.
The Open Protein Structure Annotation Network
PDB Keyword
.

3fa5

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

    Title Crystal structure of protein of unknown function (DUF849) (YP_917261.1) from PARACOCCUS DENITRIFICANS PD1222 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3fa5 Target Id
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Molecular Characteristics
    Source
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Alias Ids
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS7089,YP_917261.1, PF05853, 86696
    Molecular Weight
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Da.
    Residues
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Isoelectric Point
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Sequence
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
      BLAST   FFAS

    Structure Determination
    Method XRAY
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Chains 2
    Resolution (Å)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Rfree
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Matthews' coefficent 2.38 Rfactor 0.205
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 48.29

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
    parameter 'target' could not convert from 'list' to 'str' (click for details)
    Google Scholar output for 3fa5
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. 3-Keto-5-aminohexanoate Cleavage Enzyme
    M Bellinzoni, K Bastard, A Perret, A Zaparucha - Journal of Biological , 2011 - ASBMB
     

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Protein Summary

    Gene Pden_3495 from Paracoccus denitrificans pd1222 encodes the YP_917261.1 amino acid sequence that belongs to the DUF849 (PF05853). Genome context analysis identifies with a 0.87 scored the 3-oxoadipate enol-lactonase (Pden_3491), and the fumarate lyase (Pden_3496) genes as neighbors of Pden_3495. An 83% identical protein is annotated as putative 3-keto-5-aminohexanoate cleavage enzyme (ZP_05781575).

     

    3fa5 is highly similar to jcsg structures 3chv (DALI Zscr=49, 76% seq id, rmsd 0.74 A for 274 aligned Ca atoms), 3c6c (Z-scr=37, 34% seq id, rmsd 1.47A for 259 aligned Ca atoms), 3e49 (Zscr=40), and 3e02 (Zscr=40). The putative active site is identical to 3chv, see TOPSAN links above for annotation. A DALI weak hit (Zscr=17) with the 4-hydroxy-2-oxovalerate aldolase 1nvm is next.

     

    Notes from Pfam:

    This protein is now in family: DUF849 (PF05853) which is in clan Enolase_TIM (CL0256). the family already has some structures for it, and the clan-membership implies it is likely to be an enolase. I will amend the annotation for the DUF.

     

     

    Differences worth noting are:

    The 3fa5 crystal packing seems to suggest this protein is a dimer, while other related proteins are likely tetramers. A magnesium ion is at the metal site since the crystal was grown in high concentration of Mg++ (0.314M MgCl2). Other JCSG structures have either Zinc or Nickle ions at the equivalent position.

    Ligand Summary

    contains a Mg ion in the active site.

    Reviews

    References

     

    No references found.

    Tag page

    Files (0)

     
    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