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The Open Protein Structure Annotation Network
PDB Keyword
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3d00

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

    Title Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved alpha+beta core domain and an auxiliary C-terminal treble-clef zinc finger. Acta Crystallogr.,Sect.F 66 1335-1346 2010
    Site JCSG
    PDB Id 3d00 Target Id 383639
    Molecular Characteristics
    Source Syntrophus aciditrophicus sb
    Alias Ids TPS1773,YP_460196.1, PF02663, 92910 Molecular Weight 21426.86 Da.
    Residues 190 Isoelectric Point 6.17
    Sequence mtarnilsysyeeyvekitafhgypapgvliggfmvdlavknlpegilydaicetrtclpdavqlltpc tfgngwltvlpmglfavslydkftgegvrvfldvekmgpwqeirnwflklktkkeqdserlfkeireag pdilelrnvklkpgflekkhkgkivlcpqcreaypaqdgelclscqggspyl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.268
    Matthews' coefficent 2.33 Rfactor 0.233
    Waters 42 Solvent Content 47.14

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3d00
    1. Ligands in crystal structures that aid in functional characterization
    AE Speers, BF Cravatt - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org
     
    2. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved+ core domain and an auxiliary C-terminal treble-
    HL Axelrod, D Das, P Abdubek, T Astakhova - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    The SYN_00638 gene from Syntrophus aciditrophicus sb encodes the YP_460196 protein that belongs to the tungsten formylmethanofuran dehydrogenase, subunit E (FmdE) group (PF02663). This subunit E is co-expressed with the formylmethanofuran dehyrogenase holoenzyme (tungsten containing isoenzyme with subunits FmdA, FmdB, FmdC and FmdD), but fails to co-purify, and the function of the subunit E remains unknown. The reactions catalyzed by the Fmd holoenzyme is important for the reduction of CO2 to CH4 in autotrophic CO2 fixation. 3d00 structure is shown below.



    Pre-SCOP classifies 3d00 in the alpha+beta class, FmdE-like (super)family. A DALI search for structural similarity with 3d00 returns as top hits other FmdE-like proteins such as PDB:2glz (Z=13) and PDB:2gvi (Z=12). Next is a rather weak hit (Z=5) with a phosphoglycerate dehydrogenase (3dc2). The most similar proteins to 3d00 detected by FFAS are shown below. These include the  structure of Ta1109 protein from THERMOPLASMA ACIDOPHILUM (PDB:2gvi, cyan, TOPSAN https://jcsgwiki.jot.com/WikiHome/361192)  and the formylmethanofuran dehydrogenase subunit E-like protein Dhaf_2992 from Desulfitobacterium halfniense (PDB:2glz, magenta, TOPSAN https://www.topsan.org/WikiHome/361000). All these 3 proteins structures have been solved by the JCSG.


    The superposition of the FmdE-like structures 3d00, 2gvi and 2glz is depicted above.

    Ligand Summary

    Zinc is bound to 4 Cys residues.
    The presence of Zn has been verified by an x-ray fluorescence scan and by calculating anomalous difference Fourier maps.

    References

    Reviews

    References

     

    No references found.

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