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The Open Protein Structure Annotation Network
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3m7a

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

    Title Crystal structure of Saro_0823 (YP_496102.1) a protein of unknown function from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.22 A resolution. To be Published
    Site JCSG
    PDB Id 3m7a Target Id 396342
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS25903,SARO_25NOV03_CONTIG30_REVISED_GENE3122, PF02643, 327660 Molecular Weight 14819.28 Da.
    Residues 139 Isoelectric Point 5.66
    Sequence gtktaaeaaapavhpvsglqivpvtvtgtsgrhvfrselartsaeqakglmfrtelgdeegmiflrnpp dmatfwmrntvipldiifvgldrrvmniaanavpydetplpaagptlavleingglaarlgikpgdkvew
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.22 Rfree 0.148
    Matthews' coefficent 2.05 Rfactor 0.117
    Waters 477 Solvent Content 39.91

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Gene Saro_0823 from Novosphingobium aromaticivorans dsm 12444 translates into the YP_496102 protein, a member of the DUF192 group (PF02643), a very large (>500 homologs) family of mostly bacterial proteins, but also with homologs in several Plasmodium species. Saro_0823 is a homolog of Thermotoga maritima TM1668. The homolog in Caulobacter crescentus (CC1388) is associated with CspD, a cold shock protein (CC1387). However, the genomic context of Saro_0823 is most conserved with a putative xylose isomerase, suggesting a possible role in extracellular sugar processing. Saro_0821 is annotated as an AMP-dependent synthetase and ligase.

    3m7a structure corresponds to the C-terminal (27-165) fragment of the YP_496102 protein. It is structurally rather unique as the best hit from Dali have a Z-score of  3.8 (1nt0, 2j1t, 3kq4) and it is a likely candidate for a new fold. Interestingly, many of the top Dali hits are involved in sugar metabolism. There are no obvious active site like cavities on the protein surface of 3m7a.

     

    Note: The NCBI sequence (gi|87198845) seems to be shorter than JCSG PSCA sequence, which came from a preliminary assembly.  There is a similar structure solved by JCSG.

     

    Fig. 1 monomer of 3m7a

    PX1668C.png

    Fig. 2 surface conservation in 3m7a structure

    active-site-pX1668C.png 

    Fig. 3 sequence alignment of top blast hits fpr Saro_0823 amino acid sequence

    PX1668C-aline.png

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (3)

    FileSizeDateAttached by 
     active-site-pX1668C.png
    active site of PX1668C
    118.89 kB23:01, 17 Feb 2010qxuActions
    PX1668C-aline.png
    sequence alignment of PX1668C
    456.2 kB22:57, 17 Feb 2010qxuActions
     PX1668C.png
    monomer of PX1668C
    88.09 kB22:21, 17 Feb 2010qxuActions
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