Summary: Menaquinone biosynthesis
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This family includes two enzymes which are involved in menaquinone biosynthesis. One which catalyses the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to futalosine . These enzymes comprise two domains with alpha/beta structures, a large domain and a small domain. A pocket between the two domains may form the active site, a conserved histidine located within this pocket could be the catalytic base .
Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi T;, Science. 2008;321:1670-1673.: An alternative menaquinone biosynthetic pathway operating in microorganisms. PUBMED:18801996 EPMC:18801996
Arai R, Murayama K, Uchikubo-Kamo T, Nishimoto M, Toyama M, Kuramitsu S, Terada T, Shirouzu M, Yokoyama S;, J Struct Biol. 2009;168:575-581.: Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8. PUBMED:19602440 EPMC:19602440
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003773
This family includes two enzymes which are involved in menaquinone (vitamin K2) biosynthesis. One which catalyses the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to futalosine [PUBMED:18801996]. These enzymes comprise two domains with alpha/beta structures, a large domain and a small domain. A pocket between the two domains may form the active site, a conserved histidine located within this pocket could be the catalytic base [PUBMED:19602440].
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Periplasmic binding proteins (PBPs) consist of two large lobes that close around the bound ligand. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors .
The clan contains the following 25 members:DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate Mycoplasma_p37 NMT1 NMT1_2 NMT1_3 OpuAC PBP_like PBP_like_2 Phosphonate-bd SBP_bac_1 SBP_bac_11 SBP_bac_3 SBP_bac_5 SBP_bac_6 SBP_bac_8 TctC Transferrin VitK2_biosynth YhfZ_C
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Curation and family details
|Author:||Mian N, Bateman A, Eberhardt R|
|Number in seed:||87|
|Number in full:||2889|
|Average length of the domain:||209.00 aa|
|Average identity of full alignment:||21 %|
|Average coverage of the sequence by the domain:||91.97 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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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 VitK2_biosynth domain has been found. There are 15 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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