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The Open Protein Structure Annotation Network
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3poh

    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
    Ligands
    Metals

    Jmol

     
    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):

    Fig1.png

    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.

    Fig2.png

    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

    Reviews

    References

     

    No references found.

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    413.21 kB01:31, 19 Nov 2010debanuActions
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    511.16 kB02:01, 19 Nov 2010debanuActions
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