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The Open Protein Structure Annotation Network
PDB Keyword
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377840

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

    Site JCSG
    Status Diffraction-quality Crystals
    Target Id 377840
    Molecular Characteristics
    Source Arthrobacter sp. fb24
    Alias Ids TPS7008, Molecular Weight 23340.29 Da.
    Residues 226 Isoelectric Point 5.42
    Sequence mkiavlgtgtvgrtmagaladlghevtigtrdpkatlaraepdamgappfsqwlpehphvhlaafadvaagaelvv nategassiaaltaagaenlagkilvdianpldfshgmpptlnpvntdslgeqiqrtfpeakvvktlntmnaslm vdpgraaggdhsvfvsgndaaakaevatllkslghqdvidlgdittargaemllpvwirlwgalgtanfnfkiar
      BLAST   FFAS
    Ligand Information
    Ligands
    Metals
    Google Scholar output for

    Protein Summary

    Protein YP_830112.1 is annotated as an NADP oxidoreductase, coenzyme F420-dependent precursor and belongs to the PFAM PF03807.  The function of F420-dependent NADP reductase is the transfer of electrons from reduced coenzyme F420 into an electron transport chain. It catalyses the reduction of F420 with NADP(+) and the reduction of NADP(+) with F420H(2).

    It is predominantly a helical protein, with an additional beta sheet (Fig 1).

    FM11555A_monomer.png

    Fig 1. Monomer structure of target  YP_830112.1. NADP is shown in stick representation.

     

    The protein exists as dimer. The last helix and the b-strand form the dimerization domain (Fig 2.)

    FM11555A_dimer.png
    Fig 2. Dimerization of the protein is facilitated by the interaction between the last b-strand and the helix.

     

    PSI-blast shows a number of proteins homologous to the sequence of this target. The top hits are all annotated as  NADP oxidoreductase.                                                                                                               
    Sequences producing significant alignments:                                        Score (bits)   E-Value
    ref|YP_830112.1| NADP oxidoreductase, coenzyme F420-dependent [A...   393   e-108
    ref|ZP_02836987.1| NADP oxidoreductase coenzyme F420-dependent [...   290   4e-77
    ref|YP_001539920.1| NADP oxidoreductase coenzyme F420-dependent ...   157   5e-37
    ref|YP_001361700.1| NADP oxidoreductase coenzyme F420-dependent ...   108   3e-22
    ref|YP_001824714.1| putative oxidoreductase [Streptomyces griseu...    99   3e-19
    ref|YP_589204.1| NADP oxidoreductase, coenzyme F420-dependent [A...    99   3e-19
    ref|NP_714614.1| hypothetical protein LB070 [Leptospira interrog...    92   4e-17
    ref|YP_799330.1| Dinucleotide-binding enzyme [Leptospira borgpet...    89   2e-16
    ref|YP_802218.1| Dinucleotide-binding enzyme [Leptospira borgpet...    89   2e-16

    There are several structural homologs of this protein. SSM search return a number of proteins, namely 2raf 1jay 1jax 1yb4 2izz 1vpd 2gra 2gr9 2i9p 2cvz 2h78 3cum 2ger 2amf. FFAS results return 1jax 2raf 1z82 1evy 1txg.
    A superposition of some of these proteins is shown in Fig 3.

    all.png

    Fig 3. A superposition of a few structural homologs (2vq3 = green; 2raf = blue; 1jay = cyan) of this target (red). The bound NADP molecules are also shown.

     

    References:

    Warkentin E, Mamat B, Sordel-Klippert M, Wicke M, Thauer RK, Iwata M, Iwata S, Ermler U, Shima S. 'Structures of F420H2:NADP+ oxidoreductase with and without its substrates bound.' EMBO J. 2001 Dec 3;20(23):6561-9.
    Abstract: Cofactor F420 is a 5'-deazaflavin derivative first discovered in methanogenic archaea but later found also to be present in some bacteria. As a coenzyme, it is involved in hydride transfer reactions and as a prosthetic group in the DNA photolyase reaction. We report here for the first time on the crystal structure of an F420-dependent oxidoreductase bound with F420. The structure of F420H2:NADP+ oxidoreductase resolved to 1.65 A contains two domains: an N-terminal domain characteristic of a dinucleotide-binding Rossmann fold and a smaller C-terminal domain. The nicotinamide and the deazaflavin part of the two coenzymes are bound in the cleft between the domains such that the Si-faces of both face each other at a distance of 3.1 A, which is optimal for hydride transfer. Comparison of the structures bound with and without substrates reveals that of the two substrates NADP has to bind first, the binding being associated with an induced fit.

    Ligand Summary

    NADP


     

    Reviews

    References

     

    No references found.

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