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3of4

    Title Crystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreductase (nfnB, IL2077) from Idiomarina loihiensis L2TR at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3of4 Target Id 403059
    Molecular Characteristics
    Source Idiomarina loihiensis l2tr
    Alias Ids TPS30637,YP_156458.1, 3.40.109.10, 324420 Molecular Weight 23293.18 Da.
    Residues 208 Isoelectric Point 5.95
    Sequence myleklqqwryatadfsgahitddvldkllnttrltassyglqpyctlvirnkglreqlvnhsfgqqkv adssalvifaaktgavadivdpyiselsqqrqltneeaentrnyftqklqamsaatrkewavrqayigl gtfllaaaelevdscpmegiehdaydnilslkdlglstvfacpvgyrseadttqfqkkvrqplsrfkvvl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 1.90 Rfree 0.1937
    Matthews' coefficent 2.42 Rfactor 0.1574
    Waters 389 Solvent Content 49.21

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3of4

    Protein Summary

    The protein YP_156458.1 is annotated as nitroreductase. YP_156458.1 belongs to PFAM PFAM:PF00881 Nitroreductase. This consists of a group of FMN- or FAD-dependent and NAD(P)H-dependent enzymes able to metabolize nitrosubstituted compounds.

    The protein YP_156458.1 can bind either FMN or FAD as observed in the crystal structure. There are three monomers in the crystallographic asymmetric unit. Two monomers bind FMN and a molecule resembling a fragment of FAD. The third monomer binds FAD.

     AB_dimer.png

    Fig. 1. Monomers A and B form a dimer. Each monomer binds a FMN as shown in yellow stick representation. Adjacent to FMN is modeled an unknown ligand UNL that resembles adenine moiety of FAD.

    C_FAD_dimer.png

    Fig. 2. Chain C binds FAD and forms a dimer with its symmetry related molecule.

     

    The location of UNL in chains A and B coincides with that of adenine moiety of FAD in chain C.  A superposition of all chains is shown below to illustrate the equivalence of ligand binding.

    A_B_FMN_UNL.png
    C_FAD.png
    A_B_C.png
    Chains A,B (FMN+UNL in red spheres) Chain C (FAD) Chains A,B,C superposed

     

    There are several instances of proteins binding both FMN and FAD, but not at the same region. Also, none of these proteins (2,4-Dienoyl-CoA reductase, Deoxyribodipyrimidine Photo-lyase, Dihydropyrimidine dehydrogenase, Glutamate synthase, NADPH cytochrome P450 reductase, Nitric-oxide synthase, sarcosine oxidase) is a nitroreductase.


