Summary: ML domain
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This is the Wikipedia entry entitled "ML domain". More...
ML domain Edit Wikipedia article
ML domain | |||||||||||
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Identifiers | |||||||||||
Symbol | E1_DerP2_DerF2 | ||||||||||
Pfam | PF02221 | ||||||||||
InterPro | IPR003172 | ||||||||||
SCOP2 | 1a9v / SCOPe / SUPFAM | ||||||||||
OPM protein | 1nep | ||||||||||
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MD-2-related lipid-recognition | |||||||||||
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Identifiers | |||||||||||
Symbol | MD-2_lipid-recog | ||||||||||
Pfam | PF02221 | ||||||||||
InterPro | IPR003172 | ||||||||||
SMART | SM00737 | ||||||||||
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The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like beta-sandwich fold similar to that of E-set Ig domains. This domain is present in the following proteins:
- Epididymal secretory protein E1 (also known as Niemann-Pick C2 protein), which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes[1].
- House-dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus[2].
Human proteins containing this domain
References
- ^ Lobel P, Stock AM, Friedland N, Liou HL (2003). "Structure of a cholesterol-binding protein deficient in Niemann-Pick type C2 disease". Proc. Natl. Acad. Sci. U.S.A. 100 (5): -. PMIDÂ 12591954.
{{cite journal}}
: CS1 maint: multiple names: authors list (link) - ^ Kristensen O, Kastrup JS, Skov LK, Gajhede M, Larsen JN, Johannessen BR, Bolwig C, Spangfort M, Lund K (2005). "Structure of the house dust mite allergen Der f 2: implications for function and molecular basis of IgE cross-reactivity". FEBS Lett. 579 (5): -. PMIDÂ 15710415.
{{cite journal}}
: CS1 maint: multiple names: authors list (link)
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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.
ML domain Provide feedback
ML domain - MD-2-related lipid recognition domain. This family consists of proteins from plants, animals and fungi, including dust mite allergen Der P 2 (P49278). It has been implicate in lipid recognition, particularly in the recognition of pathogen related products. A mutation in Npc2 (Q15668) causes a rare form of Niemann-Pick type C2 disease. This domain has a similar topology to immunoglobulin domains.
Literature references
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Mueller GA, Benjamin DC, Rule GS; , Biochemistry 1998;37:12707-12714.: Tertiary structure of the major house dust mite allergen Der p 2: sequential and structural homologies. PUBMED:9737847 EPMC:9737847
Internal database links
SCOOP: | DUF1091 TRP_N |
Similarity to PfamA using HHSearch: | TRP_N |
External database links
SCOP: | 1a9v |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003172
The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like beta-sandwich fold similar to that of E-set Ig domains. This domain is present in proteins from plants, animals and fungi, including the following proteins:
- Epididymal secretory protein E1 (also known as Niemann-Pick C2 protein - Npc2), which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes [ PUBMED:12591954 ].
- House-dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus [ PUBMED:15710415 ].
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 LIG (CL0532), which has the following description:
This superfamily includes a number of lipid binding families that have a similar topology to the immunoglobulin fold. The family includes The ML domain Pfam:PF02221. It includes the uncharacterised family Pfam:PF06477.
The clan contains the following 3 members:
DUF1091 E1_DerP2_DerF2 TRP_NAlignments
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 (75) |
Full (4239) |
Representative proteomes | UniProt (7857) |
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RP15 (1207) |
RP35 (2155) |
RP55 (3490) |
RP75 (4385) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (75) |
Full (4239) |
Representative proteomes | UniProt (7857) |
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RP15 (1207) |
RP35 (2155) |
RP55 (3490) |
RP75 (4385) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Yeats C |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 75 |
Number in full: | 4239 |
Average length of the domain: | 127 aa |
Average identity of full alignment: | 19 % |
Average coverage of the sequence by the domain: | 65.03 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 134 | ||||||||||||
Family (HMM) version: | 18 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 E1_DerP2_DerF2 domain has been found. There are 78 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.