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The Open Protein Structure Annotation Network
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3e4v

    Table of contents
    1. 1. Protein Summary

    Title Crystal structure of NADH:FMN oxidoreductase like protein in complex with FMN (YP_544701.1) from METHYLOBACILLUS FLAGELLATUS KT at 1.40 A resolution. To be published
    Site JCSG
    PDB Id 3e4v Target Id 375043
    Molecular Characteristics
    Source Methylobacillus flagellatus kt
    Alias Ids TPS6825,YP_544701.1, 2.30.110.10, 92210 Molecular Weight 20718.59 Da.
    Residues 185 Isoelectric Point 5.29
    Sequence mrnelppenayrilesgpivlvstrgadgranlmtmgfhmmmqhepplvgaiigpwdyshqalsetgec vlavptvdlaetvvdigncsgdaldkfghfgltpvpaqtvdaplvrqcwanlecrvvddgwarrynlwv levqriwidtarketrlihhqgdgrfsvdgdtldlgermtkwrhlmg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.40 Rfree 0.151
    Matthews' coefficent 1.92 Rfactor 0.119
    Waters 376 Solvent Content 35.85

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Previously, this protein was annotated as a  hypothetical protein Mfla_0590. It contains a Pfam-A domain - Flavin Reducatase like domain (PF01613; residues 16-164; E-value: 0.00032) consisting of enzymes known to be flavin reductase as well as various oxidoreductase and monooxygenase components.  Additionally, this protein contains a Pfam-B domain - Pfam-B_1804 (residues 13-125; E-value: 7.8e-11)- which is in within the region of the protein that is in the Flavin Reductase like domain.  PSI-BLAST shows hits with many flavin reductases.


    There are two protomers per asymmetric unit in the crystal structure. One FMN is bound in each protomer as shown in the Fig. 1.
    dimer_FMN.png
    Fig. 1: Two protomers (A subunit: green and B subunit: cyan) are shown with FMN (blue, ball and stick).

        

    figure2.png

    Figure 2: Chain A is shown in cyan; Chain B is shown in green.  In both chains, residues 162, 164, 166, 168, 169,  171, 173, and 179 are involved in dimerization and are within 3 A of the other chain.  These residues are highlighted in orange in chain A and in magetna in chain B.

    This protein shares sequence and structural similarity to proteins from the NADH:FMN oxidoreductase like family from SCOP including flavoredoxin from D. Vulgaris (PDB code: 2d5m, 25% seq identity, sequence similarity E-value: 2e-11), Fmn-Binding Protein from P. horikoshii OT3 (PDB code: 2r6v, TOPSAN page, 28% seq identity, sequence similarity E-value: 8e-10) and a FMN-binding protein from M. thermautotrophicus (PDB code: 1eje, TOPSAN page, 26% seq identity, sequence similarity E-value: 8e-06).


    When 375043 is superposed and compared with 2eje (cyan) and 2d5m (pink), they are all very similar except that 2eje and 2d5m have a longer N-terminus which is missing in the 375043 (Fig. 2).

        

    super_an600r_1eje_2d5m.png

    Fig. 2: The superposition of 2eje (cyan) and 2d5m (pink) with the 375043 (green).

    Additionally, this protein is structural similar to  flavin reductase PheA2 (PDB code: 1rz0).  However, the FMN binding residues are not conserved in between 375043 (Gly37, Phe38, Ile52 and Gly54) and 1rz0 (Asn34, Ala35, Ser49 and Gly51).

        

    Analysis with the String Server, shows that are Mfla_0588 and Mfla_0589, which are both short-chain dehydrogenase/reductase SDR, are in the genomic neighborhood of this protein.

    References:

    1. Christendat, D.,  Yee, A.,  Dharamsi, A.,  Kluger, Y.,  Savchenko, A.,  Cort, J.R.,  Booth, V.,  Mackereth, C.D.,  Saridakis, V.,  Ekiel, I.,  Kozlov, G.,  Maxwell, K.L.,  Wu, N.,  McIntosh, L.P.,  Gehring, K.,  Kennedy, M.A.,  Davidson, A.R.,  Pai, E.F.,  Gerstein, M.,  Edwards, A.M.,  Arrowsmith, C.H. (2000) Structural proteomics of an archaeon. Nat.Struct.Biol. 7: 903-909 (2000).
    2. Van Den Heuvel, R.H.,  Westphal, A.H.,  Heck, A.J.,  Walsh, M.A.,  Rovida, S.,  Van Berkel, W.J.,  Mattevi, A. (2004) Structural Studies on Flavin Reductase PheA2 Reveal Binding of NAD in an Unusual Folded Conformation and Support Novel Mechanism of Action. J.Biol.Chem. 279: 12860-12867.

        

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