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3fkj

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

    Title Crystal structure of putative phosphosugar isomerase (NP_459564.1) from SALMONELLA TYPHIMURIUM LT2 at 2.12 A resolution. To be published
    Site JCSG
    PDB Id 3fkj Target Id 391508
    Molecular Characteristics
    Source Salmonella typhimurium lt2
    Alias Ids TPS20899,NP_459564.1, 3.40.50.10490, 384243 Molecular Weight 36725.60 Da.
    Residues 328 Isoelectric Point 5.33
    Sequence msvahenarriisdilgkqniervwfvgcggsltgfwpgkyfldceasklavgyitsnefvhatpkalg knsvvilasqqgntaetvaaarvarekgaatiglvyqpdtplceysdyiieyqwarypetvdpaqqkaa yslwlaleilaqtegyaqydelvsafgrfsdvvhgaqrqvqedaqrfaaewkdekvvymmgsgpsfgaa hqesicillemqwinsasihsgeyfhgpfeitepgtpfillqssgrtrplddrairfieryqgklqlid adklgiqdlstdvgeyfcgllhncvldvynlalatarnhplttrrymwkvey
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.12 Rfree 0.212
    Matthews' coefficent 2.21 Rfactor 0.165
    Waters 316 Solvent Content 44.45

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fkj
    1. Exchanging a single amino acid residue generates or weakens a+ 2 cellooligosaccharide binding subsite in rice _-glucosidases
    S Sansenya, J Maneesan, JR Ketudat Cairns - Carbohydrate Research, 2012 - Elsevier
     

    Protein Summary

    Gene STM_0572 from Salmonella typhimurium lt2 encodes the NP_459564 protein that contains a tandem repeat of the SIS domain (PF01380).  Genome context analysis using the STRING server predicsts that STM_0572 is functionally associated with enzymes from fructose and mannose metabolism.

    Pre-SCOP classifies 3fkj in the alpha/beta class, SIS domain superfamily, double SIS domain family (PFAM PF01380.15 SIS CL0067). 3fkj structure is similar to jcsg structure 3eua (seq id 38%, rmsd 1.3A for 319 aligned Ca atoms; Dali Z=45). The active site residues are conserved between these two proteins, thus most likely they share the same function as sugar isomerases.

    Significant structural similarity is also found with a glucosamine 6-phosphate synthase (GlmS) with bound ligand alpha-D-glucose-6-phosphate (G6P), PDB:1mor [Ref]. Structure comparison with TopMatch (273 equivalent residues, 2.15Å rmsd, 19% sequence identity) of the two protein chains reveals a highly conserved phosphate binding loop consisting of equivalent residues Ser-32/303, Ser-78/347, Gln-79/348 and further high conservation up to residue Gly-97/366 (3fkj/1mor). Furthermore, residues believed to be catalytic in 1mor (Lys-603, a Schiff base;  His-504, the ring-opening step; Glu-488, the proton transfer from C1 to C2 of the substrate G6P) are conserved. On the other hand, a distinct C-terminal motif for GlmS, DXPXXLAK[SC]VT, is not found in 3fkj.

    Figure 1. Dimeric crystal structure of 3fkj

    mg10938d-dimer.png

    Figure 2. 3fkj dimer structure (red) superimposed to 3eua (cyan)

    dimer-vs-3eua.png

    Figure 3. The putative active site of 3fkj is defined by a deep groove near the dimer interface

    mg10938d.png

    Ligand Summary

    Reviews

    References

     

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    Files (3)

    FileSizeDateAttached by 
     dimer-vs-3eua.png
    dimer (red) comparison with vs 3eua
    178.47 kB23:41, 4 Dec 2008qxuActions
     mg10938d-dimer.png
    dimer of 391508
    166.29 kB23:25, 4 Dec 2008qxuActions
     mg10938d.png
    active site of 391508
    202.01 kB23:47, 4 Dec 2008qxuActions
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