Summary: Polysaccharide lyase family 4, domain II
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Polysaccharide lyase family 4, domain II Provide feedback
FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognises and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits .
McDonough MA, Kadirvelraj R, Harris P, Poulsen JC, Larsen S; , FEBS Lett. 2004;565:188-194.: Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4. PUBMED:15135077 EPMC:15135077
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR029413
This entry represents domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognises and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits [PUBMED:15135077].
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This clan unifies several SCOP superfamilies that all share a 7 stranded beta sandwich fold.
The clan contains the following 18 members:Antigen_C CarbopepD_reg_2 CarboxypepD_reg Cna_B Dioxygenase_C DUF1416 DUF2012 DUF2606 DUF3823 DUF3869 FctA fn3_3 GramPos_pilinBB GramPos_pilinD3 PEGA phage_tail_N Transthyretin TTR-52
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Curation and family details
|Number in seed:||51|
|Number in full:||743|
|Average length of the domain:||90.30 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||15.51 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 fn3_3 domain has been found. There are 5 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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