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3k6q

    Title Crystal structure of Putative ligand binding protein (YP_753395.1) from Syntrophomonas wolfei str. Goettingen at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3k6q Target Id 391895
    Molecular Characteristics
    Source Syntrophomonas wolfei subsp. wolfei
    Alias Ids TPS26535,YP_753395.1, 325515 Molecular Weight 16044.48 Da.
    Residues 138 Isoelectric Point 4.71
    Sequence mqtinateirnnfsyyidtvvrdkpiavkrnrdvllffseqiikdllqdlkihaelskedgiiigtidg fdlvvsgeseqeviqklaedlleyaqdymndfklfynapnrkthypyilkvllssnidevkgyiyaemv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.80 Rfree 0.249
    Matthews' coefficent 2.07 Rfactor 0.193
    Waters 332 Solvent Content 40.51

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3k6q

    Protein Summary

    Gene Swol_0700 from Syntrophomonas wolfei encodes the YP_753395.1 protein. The first 32 residues show remote homology (e-val=3e-6) to the 90 residue long PFAM family PhdYeFM PF02604, the antitoxin part of the bacterial toxin/antitoxin "addiction module". The structure of this 32 residues N-terminal fragment belongs to the SCOP (super)family YefM-like; the C-terminal part (49-88) to the TTHA1013-like (super)family. HHpred and SSM match the N-terminal 1-31 residues (e-value 2.3e-5; 43% of SSE) with the N-terminal region of the antitoxin yefM (2a6q_A). However, Dali matches the same N-terminal region with a very low Z-score of 3.7. Dali matches the C-terminal region (Z=5) with the TTHA1013 protein.

     

    The 3k6q monomer structure is shown below.

     FR15089A.png

    The protein most likely assembles as a dimer, with a "swap" of the N-terminal domains as shown in two views below.

    FR15089A_dim1.pngFR15089A_dim2.png

    There is only one significant, yet weak, match in a DALI search using 3k6q as query:

    DALI Structural Similarities
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 1wv8 5.4 2.1 59 71 15 HYPOTHETICAL PROTEIN TTHA1013

     

    A superposition of 1wv8 protein on 3k6q shows that the overlap is limited to a part of the C-terminal domain.

    FR15089A_1wv82.png

    3k6q (green), 1wv8 (magenta).

     

    Note from PFAM:

    This was an interesting one, as it did not build well as a whole, and shows homology to different clans at the two ends, as indicated both by the TOPSAN info and the overlaps that I got to start with but then lost on trimming back the N-term. I have built it as a C-terminal DUF, but I might go back and see if I can't rebuild just the N-term, hoping that it is not just a signal peptide - it does not look like one. This is a family of proteins from bacteria and archaea of unknwon function. The N-terminal part of the structure from Swiss:Q0AZ30 shows remote homology to the N-terminus of the bacterial toxin/antitoxin 'addiction module', and the C-terminus is distantly related to the TTHA1013/TTHA0281 superfamily. In which case the second family will be RelB_N, as it will overlap with the antitoxin-toxin stability system:
    ID RelB_N
    AC PF12910
    DE Antitoxin of toxin-antitoxin stability system N-terminal
    AU Coggill P
    SE JCSG_target_391895_3k6q
    GA 20.90 20.90;
    TC 20.90 20.90;
    NC 20.80 20.80;
    BM hmmbuild --amino -o /dev/null HMM SEED
    SM hmmsearch -Z 9421015 -E 1000 --cpu 4 HMM pfamseq
    TP Domain
    CL CL0136

    RN [1] RM 14659018 RT New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. RA Anantharaman V, Aravind L; RL Genome Biol. 2003;4:R81.

    RN [2] RM 15864262 RT Prokaryotic toxin-antitoxin stress response loci. RA Gerdes K, Christensen SK, Lobner-Olesen A; RL Nat Rev Microbiol. 2005;3:371-382.

    This domain appears to be the N-terminus of the RelB antitoxin of toxin-antitoxin stability system or prevent-host death system. Together RelE toxin and the RelB antitoxin form a non-toxic complex. Although toxin-antitoxin gene cassettes were first found in plasmids, it is clear that these loci are abundant in free-living prokaryotes, including many pathogenic bacteria, and these toxin-antitoxin loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress [1,2].

    Literature references
    1. Anantharaman V, Aravind L; , Genome Biol 2003;4:R81.: New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. PUBMED:14659018

    Ligand Summary

    Reviews

    References

     

    No references found.

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