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3e99

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

    Title Crystal structure of the beta subunit of benzoate 1,2-dioxygenase (YP_105014.1) from BURKHOLDERIA MALLEI ATCC 23344 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3e99 Target Id 390534
    Molecular Characteristics
    Source Burkholderia mallei atcc 23344
    Alias Ids TPS14580,YP_105014.1, 3.10.450.50, 85633 Molecular Weight 19130.40 Da.
    Residues 163 Isoelectric Point 5.31
    Sequence mktidladiqaflyresrllddkawdawldcyradavfwmpswddadalvtdpqreisliyypnrqgle drvfrikterssatvpdtrtshnianveresadgdvhtvrfnwhtlsyryktvssyfgmsryaidfsgd apkivskyvvlkndyinqlidiyhi
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.223
    Matthews' coefficent 2.17 Rfactor 0.186
    Waters 142 Solvent Content 43.19

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3e99
    1. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     



    References:

    Furusawa, Y.,  Nagarajan, V.,  Tanokura, M.,  Masai, E.,  Fukuda, M.,  Senda,
    T.   (2004) Crystal Structure of the Terminal Oxygenase Component of Biphenyl
    Dioxygenase Derived from Rhodococcus sp. Strain RHA1  J.Mol.Biol.   342:
    1041-1052

    Protein Summary

    Gene benB (BMAA0186) from Burkholderia mallei atcc 23344 encodes the YP_105014 protein with sequence homology to the beta (or small) subunit of the benzoate 1,2-dioxygenase (BDO; EC 1.14.12.10; PF00866).  BDO catalyzes the stereospecific dioxygenation of the aromatic ring. This enzyme is of relevance since it can convert enviromental pollutants such as polycholorinated biphenyls. Based on genome context analysis with the String Server, this protein is in the same genomic neighborhood as and co-occurs with BMAA0187: the alpha sununit of benzoate 1,2-dioxygenase, BMAA0184: short-chain oxidoreductase, BMAA0185: benzoate 1,2-dioxygenase, ferredoxin reductase, and BMAA0188: Transcriptional regulator, CatR.  The following proteins co-occurs with BMAA0186: BMAA0200: muconate cycloisomerase; BMAA1919: putative class III extradiol-type catecholic; and BMAA0848: putative hydroxyphenylpyruvate dioxygenase.

    3e99 belongs to alpha+beta class, cystatin-like fold, NTF2-like superfamily, ring hydroxylating beta subunit family from SCOP. According to DALI, 3e99 is structurally similar to the large subunit of the biphenyl dioxygenase ( PDB:1ulj; Z=18) with rmsd of 1.4 A for 83% CA atoms. 3e99 is predicted to function as a trimer based on other similar structures. Several loops that are disordered most likely interact with the absent subunits. 

    Figure 1. Trimer oligomerization of 3e99

    MG14458B-trimer.png

    Figure 2. Comparison of 1ulj (yellow) with 3e99 (red)

    1ULJy-390534r.png

        

    Figure 3. The complete trimer structure of alpha and beta subunits of BDO (1ulj); the beta trimer is shown in spheres

    1ULJ.png

        

        


    References:

    1. Furusawa, Y.,  Nagarajan, V.,  Tanokura, M.,  Masai, E.,  Fukuda, M.,  Senda, T.   (2004) Crystal Structure of the Terminal Oxygenase Component of Biphenyl Dioxygenase Derived from Rhodococcus sp. Strain RHA1  J.Mol.Biol.   342:1041-1052, PMID: 15342255

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (3)

    FileSizeDateAttached by 
     1ULJ.png
    alpha and beta unit of 1ULJ
    171.56 kB18:49, 7 Aug 2008qxuActions
     1ULJy-390534r.png
    superimposition of 1ULJ with 390534
    75.92 kB18:51, 7 Aug 2008qxuActions
     MG14458B-trimer.png
    Trimer of 390534
    86.66 kB18:41, 7 Aug 2008qxuActions
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