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The Open Protein Structure Annotation Network
PDB Keyword
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3ljy

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

    Title Crystal structure of putative adhesin (YP_001304413.1) from Parabacteroides distasonis ATCC 8503 at 2.41 A resolution. To be published
    Site JCSG
    PDB Id 3ljy Target Id 394782
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25364,YP_001304413.1, 370928 Molecular Weight 25822.84 Da.
    Residues 242 Isoelectric Point 6.11
    Sequence aadhvkgdgkltskkisvadyneikvdgvidfnyeqsddpstvevtvdqnlhpyvnievkdrvltiafk gakvdhftkfivktnskwlaaakvsgnanfmvnspltgdetvikananslvqlketvtvgkldlnvsgs anmvvnhleadkiecdidgsgsitikkgnakegdysivssgdihafglavpqlsckvtgnglaevhatd nlkanvvgkgnirykgptavqqriigkgtveevke
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 2.41 Rfree 0.225
    Matthews' coefficent 2.72 Rfactor 0.189
    Waters 139 Solvent Content 54.76

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ljy

    Protein Summary

     Gene BDI_3085 from  Parabacteroides distasonis attc 8503, a species of anaerobic bacteria that are predominant components of the bacterial florae of mucous membrane and are a common cause of several endogenous infections, encodes the YP_001304413 protein which belongs to the DUF2807 (PF10988) family. Two other JCSG targets, Target ID 394781 and 394796, belong to this family.

    Pfam update: This is the first structural representative of what is quite a large family. Currently it matches 102 species and nearly 300 structures.

    Analysis of its genome context with STRING, provides a reliable hit (score 0.89) with the putative liprotein YP_001304412. Despite low sequence similarity, not detected on sequence level, the protein has a known fold of a right handed beta helix.

     

    There are three molecules found in the asu of the x-ray crystal structure, and the likely biomolecule is a monomer.

    monomer_A.png

    Figure 1. Monomer of 3ljy containing all beta strands (red) except a small helix at the N-terminal (cyan).

     As shown below, one molecule (chain A) is located in anti-pararrel with the other two molecules.

    Three_asu1.png

    Figure 2. There are three molecules found in the asu. One molecule (chain A, left) is located in anti-pararrel with two other chains (right and bottom). Color code: N-terminal region in blue and the C-terminal region in red.

     

    Top DALI hit, after 3jx8 (Z-scr=33) is with an acetyltransferase from N. meningitidis [Ref]:

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 2wle-C 11.5 10.0 148 211 11 PDB MOLECULE: POLYSIALIC ACID O-ACETYLTRANSFERASE; 2: 2wlf-A 11.4 10.0 148 210 10 PDB MOLECULE: POLYSIALIC ACID O-ACETYLTRANSFERASE; 3: 2wlf-C 11.4 10.1 148 211 11 PDB MOLECULE: POLYSIALIC ACID O-ACETYLTRANSFERASE; 4: 2wld-A 11.3 10.0 148 210 10 PDB MOLECULE: POLYSIALIC ACID O-ACETYLTRANSFERASE; 5: 2wlg-C 11.3 10.1 148 210 11 PDB MOLECULE: POLYSIALIC ACID O-ACETYLTRANSFERASE; 6: 2wlf-B 11.2 10.3 148 211 11 PDB MOLECULE: POLYSIALIC ACID O-ACETYLTRANSFERASE; 7: 2wle-B 11.2 10.3 148 210 11 PDB MOLECULE: POLYSIALIC ACID O-ACETYLTRANSFERASE; 8: 2wlg-B 11.0 10.0 147 209 11 PDB MOLECULE: POLYSIALIC ACID O-ACETYLTRANSFERASE; 9: 2iq7-B 10.5 3.2 177 339 6 PDB MOLECULE: ENDOPOLYGALACTURONASE; 10: 2wld-B 10.5 10.5 140 211 11 PDB MOLECULE: POLYSIALIC ACID O-ACETYLTRANSFERASE; 11: 2iq7-F 10.4 3.2 176 338 6 PDB MOLECULE: ENDOPOLYGALACTURONASE; 12: 1ib4-A 10.4 3.3 177 339 5 PDB MOLECULE: POLYGALACTURONASE; 13: 2iq7-C 10.4 3.2 178 339 7 PDB MOLECULE: ENDOPOLYGALACTURONASE; 14: 2iq7-G 10.4 3.2 178 339 6 PDB MOLECULE: ENDOPOLYGALACTURONASE; 15: 2iq7-D 10.4 3.1 178 339 6 PDB MOLECULE: ENDOPOLYGALACTURONASE; 16: 2iq7-E 10.4 3.2 178 339 6 PDB MOLECULE: ENDOPOLYGALACTURONASE; 17: 1nhc-B 10.2 3.3 176 336 3 PDB MOLECULE: POLYGALACTURONASE I; 18: 1nhc-C 10.2 3.3 176 336 3 PDB MOLECULE: POLYGALACTURONASE I; 19: 1nhc-D 10.2 3.1 176 336 4 PDB MOLECULE: POLYGALACTURONASE I; 20: 2iq7-A 10.1 3.0 172 339 6 PDB MOLECULE: ENDOPOLYGALACTURONASE;  

    Although the structure is similar to the acetyltranferease, there is no conservation of catalytic residues found. Therefore, we hypothesize that BDI_3085 would have a similar function (cell adhesion) to the other two JCSG targets above.

    Ligand Summary

    Reviews

    References

     

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