Summary: Zc3h12a-like Ribonuclease NYN domain
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Zc3h12a-like Ribonuclease NYN domain Provide feedback
This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes . It has been suggested that this domain belongs to the PIN domain superfamily . This domain has also been identified as part of the NYN domain family .
Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S;, Nature;458:1185-1190.: Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. PUBMED:19322177 EPMC:19322177
This tab holds annotation information from the InterPro database.
InterPro entry IPR021869
This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes [PUBMED:19322177]. It has been suggested that this domain belongs to the PIN domain superfamily [PUBMED:19322177]. This domain has also been identified as part of the NYN domain family [PUBMED:17114934].
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This superfamily contains a variety of nuclease enzymes, including PIN domains and the FLAP exonucleases.
The clan contains the following 18 members:5_3_exonuc_N DUF188 DUF4411 Fcf1 Mut7-C NYN NYN_YacP PIN PIN_2 PIN_3 PIN_4 PIN_5 PIN_6 PRORP RNase_Zc3h12a RNase_Zc3h12a_2 XPG_N XRN_N
We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Number in seed:||21|
|Number in full:||805|
|Average length of the domain:||146.50 aa|
|Average identity of full alignment:||38 %|
|Average coverage of the sequence by the domain:||22.37 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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There is 1 interaction 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 RNase_Zc3h12a domain has been found. There are 6 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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