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The Open Protein Structure Annotation Network
PDB Keyword
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2glz

    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
    Ligands
    Metals

    Jmol

     
    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:1.2.99.5 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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