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The Open Protein Structure Annotation Network
PDB Keyword
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2hhz

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

    Title Crystal structure of Pyridoxamine 5'-phosphate oxidase-related (ZP_00875725.1) from STREPTOCOCCUS SUIS 89-1591 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 2hhz Target Id 367043
    Molecular Characteristics
    Source Streptococcus suis 98hah33
    Alias Ids TPS1497,SSUI_28JUL04_CONTIG203_REVISED_GENE585, 2.30.110.10, 90339 Molecular Weight 17079.30 Da.
    Residues 149 Isoelectric Point 5.10
    Sequence melkdimhiledmkvgvfatldeygnpharhahitaaneegiffmtspethfydqlmgdqrvamtaise egyliqvvrvegtarpvendylktvfadnpyyqhiykdessdtmqvfqiyaghgfyhsltqghkyifsi gqgehsevral
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.231
    Matthews' coefficent 2.22 Rfactor 0.191
    Waters 63 Solvent Content 44.26

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2hhz
    1. Macromolecular modeling with rosetta
    R Das, D Baker - Annu. Rev. Biochem., 2008 - annualreviews.org
     
    2. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    3. Domain definition and target classification for CASP7
    ND Clarke, I Ezkurdia, J Kopp, RJ Read - Proteins: Structure, , 2007 - Wiley Online Library
     
    4. The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property
    E Hilario, Y Li, D Niks, L Fan - Acta Crystallographica Section D: , 2012 - scripts.iucr.org
     

    Protein Summary

    Gene SsuiDRAFT_2804 from Streptococcus suis encodes the ZP_03625340 protein that shows sequence similarity to proteins of the 'Pyridoxamin 5'-phosphate oxidase' family (PFAM:PF01243) and the 'uncharacterized conserved protein' COG (COG5015). The protein is also significantly similar to the hypothetical protein MA0739, annotated by the STRING database to be functionally related to Na+-transporting NADH-ubiquinone oxidoreductase MA0664, the F(420)H(2) dehydrogenase, subunit FpoD  MA1498, and the F(420)H(2) dehydrogenase, subunit FpoB MA1496, due to their phylogenetic co-occurence.

    2hhz has structural similarity to proteins belonging to the 'PNP-oxidase-like' family of SCOP (FMN-binding split barrel superfamily and fold).  Characterized proteins in this family are involved in electron transfer. A DALI search using 2hhz as query detects structural similarity with putative pyridoxamine-5-phosphate oxidases PDB:1t9m (Z=15), PDB:1dnl (Z=14), and PDB:1wv4 (Z=13).

    Analysis of the crystallographic packing of 2hhz using the PQS server indicates that a monomer is the biologically relevant form, despite the information contained in the PDB file, which indicates the protein to be a dimer. However, it is probable that the dimer is in fact the biologically relevant form, in agreement with other proteins with similar structures.



    Ligand Summary



    References

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