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The Open Protein Structure Annotation Network
PDB Keyword
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3m5k

    Table of contents
        1. 1.1.1. Protein Summary
    1. 2. Dali Summary
        1. 2.1.1. Ligand Summary

    Title Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (BDI_1728) from Parabacteroides distasonis ATCC 8503 at 1.86 A resolution. To be Published
    Site JCSG
    PDB Id 3m5k Target Id 396612
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS27942,YP_001303097.1, 3.40.109.10, 327091 Molecular Weight 19613.68 Da.
    Residues 171 Isoelectric Point 9.25
    Sequence qepenqtletilnrksvrkykdrpvekekidkliragmaapssrdrrpwefiivtdrkaldtmaeglpf armlketrqaivvcgdtikssnawfldcsaasqnlllaaesmglgavwtavypypdrieivrkelrlpd himplnvipvgypmqketpknkynvqqihhngw
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.86 Rfree 0.178
    Matthews' coefficent 3.49 Rfactor 0.160
    Waters 369 Solvent Content 64.79

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3m5k

    Protein Summary

    Pfam:This one is part of the Pfam Nitroreductase family (with a representative structure known already).

    Gene BDI_1728 from Parabacteroides distasonis atcc 8503 translates into the YP_001303097 protein annotated as a putative NADH dehydrogenase/NAD(P)H nitroreductase belonging to Pfam PF00881 whose members use FMN as cofactor. Analysis of the genomic neighborhood of BDI_1728 indicates a possible functional linkage (score 0.75) with a cation antiporter BDI_1727.

    SCOP classifies 3m5k in the alpha+beta class, FMN-dependent nitroreductase-like superfamily, NADH oxidase/flavin reductase family. According to a DALI search, 3m5k shows high similarity with nitroreductase 3kwk (Z=29).

    3m5k crystallizes as a dimer. Its crystal packing analysis suggests that this dimer could be the stable oligomeric form in solution. A flavin mononucleotide (FMN) molecule and an unknown ligand (UNL) (blue mesh 1sigma omit map) are modeled at the putative active site in both protomers.

     

    all.png

    Fig 1. Dimer formation for the 3m5k structure

    Dali Summary

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 3kwk-A 29.3 0.6 166 168 61 PDB MOLECULE: PUTATIVE NADH DEHYDROGENASE/NAD(P)H 2: 3e10-A 24.8 1.2 162 166 40 PDB MOLECULE: PUTATIVE NADH OXIDASE; 3: 3e10-B 24.7 1.4 163 167 40 PDB MOLECULE: PUTATIVE NADH OXIDASE; 4: 3e39-B 21.8 2.0 163 172 27 PDB MOLECULE: PUTATIVE NITROREDUCTASE; 5: 3e39-A 21.7 2.0 163 175 27 PDB MOLECULE: PUTATIVE NITROREDUCTASE; 6: 3ge5-B 20.1 1.9 160 175 26 PDB MOLECULE: PUTATIVE NAD(P)H:FMN OXIDOREDUCTASE; 7: 3koq-C 20.1 1.8 157 172 27 PDB MOLECULE: NITROREDUCTASE FAMILY PROTEIN; 8: 3ge5-A 20.0 1.9 160 176 26 PDB MOLECULE: PUTATIVE NAD(P)H:FMN OXIDOREDUCTASE; 9: 3h4o-A 20.0 1.8 157 172 27 PDB MOLECULE: NITROREDUCTASE FAMILY PROTEIN; 10: 3koq-B 20.0 1.8 157 172 27 PDB MOLECULE: NITROREDUCTASE FAMILY PROTEIN; 11: 3koq-D 19.9 1.8 157 172 27 PDB MOLECULE: NITROREDUCTASE FAMILY PROTEIN; 12: 3koq-A 19.8 1.9 157 173 27 PDB MOLECULE: NITROREDUCTASE FAMILY PROTEIN; 13: 3gb5-A 19.5 2.2 157 185 26 PDB MOLECULE: IODOTYROSINE DEHALOGENASE 1; 14: 2b67-D 19.4 1.7 158 201 23 PDB MOLECULE: COG0778: NITROREDUCTASE; 15: 3g14-B 19.4 1.4 144 179 26 PDB MOLECULE: NITROREDUCTASE FAMILY PROTEIN; 16: 3g14-A 19.4 1.3 143 176 26 PDB MOLECULE: NITROREDUCTASE FAMILY PROTEIN; 17: 1zch-A 19.3 1.9 164 249 26 PDB MOLECULE: HYPOTHETICAL OXIDOREDUCTASE YCND; 18: 2b67-A 19.3 1.6 157 201 23 PDB MOLECULE: COG0778: NITROREDUCTASE; 19: 2b67-C 19.3 1.6 156 200 23 PDB MOLECULE: COG0778: NITROREDUCTASE; 20: 2b67-B 19.3 1.7 157 200 23 PDB MOLECULE: COG0778: NITROREDUCTASE; 21: 3ek3-A 19.2 2.8 161 187 24 PDB MOLECULE: NITROREDUCTASE; 22: 3gbh-D 19.1 1.9 158 211 20 PDB MOLECULE: NAD(P)H-FLAVIN OXIDOREDUCTASE; 23: 3gbh-A 19.0 1.9 159 212 20 PDB MOLECULE: NAD(P)H-FLAVIN OXIDOREDUCTASE; 24: 3gbh-B 18.9 1.9 158 213 20 PDB MOLECULE: NAD(P)H-FLAVIN OXIDOREDUCTASE; 25: 3gbh-C 18.9 1.9 158 211 20 PDB MOLECULE: NAD(P)H-FLAVIN OXIDOREDUCTASE; 26: 3ge6-B 18.9 1.9 158 210 20 PDB MOLECULE: NITROREDUCTASE; 27: 3ge6-A 18.8 1.9 158 210 20 PDB MOLECULE: NITROREDUCTASE; 28: 2isl-A 18.8 1.7 159 219 22 PDB MOLECULE: BLUB; 29: 2isl-C 18.8 1.7 159 219 22 PDB MOLECULE: BLUB; 30: 2isk-C 18.8 1.7 159 219 22 PDB MOLECULE: BLUB; 31: 2isk-G 18.8 1.7 159 219 22 PDB MOLECULE: BLUB; 32: 2isk-D 18.8 1.7 159 219 22 PDB MOLECULE: BLUB; 33: 2isk-A 18.8 1.7 159 219 22 PDB MOLECULE: BLUB; 34: 2isl-H 18.8 1.8 159 219 22 PDB MOLECULE: BLUB; 35: 2isk-H 18.8 1.7 159 219 22 PDB MOLECULE: BLUB; 36: 2isj-A 18.7 1.7 159 219 22 PDB MOLECULE: BLUB; 37: 3gag-A 18.7 2.1 161 206 19 PDB MOLECULE: PUTATIVE NADH DEHYDROGENASE, NADPH

    Superposition of  YP_001303097.1 (green) with the DALI best hit, 3kwk (grey) is shown below.

    super_3kwk.png

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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