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2  structures 36  species 0  interactions 56  sequences 1  architecture

Family: OpcA (PF07239)

Summary: Outer membrane protein OpcA

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This is the Wikipedia entry entitled "Outer membrane protein OpcA". More...

Outer membrane protein OpcA Edit Wikipedia article

Outer membrane protein OpcA
1k24.gif
Identifiers
Symbol OpcA
Pfam PF07239
InterPro IPR009876
SCOP 1k24
SUPERFAMILY 1k24
OPM superfamily 271
OPM protein 1k24

Outer membrane adhesin OpcA protein family consists of several Neisseria species specific outer membrane proteins. Neisseria meningitidis causes meningococcal meningitis and septicemia. Opc (formerly called 5C) is one of the major outer membrane proteins and has been shown to play an important role in meningococcal adhesion and invasion of epithelial and endothelial cells, mediating attachment to host cells by binding proteoglycan cell-surface receptors.[1]

OpcA forms a 10-stranded beta-barrel with five highly mobile extracellular loops that protrude above the surface of the membrane.[2] These extracellular loops combine to form a crevice in the external surface that is lined by positively charged residues, which is predicted to be a binding site for proteoglycan polysaccharides involved in pathogenesis. Conformational changes in the extracellular loops modulate the surface of OpcA, which could affect the proteoglycan binding site.[3] These conformational changes could also lead to pore opening.

[edit] References

  1. ^ Zhu P, Klutch MJ, Derrick JP, Prince SM, Tsang RS, Tsai CM (2003). "Identification of opcA gene in Neisseria polysaccharea: interspecies diversity of Opc protein family". Gene 307: 31–40. doi:10.1016/S0378-1119(02)01208-8. PMID 12706886.
  2. ^ Derrick JP, Prince SM, Achtman M (2002). "Crystal structure of the OpcA integral membrane adhesin from Neisseria meningitidis". Proc. Natl. Acad. Sci. U.S.A. 99 (6): 3417–21. doi:10.1073/pnas.062630899. PMC 122538. PMID 11891340. //www.ncbi.nlm.nih.gov/pmc/articles/PMC122538/.
  3. ^ Sansom MS, Derrick JP, Bond PJ (2007). "Membrane Simulations of OpcA: Gating in the Loops?". Biophys. J. 92 (2): L23–5. doi:10.1529/biophysj.106.097311. PMC 1751375. PMID 17114231. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1751375/.

This article incorporates text from the public domain Pfam and InterPro IPR009876

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.

Outer membrane protein OpcA Provide feedback

This family consists of several Neisseria species specific OpcA outer membrane proteins. Opc (formerly called 5C) is one of the major outer membrane proteins and has been shown to play an important role in meningococcal adhesion and invasion of both epithelial and endothelial cells [1].

Literature references

  1. Zhu P, Klutch MJ, Derrick JP, Prince SM, Tsang RS, Tsai CM; , Gene 2003;307:31-40.: Identification of opcA gene in Neisseria polysaccharea: interspecies diversity of Opc protein family. PUBMED:12706886 EPMC:12706886


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009876

This entry represents several Neisseria species-specific OpcA-type outer membrane adhesion proteins. OpcA (formerly called 5C) was isolated from Neisseria meningitidis, causative agent of meningococcal meningitis and septicemia. An outer membrane protein embedded in the lipid bilayer, OpcA was shown to play an important role in meningococcal adhesion and invasion of both epithelial and endothelial cells, mediating attachment to host cells by binding proteoglycan cell-surface receptors [PUBMED:12706886]. OpcA forms a 10-stranded beta-barrel with five highly mobile extracellular loops that protrude above the surface of the membrane [PUBMED:11891340]. These extracellular loops combine to form a crevice in the external surface that is lined by positively charged residues, which is predicted to be a binding site for proteoglycan polysaccharides involved in pathogenesis. Conformational changes in the extracellular loops modulate the surface of OpcA, which could affect the proteoglycan binding site [PUBMED:17114231]. These conformational changes could also lead to pore opening.

Domain organisation

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Alignments

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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.

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  Seed
(2)
Full
(56)
Representative proteomes NCBI
(42)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(1)
RP75
(2)
Alignment:
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  Seed
(2)
Full
(56)
Representative proteomes NCBI
(42)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(1)
RP75
(2)
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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.

Pfam alignments:

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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_17433 (release 10.0)
Previous IDs: none
Type: Family
Author: Moxon SJ
Number in seed: 2
Number in full: 56
Average length of the domain: 202.30 aa
Average identity of full alignment: 53 %
Average coverage of the sequence by the domain: 89.45 %

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 25.2 25.0
Noise cut-off 23.9 24.9
Model length: 244
Family (HMM) version: 6
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 OpcA 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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