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 putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3etn Target Id 391616
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS14638,YP_209877.1,, 85666 Molecular Weight 21809.05 Da.
    Residues 201 Isoelectric Point 5.97
    Sequence miesiqellqkeaqavlnipvtdayekaveliveqihrkkgklvtsgmgkagqiamniattfcstgips vflhpseaqhgdlgilqendllllisnsgktreiveltqlahnlnpglkfivitgnpdsplasesdvcl stghpaevctlgmtpttsttvmtvigdilvvqtmkrteftieeyskrhhggylgeksrklcvk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.70 Rfree 0.197
    Matthews' coefficent 2.04 Rfactor 0.172
    Waters 728 Solvent Content 39.80

    Ligand Information


    Google Scholar output for 3etn
    1. Structure prediction and functional analysis of KdsD, an enzyme involved in lipopolysaccharide biosynthesis
    S Sommaruga, LD Gioia, P Tortora, A Polissi - Biochemical and biophysical , 2009 - Elsevier
    2. Probing the active site of the sugar isomerase domain from E. coli arabinose_5_phosphate isomerase via X_ray crystallography
    LJ Gourlay, S Sommaruga, M Nardini - Protein , 2010 - Wiley Online Library
    3. A unique arabinose 5-phosphate isomerase found within a genomic island associated with the uropathogenicity of Escherichia coli CFT073
    JA Mosberg, A Yep, TC Meredith, S Smith - Journal of , 2011 - Am Soc Microbiol

    Protein Summary

    The sequence of this protein matches SIS domain of PFAM family PF01380 (http://pfam.sanger.ac.uk/family?acc=PF01380). The SIS domain seems to have a common function in phopshosugar isomerization (Bateman 1999). The structure of 391616 matches closely to 1vim (Z=20.7 rmsd 2.7A for 177 Ca with seqid 23%), 1m3s, 1jeo, 2i2w, 1x94, 1viv, 3bjz etc, most of them structural genomics targets.  The biological relevant oligomer is likely tetramer, as observed in the asymmetric unit. This is consistent with the active site arrangement since the C-terminus is required for forming the active site of a neighbour promoter. A CMK (cmp-2-keto-3-deoxy-octulosonic acid) molecule is present in the  active site of 391616, the CMK is idenitified by unambiguous density. The CMK appears to be an inhibitor of 391616 (?). It is similar to Leptospira interrogans polysialic acid capsule expression protein KpsF.

     Figure 1. CMK in experimental density (density modified, 1.5 sigma)




    Bateman A; , Trends Biochem Sci 1999;24:94-95.: The SIS domain: a phosphosugar-binding domain. PUBMED:10203754

    Teplyakov A, Obmolova G, Badet-Denisot MA, Badet B, Polikarpov I; , Structure 1998;6:1047-1055.: Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain. PUBMED:9739095


    Martinez-Cruz, L.A.,  Dreyer, M.K.,  Boisvert, D.C.,  Yokota, H.,  Martinez-Chantar, M.L.,  Kim, R.,  Kim, S.H. (2002) Crystal structure of MJ1247 protein from M. jannaschii at 2.0 A resolution infers a molecular function of 3-hexulose-6-phosphate isomerase. Structure 10: 195-204


    Ligand Summary

    An CMK (cmp-2-keto-3-deoxy-octulosonic acid) is present in the active site, likely an inhibitor




    No references found.

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    CMK with experimental density
    1020.79 kB16:58, 8 Oct 2008qxuActions
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