.
The Open Protein Structure Annotation Network
PDB Keyword
.

3no5

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

    Title Crystal structure of a Pfam DUF849 domain containing protein (Reut_A1631) from Ralstonia eutropha JMP134 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3no5 Target Id 360840
    Molecular Characteristics
    Source Ralstonia eutropha jmp134
    Alias Ids TPS2812,YP_295841.1, PF05853, 285614 Molecular Weight 29530.18 Da.
    Residues 274 Isoelectric Point 5.90
    Sequence mnkpciisvaitgslprkkdnpavpitvseqvestqaafeagatlvhlhvrnddetptsnpdrfalvle girkhapgmitqvstggrsgagnergamlslrpdmaslatgsvnfptrvydnppelvdwlaaemktygi kpeveafdlsmifqaaamqaagaivgplhiqfvmgiknampvdrevlefyvqtlkrlspdatwtgagig rhqltmarwslelgghcrtglednvrldkntlapsnaalvrqvaelceeygrpvataaqareimslg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 6
    Resolution (Å) 1.90 Rfree 0.224
    Matthews' coefficent 2.55 Rfactor 0.206
    Waters 1097 Solvent Content 51.75

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3no5
    1. 3-Keto-5-aminohexanoate Cleavage Enzyme
    M Bellinzoni, K Bastard, A Perret, A Zaparucha - Journal of Biological , 2011 - ASBMB
     

    Protein Summary

    Pfam: DUF849 family. Although the precise function is unclear, this family is a member of our Enolase_TIM clan.

     

     

     The structure of target ID 360840 was determined at a resolution of 1.9 Angstroms. Primary phasing was accomplished by implemented molecular replacement using the PDB ID 3chv as a search model. This target is a member of the Prokaryotic Protein of Unknown Function DUF849 (PF05853) Pfam class. Shown below is a ribbons representation of the structure with the N-terminal end in blue and the C-terminal end in red. A zinc atom modeled into the structure is shown by the grey sphere.

    monomer.png

     The overall fold of target ID 360840 is similar to those proteins belonging to metallo-dependent hydrolase Superfamily that contain a TIM-barrel with a transition metal ion bound within the barrel with the barrel capped by a C-terminal alpha-helix. Analysis of the crystal structure using the EBI PISA webserver suggests that the dimer is a significant oligomerization state. Shown below is a ribbons representation of the dimer with the individual chains color-coded in blue and yellow respectively.

    dimer.png

     

     A DALI seach shows structural similarity between that target ID 360840 and the following table. Six of the top-scoring DALI hits are JCSG structures.

    PDB ID DALI Z-Score rmsd overlag (Angstroms) number aligned residues total residues in target % sequence identity description
    3fa5 47.7 0.7 271 276 64  Protein of unknown function (DUF849) (YP_91726.1) from Paracoccus denitrificans PD1222 at 1.9 Angstroms resolution
    3chv 47.2 0.8 271 279 66  Prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_164873.1) from Silicibacter pomeroyi DSS-3 at 1.45 Angstrom resolution
    3lot 40.5 1.5 272 310 33 Protein of Unknown Function (NP_070038.1) from Archaeoglobus fulgidus at 1.89 Angstrom  resolution
    3e02 40.4 1.4 271 310 32  Protein of Unknown Function (DUF849) (YP_555544.1) from Burkholderia Xenovorans LB400 at 1.90 Angstrom resolution.
    3e49 40.3 1.5 272 307 31  Prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_556190.1) from Burkholderia Xenovorans LB400 at 1.75 Angstrom resolution.
    3c6c 39.5 1.4 269 294 30  3-keto-5-aminohexanoate cleavage enzyme (YP_293392.1) from Ralstonia eutropha JMP134 at 1.72 Angstrom resolution.
    1nvm 17.7 3.2 217 338 9  bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate.
    3iix 16.2 2.9 219 348 17 X-ray structure of the FeFe-hydrogenase maturase HydE from Thermotoga maritima in complex with methionine and 5'-deoxyadenosine.

     

     

    PDB ID's 3chv, 3lot, 3e02, and 3e49 all contain a bound zinc. In all four of these structures, the location of the bound zinc and its ligands are conserved, and the structures suggest that the zinc binding plays a functional role.

     

     

     align1.png

     

     

     align2.png

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch