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The Open Protein Structure Annotation Network
PDB Keyword
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3fse

    Title Crystal structure of two-domain protein containing DJ-1/ThiJ/PfpI-like and ferritin-like domains. (YP_324989.1) from ANABAENA VARIABILIS ATCC 29413 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3fse Target Id 375658
    Molecular Characteristics
    Source Anabaena variabilis atcc 29413
    Alias Ids TPS6868,YP_324989.1, 1.20.1260.10, 104187 Molecular Weight 39736.06 Da.
    Residues 364 Isoelectric Point 5.66
    Sequence mtnhnnsgkkkvailieqavedtefiipcnglkqagfevvvlgsrmnekykgkrgrlstqadgttteai asefdavvipggmapdkmrrnpntvrfvqeameqgklvaavchgpqvliegdllrgkqatgfiaiskdm mnagadyldealvvdgnlitsrepgdlaifttailsrlgyggkdaalpdekdrnaewwkladawggstk gdivrglntalggeryslealekytekesdveakalfqemitnkqrhieyletyltrlgekpslsania nqyakvktaltgsddiyqirsalgdiqtgigdignlcamytdpiataifkeiykdlvkyeqrlvslyrt rtnatvqppkpttgaavsm
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.90 Rfree 0.219
    Matthews' coefficent 2.08 Rfactor 0.176
    Waters 461 Solvent Content 40.79

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fse
    1. The Ferritin-like superfamily: Evolution of the biological iron storeman from a rubrerythrin-like ancestor
    SC Andrews - Biochimica et Biophysica Acta (BBA)-General Subjects, 2010 - Elsevier
     
    2. Experimental and computational studies indicate the mutation of Glu12 to increase the thermostability of oligomeric protease from Pyrococcus horikoshii
    D Zhan, W Han, Y Feng - Journal of Molecular Modeling, 2011 - Springer
     

    Protein Summary

    The gene Ava_4496 (YP_324989.1) from Anabaena variabilis is annotated as a peptidase C56, PfpI. It contains two domains. The first ~ 200 residues belong to the PF01965 which is the family of protease PfpI. The second half of the protein belongs to PF09537 which is a domain of unknown function DUF2383.

    Pre-SCOP classifies the N-terminal domain (1-176) in the alpha/beta class, class I glutamine amidotransferase-like superfamily, DJ-1/PfpI family; and the C-terminal domain (209-339) in the all alpha class, ferritin-like (super)family.

    3fse monomer structure splits into two domains, as shown below. The magenta colored N-terminal domain is the peptidase domain while the four-helix bundle (green) is the DUF2383.

    FL10835A.png

    The protein crystallizes as a dimer which may also represent its solution oligomeric state. The peptidase domain is involved in the dimer formation.

    FL10835A_dimer.png

    According to a DALI search, there are several similar structures to this protein peptidase domain. Most of them are DJ-1 proteases involved in the human Parkinson's desease. A superposition of some of these structures is shown below.

    all.png

    Color code for the structural superposition of the N-terminal peptidase domain: 3fse (green), 1g2i (Z=31; cyan), 1j42 (Z=27; magenta), 1oi4 (Z=30; yellow).

     

    A comparison with the DJ-1 protein 2rk6 (Z=27) reveals that a conserved Cys residue (111 in 3fse) is oxidized. This residue is located in the peptidase domain. The oxidation state of this Cys residue may be functionally relevant.

    FL10835A_2rk6.png  FL10835A_csx.png

    Oxidized Cys 111 of 3fse (green) superimposed                 Location of Cys 111 in the peptidase domain

    to Cys 106 of 2rk6 (grey).

     

    The C-terminal DUF2383 is structurally similar to an uncharacterized protein (PDB:2ib0) from Mycobacterium tuberculosis and several DPS ferritin-like proteins. It is unlikely that YP_324989 has the same function as DPS ferritin-like proteins, because in contrast to YP_324989, such proteins have functionally conserved histidines.

