The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of a putative dipeptidyl aminopeptidase IV (BACOVA_01349) from Bacteroides ovatus ATCC 8483 at 2.48 A resolution. To be published
    Site JCSG
    PDB Id 4q1v Target Id 420002
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS82723,ZP_02064383.1 Molecular Weight 80246.55 Da.
    Residues 709 Isoelectric Point 6.17
    Sequence qetkkptleelipggesylyaenlyglqwwgdecikpgvdtlysiqpktgketmvitreqinkvleenk agklshlysvrfpwtdkaqmlftiagkfivynfknnqvvstfkpkdgannedycaasgnvaytidnnly vnekavtnepegivcgqtvhrnefginkgtfwspkgnllafyrmdesmvtqyplvditarvgevnnvry pmagmtshqvkvgiynpatgksiylnagdptdryftniswapdekslylievnrdqnhaklcqynaetg epmgvlyeemhpkyvepqnpivflpwdptkfiyqsqrdgynhlylfetnaanmkgetynsanggsyfqa gkvkqltkgnwlvseilgfntkrkeviftaveglrsghfavnvsngkisqpfenckesehsgtlsasgt ylidrystkdqprvinlvdtknfketanlltaenpydgyqmpsietgtikaadgttdlhyrlmkpanfd pakkypvivyvyggphaqcvtggwqngargwdtymaskgyimftidnrgssnrgltfenatfrrlgiee gkdqvkgveflkslpyvdserigvhgwsfgghmttalmlrypeifkvgvaggpvidwgyyeimygerym dtpesnpegykecnlknladqlkghlliihddhddtcvpqhtlsfmkacvdartypdlfiypchkhnva grdrvhlhekitryfeqnl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.48 Rfree 0.2074
    Matthews' coefficent 3.03 Rfactor 0.1712
    Waters 641 Solvent Content 59.37

    Ligand Information



    Protein Summary




    A unique 8-bladed ß-propeller formed from a N-terminal domain (470 residues) which connects to the serine protease domain ( 471-732).

    The C-terminal domain faces the huge internal predominantly acidic cavity inside of the propeller (~16A in diameter). The largest irregularity within the 8-blade wheel forms a cavity which suppose to control the accsess to the substrate. Both molecules in ASU contain a light metal near Asp285 and Asp645, which physically connects the propeller with the protease domain in addition to the short anker loop 470-476 and the N-terminal portion 26-39, which intercalates the protease domain. The metal center is located ~20A away from the catalytic center (S603, D678 and H710) almost 180deg on the opposite site where the domains are joined together.

    FFAS data base using PDB bank as template asigns the nearest hopmology of 43% seqID to putative dipeptidyl aminopeptidase IV from the pathogenic Porphyromonas gingivalis bacteria (2d5l pdb code). The next nearest protein similar to the SP16867A is the human fibroblast activation protein, alpha subunit (1z68) with 20% seqID. The catalytic triad consisting of S603, D678 and H710 is absolutely conserved in all 3. The function of the homologs is well known. The serine protease activity in the homologs is related to several serious diseases.

    Dali server euqally confirms the PROFUNC and FFAS results, linking the SP16867A target to the putative DIPEPTIDYL AMINOPEPTIDASE IV (2d5l) with rmsd of 1.9A. The structural similarity to the 1z68 human FIBROBLAST ACTIVATION PROTEIN results in 3.1A rmsd. Almost all DIPEPTIDYL PEPTIDASEs 4 within PDB bank range in the same rmsd values of ~3A.

    Ligand Summary




    No references found.

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    N- and C-terminal domains with the 3 catalytic residues
    488.1 kB21:16, 5 Mar 2014cbtrameActions
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