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78  structures 1419  species 0  interactions 4239  sequences 68  architectures

Family: E1_DerP2_DerF2 (PF02221)

Summary: ML 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 "ML domain". More...

ML domain Edit Wikipedia article

ML domain
Identifiers
SymbolE1_DerP2_DerF2
PfamPF02221
InterProIPR003172
SCOP21a9v / SCOPe / SUPFAM
OPM protein1nep
MD-2-related lipid-recognition
Identifiers
SymbolMD-2_lipid-recog
PfamPF02221
InterProIPR003172
SMARTSM00737

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:

Human proteins containing this domain

LY86; LY96; MMD-1;

References

  1. ^ 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): -. PMID 12591954.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ 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): -. PMID 15710415.{{cite journal}}: CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR003172

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.

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

  1. 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

External database links

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_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
(75)
Full
(4239)
Representative proteomes UniProt
(7857)
RP15
(1207)
RP35
(2155)
RP55
(3490)
RP75
(4385)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(75)
Full
(4239)
Representative proteomes UniProt
(7857)
RP15
(1207)
RP35
(2155)
RP55
(3490)
RP75
(4385)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(75)
Full
(4239)
Representative proteomes UniProt
(7857)
RP15
(1207)
RP35
(2155)
RP55
(3490)
RP75
(4385)
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: Yeats C
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Yeats C
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 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 22.7 22.7
Trusted cut-off 22.7 22.7
Noise cut-off 22.6 22.6
Model length: 134
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Viruses Viruses Unclassified Unclassified
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 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.

Protein Predicted structure External Information
A0A077Z0I4 View 3D Structure Click here
A0A077Z3A9 View 3D Structure Click here
A0A077ZBC2 View 3D Structure Click here
A0A077ZES0 View 3D Structure Click here
A0A077ZIB9 View 3D Structure Click here
A0A0D2E5H0 View 3D Structure Click here
A0A0K0E416 View 3D Structure Click here
A0A0K0EAD9 View 3D Structure Click here
A0A0K0EBH5 View 3D Structure Click here
A0A0K0ESC0 View 3D Structure Click here
A0A0R0H3H7 View 3D Structure Click here
A0A175VV36 View 3D Structure Click here
A0A1C1CSA2 View 3D Structure Click here
A0A1D6F9G8 View 3D Structure Click here
A0A286YA46 View 3D Structure Click here
A0A2K6VGW0 View 3D Structure Click here
A0A3P7DUG1 View 3D Structure Click here
A0A3P7F1E8 View 3D Structure Click here
A0A3Q0KU93 View 3D Structure Click here
B3DFW4 View 3D Structure Click here
B4FEI9 View 3D Structure Click here
C0NNF2 View 3D Structure Click here
C1GYS5 View 3D Structure Click here
C6SXR8 View 3D Structure Click here
C6SZX0 View 3D Structure Click here
C6T049 View 3D Structure Click here
D4AYQ6 View 3D Structure Click here
F4J7G5 View 3D Structure Click here
F7FJQ3 View 3D Structure Click here
I1JGG0 View 3D Structure Click here
K7LVU6 View 3D Structure Click here
O17271 View 3D Structure Click here
O48704 View 3D Structure Click here
O94183 View 3D Structure Click here
O97763 View 3D Structure Click here
P0CP28 View 3D Structure Click here
P17900 View 3D Structure Click here
P49278 View 3D Structure Click here
P58754 View 3D Structure Click here
P61916 View 3D Structure Click here