here
F6NZ60 View 3D Structure Click here
I1JRE0 View 3D Structure Click here
I1JS15 View 3D Structure Click here
I1KAQ7 View 3D Structure Click here
I1KMP3 View 3D Structure Click here
I1KPR8 View 3D Structure Click here
I1M9V9 View 3D Structure Click here
I1MRT3 View 3D Structure Click here
I1MWC4 View 3D Structure Click here
I1NC04 View 3D Structure Click here
I1NCN7 View 3D Structure Click here
I1NE02 View 3D Structure Click here
K7KLY3 View 3D Structure Click here
K7LXA6 View 3D Structure Click here
K7U924 View 3D Structure Click here