Summary: Flavivirus non-structural protein NS2B
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Flavivirus non-structural protein NS2B Provide feedback
Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex.
Literature references
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Stocks CE, Lobigs M; , J Virol 1998;72:2141-2149.: Signal peptidase cleavage at the flavivirus C-prM junction: dependence on the viral NS2B-3 protease for efficient processing requires determinants in C, the signal peptide, and prM. PUBMED:9499070 EPMC:9499070
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Yamshchikov VF, Compans RW; , J Virol 1995;69:1995-2003.: Formation of the flavivirus envelope: role of the viral NS2B-NS3 protease. PUBMED:7884844 EPMC:7884844
This tab holds annotation information from the InterPro database.
InterPro entry IPR000487
Pathogenic members of the flavivirus family [E1], including West Nile Virus (WNV) and Dengue Virus (DV), are growing global threats for which there are no specific treatments. The genome encodes three structural proteins found in the mature virion (C, prM, and E) and seven "nonstructural" (i.e., not part of the virion architecture) proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5). Full-length NS3 is a bifunctional protein. The N-terminal 175 residues comprise a chymotrypsin-like protease, "NS3pro", while the C-terminal portion is a helicase ("NS3hel"). The NS2B protein, which is located in the polypeptide precursor immediately upstream of the NS3pro domain, functions as the cofactor for NS3pro. A 35-48 residue central portion is required for protease activity in vitro, while N- and C-terminal flanking hydrophobic regions are predicted to anchor the NS2B-NS3 complex into the host endoplasmic reticulum membrane. The two component flaviviral enzyme NS2B-NS3 cleaves the viral polyprotein precursor within the host cell, a process that is required for viral replication [ PUBMED:17400917 , PUBMED:19693793 , PUBMED:20042502 ]. The NS3pro domain forms peptidase family S7 (flavivirin family) of clan PA [E2].
The NS3pro has a classical serine protease catalytic triad (His, Asp, and Ser). The enzymatic activity of NS3pro is enhanced by interacting with the central 40 amino acid of NS2B which acts as an essential cofactor. The NS3pro domain has an overall structure of two barrels made of six beta sheets each, with the active site located in the cleft between the barrels. The NS2B hydrophilic core cofactor contributes one of the N-terminal beta sheets [ PUBMED:17400917 , PUBMED:19693793 , PUBMED:20042502 ].
This entry represents a domain cover the entire flavivirus NS2B and NS3pro domains.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | virion component (GO:0044423) |
Molecular function | serine-type endopeptidase activity (GO:0004252) |
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.
Seed (2) |
Full (4) |
Representative proteomes | UniProt (10365) |
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RP15 (3) |
RP35 (4) |
RP55 (4) |
RP75 (4) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (2) |
Full (4) |
Representative proteomes | UniProt (10365) |
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RP15 (3) |
RP35 (4) |
RP55 (4) |
RP75 (4) |
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Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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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
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Curation
Seed source: | Pfam-B_156 (release 3.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Finn RD |
Number in seed: | 2 |
Number in full: | 4 |
Average length of the domain: | 126.8 aa |
Average identity of full alignment: | 38 % |
Average coverage of the sequence by the domain: | 4.76 % |
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: | 127 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
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 Flavi_NS2B domain has been found. There are 107 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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