The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of Putative protoporphyrinogen oxidase (YP_001813199.1) from Exiguobacterium sp. 255-15 at 2.06 A resolution. To be published
    Site JCSG
    PDB Id 3lov Target Id 396730
    Molecular Characteristics
    Source Exiguobacterium sibiricum 255-15
    Alias Ids TPS25448,YP_001813199.1, 332878 Molecular Weight 52425.73 Da.
    Residues 474 Isoelectric Point 4.87
    Sequence msskrlvivgggitglaaayyaerafpdlnitlleagerlggkvatyredgftiergpdsyvarkhilt dlieaiglgeklvrnntsqafildtgglhpipkgavmgiptdldlfrqttllteeekqevadlllhpsd slripeqdiplgeylrprlgdalvekliepllsgiyagnidqmstfatypqfvaneqkagslfegmrlm rpldqlpqtpqttikatgqflsletgleslierleevlerseirletpllaisredgryrlktdhgpey adyvlltiphpqvvqllpdahlpeleqltthstatvtmifdqqqslpiegtgfvvnrrapysitactai dqkwnhsapdhtvlrafvgrpgndhlvhesdevlqqavlqdlekicgrtlepkqviisrlmdglpaytv ghadriqrvreevlaqypgiylaglaydgvglpdcvasaktmiesieleqshtdesvnet
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.06 Rfree 0.241
    Matthews' coefficent 2.79 Rfactor 0.197
    Waters 308 Solvent Content 55.91

    Ligand Information


    Google Scholar output for 3lov
    1. Data processing and analysis with the autoPROC toolbox
    C Vonrhein, C Flensburg, P Keller, A Sharff - Section D: Biological , 2011 - scripts.iucr.org
    2. FAD-binding site and NAD (P) reactivity in human renalase, a new enzyme involved in blood pressure regulation
    M Milani, F Ciriello, S Baroni, V Pandini - Journal of Molecular , 2011 - Elsevier

    Protein Summary

    This protein is a protoporphyrinogen oxidase (PPO) based on high sequence similarity to B. subtilis enzyme 3i6d (40% id, Pubmed id: 19944166), which an important enzyme in the biosynthesis of heme/chlorophyll. It is also homologous to plant PPO (PDB 1sez, 21% seq, Pubmed  15057273).


    As expected, the structure is highly similar to the BsPPO. There is no ligand in the jcsg structure, except for co-factor FAD. The main value of this structure is that is an apo form, which displays a closed active site, suggesting conformational changes are needed for substrate binding.


    This protein is now in family PF01593.17 Amino_oxidase CL0063 along with other structures.


    Fig 1. PPO with FAD

    Ligand Summary




    No references found.

    Tag page

    Files (1)

    FileSizeDateAttached by 
    ge8204a monomer
    165.63 kB20:48, 1 Feb 2010qxuActions
    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