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The Open Protein Structure Annotation Network
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2qj8

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

    Title Crystal structure of uncharacterized protein mlr6093 (NP_106651.1) from Mesorhizobium loti at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 2qj8 Target Id 375129
    Molecular Characteristics
    Source Mesorhizobium loti maff303099
    Alias Ids TPS1649,NP_106651.1, 3.40.630.10, 104002 Molecular Weight 35653.82 Da.
    Residues 331 Isoelectric Point 5.78
    Sequence mseaphltfdldtpgvstghlvvpkgadcealslpvfscnrgegpsllitggnhgnelqgpilarrlvk wlpeaqrcgriiivpeinplavqawtrntpidgknlnrvfpgrsdgsvseriadaisrlllpvvdtvld lhsfgptwdcapsiishpiadidqmtktvsiskafklpvtllwehnetdgmfdtlvhrqgktfictefg ggvvsaealtiyeagvrnglialglvkgkaeyptfrqqktgqtlettssdqlkspspgifeprcsvmde veqgdvvgvlhpmgslsaasidiraqskstvfairsamyvqgneevailarplar
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.254
    Matthews' coefficent 2.29 Rfactor 0.207
    Waters 282 Solvent Content 46.30

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2qj8
    1. FAMSD: A Powerful Protein Modeling Platform that Combines Alignment Methods, Homology Modeling, 3D Structure Quality Estimation and Molecular
    K Kanou, M Iwadate, T Hirata, G Terashi - Chemical & , 2009 - bioinf.jku.at
     
    2. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     

    Protein Summary

    The mlr6093 gene (PF04952, cl11393, cd06252) from Mesorhizobium loti encodes for a putative succinylglutamate desuccinylase (EC:3.5.1.96), a metallocarboxypeptidase involved in the catabolism of arginine. Mutations in this family are known to cause Canavan disease, a neurodegenerative disorder. A possible functional linkage (score 0.75), based on co-ocurrence, is found with a probable dipeptidase (mlr7141).

    The 2qj8 structure is quite complex and a single chain could be broken into two domains, one alpha/beta/alpha sandwich and the other a pure beta structure. At the time of writing, neither SCOP nor CATH has characterized this protein structure. Similar structures determined by the PSI are PDB:3cdx (see topsan),  PDB:3fmc (see topsan), and PDB:3na6 (see topsan). DALI top hits for 2qj8 are with PDB:3cdx (Z-scr=35), PDB:3fmc (Z-scr=24) and PDB:2bco (Z-scr=19, 21% seq. identity), all putative succinylglutamate desuccinylases. Comparing the Zn2+ binding sites of 2bco and another structurally related protein, PDB:1yw4, shows that this must be accomplished by residues His-54, Glu-57, and His-140 in 2qj8, even though there is no zinc ion present at this location. In this model, the side-chains of these three residues would need to reorientate significantly, resulting in different rotamers and possible changes of the binding loop backbone.

    Ligand Summary


    References

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    References

     

    No references found.

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