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2  structures 63  species 1  interaction 120  sequences 5  architectures

Family: VOMI (PF03762)

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
PDB 1vmo EBI.jpg
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
SCOP 1vmo
SUPERFAMILY 1vmo

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 backbone of 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

  1. ^ 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. 
  2. ^ 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. 
  3. ^ Shimizu T, Vassylyev DG, Kido S, Doi Y, Morikawa K (March 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. 
  4. ^ Shimizu T, Morikawa K (January 1996). "The beta-prism: a new folding motif". Trends Biochem. Sci. 21 (1): 3–6. doi:10.1016/s0968-0004(06)80018-6. PMID 8848836. 

This article incorporates text from the public domain Pfam and InterPro IPR005515

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.

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

  1. 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

  2. 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

This tab holds annotation information from the InterPro database.

InterPro entry IPR005515

VOMI binds tightly to ovomucin fibrils of the egg yolk membrane. The structure [PUBMED:8131734] 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 [PUBMED:8848836].

Gene Ontology

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Domain organisation

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Alignments

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Full
(120)
Representative proteomes NCBI
(127)
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(37)
RP35
(43)
RP55
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RP75
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  Seed
(22)
Full
(120)
Representative proteomes NCBI
(127)
Meta
(1)
RP15
(37)
RP35
(43)
RP55
(60)
RP75
(78)
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  Seed
(22)
Full
(120)
Representative proteomes NCBI
(127)
Meta
(1)
RP15
(37)
RP35
(43)
RP55
(60)
RP75
(78)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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.

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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: Pfam-B_3481 (release 7.0)
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 22
Number in full: 120
Average length of the domain: 149.20 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 64.05 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.5 25.5
Noise cut-off 23.6 23.9
Model length: 176
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

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VOMI

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 seqence.

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