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The Open Protein Structure Annotation Network
PDB Keyword
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4ogz

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of a putative alpha-galactosidase/melibiase (BF4189) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 4ogz Target Id 418282
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS82509,YP_213754.1, 326686 Molecular Weight 52528.11 Da.
    Residues 472 Isoelectric Point 5.33
    Sequence sevrtaifegkpcinpphvvgnypatpflfyiptsgerpikwhaenlpkglkldketgiikgkvvekgt ykvmlkaenalgtdtqellinigdellltppmgwnswntfgrhlteelllqtadamvengmrdlgyayi niddfwqlpergadghiqidktkfprgikyvadylhergfklgiysdaadktcggvcgsygyeeidard faswgvdllkydycnapagrveameryekmgralratdrsivfsicewgqrepwkwakkvgghlwrvsg digdlwnrstdekgglrgilnileinaplseyarpggwndpdmlvvgiggksksigyesegctneqyqs hfalwcmmaspllcgndvrqmndstlqillnkdliainqdplgiqaerairadhydvwvkplsdgskai aclnrisgpvdvelnvktveglsldrvydviegslvaeastgwvvklapgeckvfick
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.00 Rfree 0.2006
    Matthews' coefficent 2.07 Rfactor 0.1692
    Waters 464 Solvent Content 40.44

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Shown below is a ribbons representation of the structure of target id 418282 color coded with the N-terminal end in blue and the C-terminal end in red.

    SP3088D_monomer.png

     

     

     

     


    A search of the Pfam database using the sequence of target id 418282 shows that the sequence is associated with two Pfam entries. The structure is composed of residues 25-496. Residues 12-40 (mostly missing from the structure) can be classified in the He_PIG_assoc (PF10632) Pfam family. This domain has been named NEW1 but its actual function is not known. It is found on proteins which are bacterial galactosidases.  The domain is associated with the He_PIG family, PF05345 a putative Ig-containing domain. The second Pfam domain belongs to the Melibiase (PF02065) Pfam family, usually associated with glycoside hydrolaxses.  Analysis of the structures shows that it is composed of three domains. Starting at the N-terminal and C-terminal ends respectively, residues 35-115 and residues  415-496 are Ig-like domains.  The largest domain, residues 120-409 shows a TIM beta/alpha-barrel fold and the (trans)glycosidase Superfamily, and the Amylase catalytic domain family.

    The structure of target id 418212 shows dozens of significant DALI hits. The top-scoring DALI hit is PDB id 1uas, rice alpha-galactosidase [Ref] (DALI Z-score 50.7, alignment length 355, rmsd=1.5 Angstroms, seq id.=41%). The structure is similar to other JCSG targets including PDB ID 3cc1 and target id 419777 (DALI Z-score 301., rmsd=2.3 Angstroms, length of alignment=331, %seq id=25%). Shown below is a superpositioning of the structures of target id 418282 (green) and PDB id 3cc1 (cyan)

     

    3cc1_superposition.png

     

    Compared with PDB ID 3cc1, target id 418212 shows an extra N-terminal Ig-like domain.

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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