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3ge5

    Title Crystal structure of putative NAD(P)H:FMN oxidoreductase (NP_904626.1) from PORPHYROMONAS GINGIVALIS W83 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3ge5 Target Id 391162
    Molecular Characteristics
    Source Porphyromonas gingivalis w83
    Alias Ids TPS24303,NP_904626.1, 3.40.109.10 Molecular Weight 20493.52 Da.
    Residues 179 Isoelectric Point 5.96
    Sequence mkqipqdfrliedffrtrrsvrkfidrpveeeklmaileagriapsahnyqpwhflvvreeegrkrlap csqqpwfpgapiyiitlgdhqrawkrgagdsvdidtsiamtymmleahslglgctwvcafdqalcseif dipshmtpvsilalgygdptvppreafnrktieevvsfekl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.172
    Matthews' coefficent 2.31 Rfactor 0.145
    Waters 500 Solvent Content 46.85

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ge5
    1. A remote arene-binding site on prostate specific membrane antigen revealed by antibody-recruiting small molecules
    AX Zhang, RP Murelli, C Barinka, J Michel - Journal of the , 2010 - ACS Publications
     

    Protein Summary

    Gene PG0310 from Porphyromonas gingivalis w83 encodes the NP_904626 protein from the nitroreductase family  (PF00881). Its genomic neighbor, PG0311, is annotated as glycosyl transferase group 2 family protein.

    Pre-SCOP classifies 3ge5 in the alpha+beta class, FMN-dependent nitroreductase-like superfamily, NADH oxidase/flavin reductase family. 3ge5 crystallizes as a dimer and its packing analysis suggests that this dimer should be the stable oligomeic form in solution. A flavin mononucleotide (FMN) cofactor and an unknown ligand (UNL) are modeled  into the putative active site of both protomers.

     

     dimer_103409.png

    Fig 1. Dimer of 3ge5 in asu.  

     

    During the refinement, the FMN restraints dictionary was modified to allow bending of the isoalloxazine ring along the N5-N10 virtual axis resulting in an improved fit between the FMN coordinates and the electron density. The omit maps of two UNLs are shown in the figures below (Fig 2a-b).

     

    unl1.png

     

    Fig 2a. UNL-1 (green stick) and omit map (1 sigma level) in the protomer A are shown here. UNL-1 resembles benzoate or nitrobenzene.

    unl2.png

    Fig 2b. UNL-2 (cyan stick) and omit map (1 sigma level) in the protomer B are shown here. UNL-2 resembles benzoate or nitrobenzene derivatives.

    According to DALI, other protein structures that are most similar in terms of structure to 3ge5 are: putative nitroreducatase (3e39, Z=21.0, 2.3A rmsd, 166 Ca aglined, 27%id), putative NADH oxidase (3e10, Z=19.9, 1.9A rmsd, 146 Ca aglined, 31%id), nitroreductase (1nec, Z=19.9, 1.9A rmsd, 164 Ca aglined, 21%id) and the oxidoreducatse 1v5z (Z=18). The superposition of 3ge5 dimer with those of 3e39 and 3e10 is shown below. 

     

     

     

     super_3e39_3e10.png

     

     Fig 3. Superposition of 3ge5 (green) dimer with those of 3e39 (light blue) and 3e10 (light pink). Please notice that the dimer formation of the three structures is almost identical.  They all contain a FMN molecule in the active site.

     

    By Piotr Kozbial:

    MG0383R-DALI (1).png

    Figure 4. Structure based alignment. Uppercase means structurally equivalent positions with 3ge5 (labeled here as 0310A). Lowercase means insertions relative to 3ge5. The most frequent amino acid type is coloured in each column.

    The binding cleft

    NP_904626.1 encode by  locus PG_0310 has FMN-binding cleft similar to that of PDB:1v5z

      PG_0310 1V5Z - FMN Deformation (+ coef.) Deviation (Å) Depth difference Weight
    delta_plus backbone SER 46 A backbone SER 41 B 1.6% (4.41) 0.130 0.032 0.6
    delta_minus   ASN 49 A   ASN 44 B 4.7% (4.50) 0.271 0.034 0.6
    delta_plus backbone ASN 166 B backbone SER 207 A 5.7% (4.77) 0.248 0.130 0.6
    delta_plus h12 ARG 167 B h12 ARG 208 A 3.1% (4.99) 0.092 0.014 0.6
    delta_plus h22 ARG 167 B h22 ARG 208 A 3.6% (4.70) 0.226 0.020 0.6
    guanidinium   ARG 167 B   ARG 208 A 2.8% (6.48) 0.148 0.009

     


    PG_0310
    [PDB file] | [RasMol] | [PDB] | [PDBsum]
    1V5Z - FMN

    OXIDOREDUCTASE - BINDING OF COUMARINS TO NAD(P)H:FMN OXIDOREDUCTASE
    Matched annotations Weighted number of SuMo groups Number of SuMo groups Volume
    FMN 2/2 binding site [automatic] [details] 11% (2.65 / 23.4) 11% (4 / 35) 13% (2.65 / 20.35)
    Matched annotations Weighted number of SuMo groups Number of SuMo groups Volume
    FMN 2/2 binding site [automatic] [details] 27% (3.85 / 14.45) 26% (6 / 23) 33% (3.84 / 11.73)
    MG0383R-1-CFADNK-1-7283.png MG0383R-2-CFADNK-1-7283.png

    Ligand Summary

    Flavin mononucleotide (FMN), unknown ligand (UNL), sulfate (SO4) and ethylene glycol (EDO) are modeled at the putative active site in both protomers.

    Reviews

    References

     

    No references found.

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