The Open Protein Structure Annotation Network
PDB Keyword


    Table of contents
    1. 1. Topsan Members
    2. 2. Summary

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    Topsan Members

    Tag pages as 'PF01936' to appear in this list.

    Name Annotation Author(s)


    Pfam family PFAM:PF01936 {Protein of unknown function DUF88} with 678 members in NR database and additional 379 members in the metagenomic datasets is represented in Archaea, and Bacteria. Its HMM logo provides evidence of the conservation of 6 Asp residues along the sequence, indicative of a putative metal binding site.

    The first structural representative solved (PDB Id: TOPSAN:2qip) was subject to FATCAT structural similarity search that indicated similarity to SCOP (v. 1.73) domain SCOP:d1xo1a2 classified as PIN domain-like fold. A HHpred search with 2qip reports a weak hit (P-val=2e-5) with T5 phage 5'-exonuclease 1exn that contains a N-terminal PIN domain-like fold. The same search in DALI gives only weak hits (Z=8) with the exonuclease 1exn, the exodeoxyribonuclease 1ut8 and the Taq polymerase 1tau, all showing the PIN fold. Based on marginal prediction from FFAS confirmed by structural similarity, one can argue that this family is remotely homologous to other families with this fold.

    Based on existing annotations narrowed by structural similarity, one can hypothesize that this family binds nucleic acids or is involved in signaling [Ref].




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