The Open Protein Structure Annotation Network
PDB Keyword


    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 2glz Target Id 361000
    Molecular Characteristics
    Source Desulfitobacterium hafniense dcb-2
    Alias Ids TPS1459,DHAF_12NOV03_CONTIG982_REVISED_GENE4728, PF02663, 90203 Molecular Weight 17356.01 Da.
    Residues 152 Isoelectric Point 5.95
    Sequence mcvektpwelvidfhghtcpdialgyriaqlaqremgirpapdseclvkaytqscaldaiqvlnkatig rhaliieethrymyqfhftgtqdihqftvspavldhletlrhpdlsprerqnkvlegvqyvltleesaf chydkipgqlskiv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.45 Rfree 0.198
    Matthews' coefficent 2.82 Rfactor 0.171
    Waters 431 Solvent Content 56.35

    Ligand Information


    Google Scholar output for 2glz
    1. A novel structural motif and structural trees for proteins containing it
    AM Kargatov, AV Efimov - Biochemistry (Moscow), 2010 - Springer
    2. Ligands in crystal structures that aid in functional characterization
    AE Speers, BF Cravatt - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org
    3. 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 gene Dhaf_2992 from Desulfitobacterium hafniense dcb-2 encodes the YP_002459451 protein, a putative subunit E of the formylmethanofuran dehydrogenase PF02663 EC: COG2191

    The 2glz structure belongs to the class of alpha and beta (a+b) proteins and reveals FmdE/GAPDH domain-like fold SCOP55346, inside the FmdE-like (super)family. DALI top hit (Z=16) is with the structure of the homologous enzyme (20% seq. id.) from Thermoplasma acidophilum PDB:2gvi, solved by the JCSG, see Topsan. Next  is the tungsten formylmethanofuran dehydrogenase PDB:3d00 (Z=13). Each 2glz chain is bound to metals Zn and Ni via the side chain of conserved residues H15, H17, C19 and C55.

    The FmdE enzyme  catalyzes the reaction: formylmethanofuran + H2O + acceptor --> CO2 + methanofuran + reduced acceptor.  It requires  2 cofactors: molybdenum or tungsten, and pterin.  The enzyme participates in folate biosynthesis.  

    Ligand Summary





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