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The Open Protein Structure Annotation Network
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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 378383
    Molecular Characteristics
    Source Paracoccus denitrificans pd1222
    Alias Ids TPS7089,YP_917261.1, PF05853, 86696 Molecular Weight 30560.06 Da.
    Residues 281 Isoelectric Point 5.54
    Sequence msdpagkpciicvaitgslptkennpavpitlaeqvestheafeagasiahchvrddegrptsdpdrfa alkeglerhcpgmivqlstggrsgagqargamlplcpdmaslsvgsnnfptrvyenppdlvdwlaaeml kydikpeieafdlshilqakrmagdgrlagtpyvqfvmgvrnampadrdvfdyyihtvrrlfgedapwc aagigpsqivlnewaissgghartglednvrldrdrlapsnaalvgravelcekyerpvatwrqarqil glrmv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.90 Rfree 0.248
    Matthews' coefficent 2.38 Rfactor 0.205
    Waters 421 Solvent Content 48.29

    Ligand Information
    Ligands
    Metals

    Jmol

     
    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
     

    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.

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