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The Open Protein Structure Annotation Network
PDB Keyword
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3h8u

    Title Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3h8u Target Id 391713
    Molecular Characteristics
    Source Klebsiella pneumoniae subsp. pneumoniae mgh 78578
    Alias Ids TPS18376,YP_001338853.1, 2.60.120.10, 87439 Molecular Weight 13245.15 Da.
    Residues 124 Isoelectric Point 5.49
    Sequence mgvnmraetesrifsvdeyvrpsngepirsvvletndsvvvvwhahpgqeiashvhphgqdtwtvisge aeyhqgngivthlkagdiaiakpgqvhgamnsgpepfifvsvvapgnagfalaek
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.80 Rfree 0.196
    Matthews' coefficent 2.23 Rfactor 0.152
    Waters 209 Solvent Content 44.96

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3h8u

    Protein Summary

    This sequence matches Pfam family Cupin_2 PF07883, which has many structures.  The Cupin superamily is functionally very diverse [Ref].

     

     

     

    The fold arrangement of this dimeric structure is of no novelty since many (79) functionally related targets of the cupin family with the conserved beta barrel motif (Fig1.), have already been deposited in the Protein Data Bank (alone JCSG deposited in the last 2 years 2pfw, 1vj2, 2ozj, 3es1, 3ebr, 3es4, 3d82, 2nvn, all with unknown function). Exact composition of the MG7319A is: 3 antiparallel beta sheets, 2 beta hairpins, 5 beta bulges, 11 strands, 2 helices, 10 beta turns and 2 gamma turns, that includes in total 48.4% of Strands, shown below together with the 3D fold.

    Ligand Summary

     

    Results from DALI search

    No: Chain Z rmsd lali nres %id Description

    1: 1v70-A 16.4 1.6 104 105 22 MOLECULE: PROBABLE ANTIBIOTICS SYNTHESIS PROTEIN;

    3: 3eqe-A 14.1 2.8 115 156 17 MOLECULE: PUTATIVE CYSTEIN DEOXYGENASE;

    4: 2ilb-A 13.7 1.8 101 114 21 MOLECULE: TETRACENOMYCIN POLYKETIDE SYNTHESIS PROTEIN;

    5: 2oa2-A 13.3 2.2 102 132 18 MOLECULE: BH2720 PROTEIN;

     

     

     

    It is a very tightly bound dimer with a long N-terminal arm stretching over the dimeric partner continuing its beta sheet and closing the barrel cavity, as indicated on the Fig.1.

    Each domain has a HIS CLUSTER: 54,56,96 in the mouth of the beta-barrel, where in homolog structures a metal-binding site resists, all the HIS residues are labeled for one monomer in the Fig.2 with the red color. The typical 4 HIS metal-coordination found in cupins is not confirmed here, since no metal was found in this structure. Instead a three HIS's and ASP conformation like in SOD and Mn/Fe class of proteins, appears in this case.

     

     

     

    Sequence search vs existing PDB entries. Chains A, B found:

    40 matching sequences found by FASTA search

     

    PDB code E-value %-tage id Overlap Name

    1. 1o4t(A)0.032 28.80066Crystal structure of putative oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 a resolution

    2. 2.2vqa(A)0.079 30.80078Protein-folding location can regulate mn versus cu- or zn- binding. Crystal structure of mnca.

    3. 3.2pfw(A)0.09 28.100114Crystal structure of cupin 2 conserved barrel domain protein (yp_751781.1) from shewanella frigidimarina ncimb 400 at 1.90 a resolution

    4. 1v70(A)0.62 30.90068Crystal structure of probable antibiotics synthesis protein from thermus thermophilus hb8

    5. 5.2dct(A)0.62 30.90068Crystal structure of the tt1209 from thermus thermophilus hb8

     

     

    50 matching sequences found by BLAST search:

    Ref. no. E-value %-tage id Overlap Name

    1. A6TJ50_KLEP7100.000122A6TJ50 Putative uncharacterized protein OS=Klebsiella pneumoniae

    2. 2.A4VPS7_PSEU589.344122A4VPS7 Uncharacterized conserved protein, contains double-stranded

    3. 3.A6N8V6_9BACT83.761117A6N8V6 Cupin 2 OS=uncultured bacterium PE=4 SV=1

    4. 4.A4JV17_BURVG75.652115A4JV17 Cupin 2, conserved barrel domain protein OS=Burkholderia

    5. 5.A7MRB5_ENTS874.783115A7MRB5 Putative uncharacterized protein OS=Enterobacter sakazakii

    6.  

      Ligand-binding templates.
    7. 19 significant hits out of 98313 ligand-binding templates.
      1. 243.539 _CUc0024 1gqg Quercetin 2,3-dioxygenase in complex with the inhibitor diethyldithiocarbamate
        Het Group CU

      2. 235.094GOLc11101zx5The structure of a putative mannosephosphate isomerase from archaeoglobus fulgidus
        Het Group GOL

      3. 226.625 OXLc0029 1o4t Crystal structure of putative oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 a resolution
        Het Group OXL

      4. 216.984 _CUc0075 1s4c Yhch protein (hi0227) copper complex
        Het Group CU

      5. 214.594 _FEc0185 2d40 Crystal structure of z3393 from escherichia coli o157:h7
        Het Group FE

       

      DNA-binding templates.

      1 significant hit out of 2856 DNA-binding templates.

      1. 116.031c007801fjfStructure of the thermus thermophilus 30s ribosomal subunit
        DNA-binding template (44 of 96 from 1fjf)

      2. CHARGE - distribution (as Chimera UCSF with charges calculated by Delphi) attached in Fig. 3).

    Reviews

    References

     

    1. (No Results)

       


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