    A Blast search using the C-terminal domain gives hits with proteases:
                                                                                                                                          Score     E
    Sequences producing significant alignments:                       (Bits)  Value
    ref|NP_484936.1|  hypothetical protein alr0893 [Nostoc sp. PCC...   309    5e-83
    ref|YP_001869466.1|  PfpI family intracellular peptidase [Nost...   260    3e-68
    ref|ZP_01628948.1|  Peptidase C56, PfpI [Nodularia spumigena C...   246    3e-64
    gb|EDX78150.1|  intracellular protease, PfpI family, putative ...   130    3e-29
    ref|YP_001804854.1|  ThiJ/PfpI peptidase C56 family protein [C...   128    1e-28
    ref|YP_002378418.1|  intracellular protease, PfpI family [Cyan...   128    2e-28
    ref|YP_001522052.1|  DJ-1/PfpI family protein [Acaryochloris m...   127    4e-28
    ref|ZP_01622636.1|  Peptidase C56, PfpI [Lyngbya sp. PCC 8106]...   124    2e-27
    ref|ZP_03137468.1|  intracellular protease, PfpI family [Cyano...   119    8e-26
    gb|EDX87616.1|  DJ-1/PfpI family [Synechococcus sp. PCC 7335]       110    3e-23

    The structures similar to 3fse C-terminal domain are listed below, for both DALI and SSM searches.

    C-terminal domain's DALI search top hits


    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 2ib0 17.1 2.1 134 142 10 CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN
    2 1dps 17.1 2.1 135 154 12 DPS
    3 2yw7 17.0 2.1 133 147 10 STARVATION-INDUCED DNA PROTECTING PROTEIN
    4 2yw6 17.0 2.3 137 150 9 DNA PROTECTION DURING STARVATION PROTEIN
    5 1jts 16.9 2.1 135 155 13 DNA PROTECTION DURING STARVATION PROTEIN
    6 1l8i 16.8 2.1 135 155 13 DNA PROTECTION DURING STARVATION PROTEIN
    7 1jre 16.8 2.1 135 155 13 DNA PROTECTION DURING STARVATION PROTEIN
    8 1f33 16.8 2.1 135 156 13 DNA PROTECTION DURING STARVATION PROTEIN
    9 2v15 16.7 2.2 136 152 12 DNA PROTECTION DURING STARVATION PROTEIN
    10 2cf7 16.7 2.2 136 152 12 DPR
    C-terminal domain's SSM search hits


    N PDB Q-score RMSD TITLE
    1 2ib0 0.5376 1.642 A CONSERVED HYPOTHETICAL PROTEIN, RV2844, FROM MYCOBACTERIUM TUBERCULOSIS
    2 2yw6 0.5317 1.275 STRUCTURAL STUDIES OF N TERMINAL DELETION MUTANT OF DPS FROM MYCOBACTERIUM SMEGMATIS
    3 2yw7 0.5284 1.126 C-TERMINAL DELETION MUTANT OF MYCOBACTERIUM SMEGMATIS DPS
    4 1jts 0.5149 1.215 DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN
    5 2cf7 0.5005 1.536 ASP74ALA MUTANT CRYSTAL STRUCTURE FOR DPS-LIKE PEROXIDE RESISTANCE PROTEIN DPR FROM STREPTOCOCCUS SUIS.

     

    A superposition of these structures is shown below.

    C-term.png

    3fse DUF2383 (green), 1dps (cyan), 1f33 (lightmagenta), 1jre (yellow), 1jts (salmon), 1l8i (lightgrey), 2cf7 (slate), 2ib0 (orange), 2v15 (lime), 2yw6 (deepteal), 2yw7 (hotpink), 1dps (yelloworange), 1f33 (violetpurple), 1jre (grey70), 1jts (marine), 1l8i (olive), 2cf7 (smudge), 2ib0 (teal), 2v15 (dirtyviolet), 2yw6 (wheat), 2yw7 (deepsalmon).

     

    References:

    • Halio SB, Blumentals II, Short SA, Merrill BM, Kelly RM; , J Bacteriol 1996;178:2605-2612.: Sequence, expression in Escherichia coli, and analysis of the gene encoding a novel intracellular protease (PfpI) from the hyperthermophilic archaeon Pyrococcus furiosus. PUBMED:8626329


     

     

     

     

     

    Ligand Summary

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