The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of an endo-beta-N-acetylglucosaminidase (BT_3987) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.55 A resolution. To be published
    Site JCSG
    PDB Id 3poh Target Id 417165
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS58820,NP_812898.1, 324621 Molecular Weight 49091.34 Da.
    Residues 450 Isoelectric Point 4.72
    Sequence ddlevgknidesaysgiyennaylrdgksnlvskvvelhgetyattvkmglsktpntatsakvkidaay letynkahntdfalypqdlvtfanegiltvnantksaevemtirageglqedktyaipvaisdqssdit ikdedakhciylvkdmrnagdaykgegvmqgylffevndvnplntlsfqlengkllwdvvvlfaaniny daeagrprvqcnpnvqylldnnetllqplrrrgvkvllgllgnhditglaqlseqgakdfarevaqyck aynldgvnyddeysnspdlsnpsltnpstaaaarlcyetkqampdklvtvfdwgqmygvatvdgvdake widivvanygsaaypigqmtkkqcsgismefnlggggslsaskaqsmidggygwfmgfapspakygsvf srlqgggevlygsnvaaptifykkndptpykypddl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.55 Rfree 0.1636
    Matthews' coefficent 2.16 Rfactor 0.1361
    Waters 643 Solvent Content 42.98

    Ligand Information


    Google Scholar output for 3poh
    1. High Resolution Crystal Structure of the Endo-N-Acetyl-_-D-Glucosaminidase Responsible for the Deglycosylation of Hypocrea jecorina Cellulases
    I Stals, S Karkehabadi, S Kim, M Ward - PloS one, 2012 - dx.plos.org

    Protein Summary

    This target is annotated as endo-beta-N-acetylglucosaminidase F1 precursor belonging to Pfam PF08522 comprised of domain of unknown function, DUF1735.This protein has the UniProt id Q8A0N4 (Q8A0N4_BACTN). Some information about putative function (carbohydrate metabolism) can be found on the UniProt page. It has an N-terminal signal peptide (Phobius prediction) and so it a secreted protein.

    According to Pfam, the DUF1735 domain is found only in bacteria, specifically, only in bacteroidetes, and is present in ~150 proteins in 9 architectures. The protein also has a domain from the glycosyl hydrolases family 18, Pfam PF00704.

    The protein is present as a monomer in the crystal structure and a ribbon representation is shown below (colored in blue to red from the N- to C-terminus):


    According to FFAS, this protein has ~40% sequence identity and ~28% seq id over ~50% of the length to the endo-beta-N-acetylglucosaminidase F1(PDB 2ebn) and endo-beta-N-acetylglucosaminidase H (PDB 1edt), respectively.

    A superimpostion of the structure of this protein (red, below) with that of the 2ebn (cyan) and 1edt (white) illustrates the unique portion of this protein, which is the N-terminal DUF1735 domain from residues 42-185, after which the glycosyl hyrdolase family 18 domain (probably involved in breaking bonds between carbohydrates) starts.


    Maybe the N-terminal DUF1735 could be involved in recognition of the carbohydrates on which the glycosyl hydrolase acts.

    A search for other proteins of structure similar to the N-terminal 42-185 residues of this proteins using DALI results in the 3 top hits with other JCSG structures classified in the DUF1735 Pfam family, probably due to the presence of this domain. They have PDB ids 3p02, 3nqk and 3n91 (Z-scores > 10.0 and r.m.s.d ~3 A). The next hits with Z-scores > 8.0 are with some sodium/calcium exchange proteins (PDB ids 3ead, 3e9t, etc.) and with integrin beta-4 (PDB ids 3h6a, 3fso, etc.).

    Ligand Summary




    No references found.

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