    There are several structural homologs of this protein.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID Description (JCSG structures highlighted in red)
    1 1nec 24.5 2.1 205 216 22 Protein (nitroreductase)
    2 1kqd 24.5 2.2 205 216 22 Oxygen-insensitive Nad(p)h Nitroreductase
    3 1kqc 24.5 2.3 206 216 22 Oxygen-insensitive Nad(p)h Nitroreductase
    4 1kqb 24.5 2.2 206 216 22 Oxygen-insensitive Nad(p)h Nitroreductase
    5 1ylu 24.4 2.2 205 216 22 Oxygen-insensitive Nad(p)h Nitroreductase
    6 3hzn 24.3 2.4 208 220 23 Oxygen-insensitive Nad(p)h Nitroreductase
    7 1oo5 24.3 2.3 206 217 22 Oxygen-insensitive Nad(p)h Nitroreductase
    8 1icv 24.3 2.2 205 216 22 Oxygen-insensitive Nad(p)h Nitroreductase
    9 1icr 24.3 2.2 206 216 22 Oxygen-insensitive Nad(p)h Nitroreductase
    10 1ylr 24.2 2.3 205 216 22 Oxygen-insensitive Nad(p)h Nitroreductase
    11 1yki 24.2 2.4 207 217 22 Oxygen-insensitive Nad(p)h Nitroreductase
    12 1ooq 24.1 2.3 206 216 22 Oxygen-insensitive Nad(p)h Nitroreductase
    13 1oo6 24.1 2.3 207 217 22 Oxygen-insensitive Nad(p)h Nitroreductase
    14 1idt 24.1 2.3 206 216 22 Minor Fmn-dependent Nitroreductase
    15 1icu 24.1 2.2 206 217 22 Oxygen-insensitive Nad(p)h Nitroreductase
    16 1oon 24.0 2.3 205 216 22 Oxygen-insensitive Nad(p)h Nitroreductase
    17 1ds7 24.0 2.3 207 217 22 Fmn-dependent Nitroreductase
    18 2b67 23.4 2.1 199 201 15 Cog0778 Nitroreductase
    19 3bem 23.1 2.2 202 207 20 Putative Nad(p)h Nitroreductase Ydfn
    20 1vfr 23.1 2.2 206 217 24 Nad(p)h\fmn Oxidoreductase
    21 1v5y 23.1 2.2 207 217 24 Major Nad(p)h-flavin Oxidoreductase
    22 1v5z 23.0 2.2 207 217 24 Major Nad(p)h-flavin Oxidoreductase
    23 1nox 23.0 1.9 197 200 22 Nadh Oxidase
    24 3gbh 22.6 2.2 202 212 15 Nad(p)h-flavin Oxidoreductase
    25 3gag 22.1 2.5 200 205 19 Putative Nadh Dehydrogenase, Nadph
    26 3ge6 21.9 2.5 202 210 16 Nitroreductase
    27 2hay 21.9 2.7 202 217 22 Putative Nad(p)h-flavin Oxidoreductase
    28 3gb5 19.7 1.7 158 185 15 Iodotyrosine Dehalogenase 1
    29 3eof 18.5 2.5 175 246 20 Putative Oxidoreductase
    30 3e39 18.4 2.3 163 175 18 Putative Nitroreductase
    31 2bkj 18.4 2.4 174 230 17 Flavin Reductase
    32 1zch 18.4 2.6 180 249 14 Hypothetical Oxidoreductase Ycnd
    33 1f5v 18.4 2.4 176 240 23 Oxygen-insensitive Nadph Nitroreductase
    34 1bkj 18.4 2.4 175 230 17 Nadph-flavin Oxidoreductase
    35 3m5k 18.2 2.1 160 168 12 Putative Nadh Dehydrogenase/nad(p)h Nitroreductas
    36 3ge5 18.2 2.4 167 176 16 Putative Nad(p)hfmn Oxidoreductase
    37 3kwk 17.8 2.1 159 168 11 Putative Nadh Dehydrogenase/nad(p)h
    38 3h4o 17.7 2.8 166 172 19 Nitroreductase Family Protein
    39 3gfd 17.7 2.0 166 221 14 Iodotyrosine Dehalogenase 1
    40 3koq 17.6 3.0 167 172 19 Nitroreductase Family Protein
    41 3gh8 17.6 2.6 169 222 14 Iodotyrosine Dehalogenase 1
    42 2h0u 17.6 2.7 176 196 26 Nadph-flavin Oxidoreductase
    43 3g14 17.5 2.4 133 179 19 Nitroreductase Family Protein
    44 3e10 17.4 1.8 129 167 18 Putative Nadh Oxidase
    45 2fre 17.3 2.7 170 198 16 Nad(p)h-flavin Oxidoreductase
    46 2isl 16.9 2.8 170 219 14 Blub
    47 2isk 16.8 2.8 170 219 14 Blub
    48 2isj 16.8 2.8 170 219 14 Blub
    49 3gfa 16.5 2.9 164 197 15 Putative Nitroreductase
    50 3ek3 16.4 2.0 158 187 16 Nitroreductase
    51 3eo8 15.6 2.8 133 219 17 Blub-like Flavoprotein
    52 3gr3 15.4 2.3 163 226 15 Nitroreductase
    53 1ywq 15.4 3.1 173 199 10 Nitroreductase Family Protein
    54 3hoi 15.3 2.4 146 193 16 Fmn-dependent Nitroreductase Bf3017
    55 2r01 15.1 2.3 158 195 17 Nitroreductase Family Protein
    56 2ifa 15.1 3.3 173 200 13 Hypothetical Protein Smu.260
    57 2i7h 14.9 2.9 163 187 14 Nitroreductase-like Family Protein
    58 1yw3 14.8 3.4 173 201 12 Hypothetical Protein Smu.260
    59 3k6h 13.7 3.3 164 191 11 Nitroreductase Family Protein
    60 3hj9 13.7 2.6 149 210 16 Oxidoreductase
    61 3bm1 13.4 3.3 158 177 13 Protein Ydja
    62 3bm2 12.2 3.1 144 166 14 Protein Ydja
    63 3eo7 11.7 2.3 126 487 17 Putative Nitroreductase
    64 1vkw 8.9 2.5 95 217 15 Putative Nitroreductase
    65 1in0 5.9 4.0 95 162 6 Yajq Protein

     

     

    A superposition of three structures are shown below.

    0MJ14489A_1nec_1kqd_1idt.png

    YP_156458.1 (green), 1nec (cyan), 1kqd (magenta), 1idt (yellow)
     

    Ligand Summary

    Reviews

    References

     

    No references found.

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