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3e10

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

    Title Crystal structure of Putative NADH Oxidase (NP_348178.1) from CLOSTRIDIUM ACETOBUTYLICUM at 1.40 A resolution. To be published
    Site JCSG
    PDB Id 3e10 Target Id 390674
    Molecular Characteristics
    Source Clostridium acetobutylicum atcc 824
    Alias Ids TPS14595,NP_348178.1, 3.40.109.10, 85709 Molecular Weight 19277.24 Da.
    Residues 167 Isoelectric Point 6.64
    Sequence mdiinnrrsirnykgkkvekekiekllraamqapsagnqqpwefivledrenidklsnfskyanslkta plaivlladeekmkisemweqdmaaaaenilleaayldlgavwlgaqpieervknlkemfnlksnikpf cvisvgypensenkfidrfdakrihieky
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.40 Rfree 0.168
    Matthews' coefficent 2.26 Rfactor 0.130
    Waters 519 Solvent Content 45.67

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3e10
    1. Architecture of the RNA polymerase IITFIIF complex revealed by cross-linking and mass spectrometry
    ZA Chen, A Jawhari, L Fischer, C Buchen, S Tahir - The EMBO , 2010 - nature.com
     
    2. Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex
    K Xiang, T Nagaike, S Xiang, T Kilic, MM Beh - Nature, 2010 - nature.com
     
    3. Drosomycin-like defensin, a human homologue of Drosophila melanogaster drosomycin with antifungal activity
    A Simon, BJ Kullberg, B Tripet - Antimicrobial agents , 2008 - Am Soc Microbiol
     
    4. Structure and function of P19, a high-affinity iron transporter of the human pathogen Campylobacter jejuni
    ACK Chan, TI Doukov, M Scofield - Journal of molecular , 2010 - Elsevier
     
    5. CHEMICAL INFORMATION BASED ELASTIC NETWORK MODEL: A NOVEL WAY TO IDENTIFICATION OF VIBRATION FREQUENCIES IN PROTEINS.
    SK Raj - 2008 - scholarworks.umass.edu
     
    6. Iron transport in two pathogenic Gram-negative bacteria
    ACK Chan - 2011 - circle.ubc.ca
     
    7. Protein/(poly) peptide libraries
    A Knappik, P Pack, L Ge - EP Patent 2,058,400, 2009 - freepatentsonline.com
     
    8. Vectors/DNA-sequences from human combinatorial antibody libraries
    A Knappik, P Pack, L Ge - EP Patent 1,143,006, 2008 - freepatentsonline.com
     

    Protein Summary

    CA_C1551 gene from Clostridium acetobutylicum encodes the NP_348178 protein, a putative NADH oxidase (nitroreductase family protein, CATH 3.40.109.10 and the nitroreductase family (PF00881) (E-value: 1.7e-36).

    Pre-SCOP classifies 3e10 structure in the alpha+beta class, FMN-dependent nitroreductase-like superfamily, NADH oxidase/flavin reductase family. 3e10 closest related protein structures, 3e39 and 3kwk, were also solved by JCSG. 3e10 and 3e39 proteins share 25% seq id. The structures of individual monomers are similar (rmsd 1.43A for 148 aligned Ca, 32% seq id; Dali Z=20) except two regions near the flavin and the C-terminal extension loop which helps the dimer formation and FMN binding. There a small rigid body movement between the two dimers.

    3e10 is structurally similar (based on SSM) to: a Nitroreductase Family Protein from Streptococcus pneumoniae (PDB id: 2b67, topsan page, rmsd 1.62 A for 146 aligned Ca, 22% seq id; Dali Z=19), NADH oxidase from Thermus thermophilus (PDB id: 1nox, rmsd 1.52 A for 143 aligned Ca, 26% seq id; Z=18), a Nitroreductase-like Family Protein from Bacillus cereus (PDB id: 2i7h, topsan page; Z=18), a putative NAD(P)H-Flavin Oxidoreductase from Streptococcus pyogenes M1 GAS (PDB id: 2hay, topsan page; Z=18), a putative nitroreductase (SMU.260) in complex with FMN from Streptococcus mutans (PDB id: 2ifa, topsan page; Z=18), (PDB id: 2h0u, topsan page).

    The overall structure of 3e10 is similar to 1nox, both lack a loop "cap" protecting the active site in 2b67. Each monomer has an a+b class of fold which belongs to NADH oxidase/flavin reductase family. Each monomer contains 1 FMN located near the dimer interface. The poses of FMN are highly conserved in these homologs. One HEPES was identified near the flavin which may functionally relevant. The loops around flavin seems to display more varieties.

    The gene CA_C1551 from Clostridium acetobutylicum encodes the NP_348178 protein that belongs to the nitroreductase family (PF00881).

    SCOP classifies 3e10 in the alpha+beta class, FMN-dependent nitroreductase-like superfamily, NADH oxidase/flavin reductase family. DALI top hit is with putative nitroreductases 3kwk (Z=24), 3e39 (Z=21) and 3koq (Z=20).

    3e10 crystal structure shows a molecule of bound FMN per chain.


    References:

    Hecht, H.J.,  Erdmann, H.,  Park, H.J.,  Sprinzl, M.,  Schmid, R.D.   (1995) Crystal structure of NADH oxidase from Thermus thermophilus.  Nat.Struct.Biol. 2: 1109-1114

     

    Ligand Summary

     

     

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     MG0383C-active.png
    Stereo view of the active site
    174.97 kB18:43, 30 Jul 2008qxuActions
     MG0383C.png
    Dimer
    92.32 kB18:43, 30 Jul 2008qxuActions
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