Summary: Vitelline membrane outer layer protein I (VOMI)
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This is the Wikipedia entry entitled "Vitelline membrane outer layer protein I (VMO-I)". More...
Vitelline membrane outer layer protein I (VMO-I) Edit Wikipedia article
VOMI | |||||||||
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![]() crystal structure of vitelline membrane outer layer protein i (vmo-i): a folding motif with homologous greek key structures related by an internal three-fold symmetry | |||||||||
Identifiers | |||||||||
Symbol | VOMI | ||||||||
Pfam | PF03762 | ||||||||
InterPro | IPR005515 | ||||||||
SCOP2 | 1vmo / SCOPe / SUPFAM | ||||||||
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In molecular biology, this entry refers to a protein domain called, the Vitelline membrane outer layer protein I (VMO-I). It is a structure found on the outside of an egg, in the vitelline membrane.
Function
The major role of the vitelline membrane is to prevent the mixing of the yolk and albumen and also act as an important anti-microbial barrier, as indicated by the high content of lysozyme in the outer layer [1] Vitelline membrane outer layer protein I (VMO-I) binds tightly to ovomucin fibrils, which construct the backboneof the outer layer membrane. VMO-I has considerable activity to synthesize N-acetylchito-oligosaccharide from N-acetylglucosamine hexasaccharides but no hydrolysis activity. VMO-I is composed of 163 aa[2]
Structure
The structure [3] consists of three beta-sheets forming Greek key motifs, which are related by an internal pseudo three-fold symmetry. Furthermore, the structure of VOMI has strong similarity to the structure of the delta-endotoxin, as well as a carbohydrate-binding site in the top region of the common fold.[4] VMO-I revealed a unique structure of the P-prism fold, a new type of multi-sheet assembly
References
- ^ Sricharoen S, Kim JJ, Tunkijjanukij S, Söderhäll I (2005). "Exocytosis and proteomic analysis of the vesicle content of granular hemocytes from a crayfish". Dev Comp Immunol. 29 (12): 1017–31. doi:10.1016/j.dci.2005.03.010. PMID 15975654.
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: CS1 maint: multiple names: authors list (link) - ^ Kido S, Doi Y, Kim F, Morishita E, Narita H, Kanaya S; et al. (1995). "Characterization of vitelline membrane outer layer protein I, VMO-I: amino acid sequence and structural stability". J Biochem. 117 (6): 1183–91. PMID 7490258.
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(help)CS1 maint: multiple names: authors list (link) - ^ Shimizu T, Vassylyev DG, Kido S, Doi Y, Morikawa K (1994). "Crystal structure of vitelline membrane outer layer protein I (VMO-I): a folding motif with homologous Greek key structures related by an internal three-fold symmetry". EMBO J. 13 (5): 1003–10. PMC 394907. PMID 8131734.
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ignored (help)CS1 maint: multiple names: authors list (link) - ^ Shimizu T, Morikawa K (1996). "The beta-prism: a new folding motif". Trends Biochem. Sci. 21 (1): 3–6. PMID 8848836.
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ignored (help)
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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.
Vitelline membrane outer layer protein I (VOMI) Provide feedback
VOMI binds tightly to ovomucin fibrils of the egg yolk membrane. The structure [1] that consists of three beta-sheets forming Greek key motifs, which are related by an internal pseudo three-fold symmetry. Furthermore, the structure of VOMI has strong similarity to the structure of the delta-endotoxin, as well as a carbohydrate-binding site in the top region of the common fold [2].
Literature references
-
Shimizu T, Vassylyev DG, Kido S, Doi Y, Morikawa K; , EMBO J 1994;13:1003-1010.: Crystal structure of vitelline membrane outer layer protein I (VMO-I): a folding motif with homologous Greek key structures related by an internal three-fold symmetry. PUBMED:8131734 EPMC:8131734
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Shimizu T, Morikawa K; , Trends Biochem Sci 1996;21:3-6.: The beta-prism: a new folding motif. PUBMED:8848836 EPMC:8848836
External database links
SCOP: | 1vmo |
This tab holds annotation information from the InterPro database.
InterPro entry IPR005515
Vitelline membrane outer layer protein I (VMO-I) is one of the proteins found in the outer layer of the vitelline membrane of eggs. VMO-I, lysozyme, and VMO-II are bound tightly to ovomucin fibrils of the egg yolk membrane. The structure of VMO-I [ PUBMED:8131734 ] consists of three beta-sheets forming Greek key motifs, which are related by an internal pseudo three-fold symmetry. It is a member of the beta-prism-fold family and the structure of VOM-I has strong similarity to the structure of the delta-endotoxin, as well as a carbohydrate-binding site in the top region of the common fold [ PUBMED:8848836 ]. VMO-I has been shown to synthesize N-acetylchito-oligosaccharides from N-acetylglucosamine.
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 Man_lectin (CL0568), which has the following description:
This familu of lectins has a beta-prism fold [1-2].
The clan contains the following 5 members:
Beta-prism_lec Endotoxin_M Endotoxin_mid Jacalin VOMIAlignments
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 (36) |
Full (815) |
Representative proteomes | UniProt (1519) |
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RP15 (241) |
RP35 (393) |
RP55 (702) |
RP75 (865) |
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HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (36) |
Full (815) |
Representative proteomes | UniProt (1519) |
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RP15 (241) |
RP35 (393) |
RP55 (702) |
RP75 (865) |
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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: | Pfam-B_3481 (release 7.0) |
Previous IDs: | none |
Type: | Repeat |
Sequence Ontology: | SO:0001068 |
Author: |
Finn RD |
Number in seed: | 36 |
Number in full: | 815 |
Average length of the domain: | 147.5 aa |
Average identity of full alignment: | 39 % |
Average coverage of the sequence by the domain: | 52.09 % |
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: | 167 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
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 VOMI domain has been found. There are 2 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.