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The Open Protein Structure Annotation Network
PDB Keyword
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4kh8

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

    Title Crystal structure of a hypothetical protein (EF0376) from Enterococcus faecalis V583 at 1.60 A resolution. To be published
    Site JCSG
    PDB Id 4kh8 Target Id 420205
    Molecular Characteristics
    Source Enterococcus faecalis v583
    Alias Ids TPS78307,NP_814167.1 Molecular Weight 36100.68 Da.
    Residues 317 Isoelectric Point 4.73
    Sequence yvpqsvdnpnnlgdlpeylrsvgirqdeglsekdwagtrvydrngndltdenqnllhaikfdattsfye ffdketgestgdegtffmtagitdvsrlviisetknyqgvyplrtlyqdtftyrqmgkdkngndievfv enkatsgpvygrpqpypnnrprtleftngrramteqtgqidvnrqgdeiigktsfdgtpqllwngtkvv dkdgndvtsanqnfislakfdqdsskyeffnlqtgetrgdygyfkvgnqnkfrahvsigtnrygavlel telndnrftytrmgkdnegndiqvyvehepyqgtfnpeftf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.60 Rfree 0.1727
    Matthews' coefficent 2.25 Rfactor 0.1408
    Waters 352 Solvent Content 45.29

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    I have not built from this as a search shows it to have a highly significant match to: built recently by Adam Godzik Sequence [E6FWM7] overlap NEW NEW/31-347 JALIGN with DUF4822 PF16103/219-335 FULL Sequence [E6FWM7] overlap NEW NEW/31-347 JALIGN with DUF4822 PF16103/53-171 FULL Sequence [E6FWM7] overlap NEW NEW/31-347 JALIGN with DUF4822 PF16103/53-171 SEED Sequence [E6FWM7] overlap NEW NEW/31-347 JALIGN with DUF4822 PF16103/219-335 SEED pfam3a [319692]91% pfinfo PF16103
    ID DUF4822
    AC PF16103
    DE Domain of unknown function (DUF4822)
    AU Godzik A
    SE JCSG target SP18758A
    GA 25.00 25.00;
    TC 46.80 28.10;
    NC 21.30 21.00;
    BM hmmbuild -o /dev/null HMM SEED
    SM hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
    TP Domain
    CL CL0116
    CC A lipocain-like domain found in functionally uncharacterised
    CC bacterial proteins, often as a repeat of two domains. Proteins with
    CC this domain are found in a wide range of bacteria and are often
    CC annotated as S-layer proteins, but the orgin of this annotation is
    CC not clear.
    Marco is very interested inthe lipocalins and lipocains, so he will be keen to see the strucutre when its is solved.

     

     

     

    Hypothetical protein EF0376 from Enterococcus faecalis  consists of two repeats of the newly defined Pfam family DUF4822 (PF16103), which was classified in the lipocain-like clan due to structural similarity to other lipocains (the top hit for both N-term and C-term is 1z24, lipid binding protein, score 159.34, p = 5.4E-5)

    The structure alignment  N-terminus domain  (green color)  and C-terminus domain (aquamarine) confirms their high similarity.

    sp18758A_2.png

     

    sp18758A_N.sp18758A_3.png

     

     

     

    The structure shows that the N-terminal domain is comprised of residues 37-200 and the C-terminal domain is comprised of residues 201-347. The two domains overlap with an rmsd of 1.8 Angstroms with a 40% sequence id between the two domains.

    A structural similarity search shows the structure of target id 420205 represents the first reported structure of two repeating lipocalin-like  domains. Shown below is are the top-scoring structures in the PDB similar to that of target id 420205

    PDB ID target length P-value twist opt-length opt-rmsd (Ang) alignment length gap Seq id (%) Description
    3ebk 165 6.72e-04 0 103 3.06 144 41 5.6 Crystal structure of major allergens, Bla g 4 from cockroaches[Ref]
    1z24 189 1.28e-03 0 106 3.01 151 45 5.3 The molecular structure of insecticyanin from the tobacco hornworm Manduca sexta L. at 2.6 A resolution.[Ref]
    1d2u 184 1.45e-03 0 113 3.34 192 79 5.7 1.15 A CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS[Ref]
    1u17 185 1.60e-03 0 110 3.16 192 82 6.25 1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme complexed with two molecules imidazole
    2cm4 145 1.60e-03 0 101 3.01 138 37 4.35 THE COMPLEMENT INHIBITOR OMCI IN COMPLEX WITH RICINOLEIC ACID[Ref]
    3hty 94 1.60e-03 0 86 3.14 132 46 5.30 Crystal structure of hypothetical protein BT_0869 from Bacteroides thetaiotaomicron VPI-5482 (NP_809782.1) at 1.95 A resolution
    1bbp 173 3.54e-03 0 102 3.08 148 46 9.46 MOLECULAR STRUCTURE OF THE BILIN BINDING PROTEIN (BBP) FROM PIERIS BRASSICAE AFTER REFINEMENT AT 2.0 ANGSTROMS RESOLUTION.[Ref]
    1iiu 174 3.58e-03 0 102 3.08 154 52 5.84 Chicken plasma retinol-binding protein (RBP)[Ref]
    2hzq 166 4.02e-03 0 97 3.02 144 47 5.56 Crystal structure of human apolipoprotein D (ApoD) in complex with progesterone[Ref]
    3fmz 174 4.78e-03 0 101 3.08 153 52 5.88 Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand[Ref]
    1euo 180 5.33e-03 0 93 3.07 133 40 4.51 Crystal structure of nitrophorin 2 (prolixin-S)[Ref]

    The structural similarity shows that the structure of target id 420205 shows similarity to another JCSG target, PDB id 3hty. Target id 420205 shows two additional paralogs in Enterococcus faecalis v583.

     

     

    Further analysis shows that there are two large cavities on both the N-terminal and C-terminal domains that most likely correspond to ligand binding sites. These cavities represent those found on other lipocalin structures. Shown below are residues that comprise the cavity on the N-terminal domain.

     

    cavity_N_term.bmp

     

     

     

    Shown below is the putative ligand binding cavity on the C-terminal domain.

    cavity_C_term.bmp

     

     

     

    Comparison of the two cavitues shows that they are different. The cavity on the N-terminal domain shows more hydrophobic sidechains, whereas the cavity on the C-terminal domain shows fewer residues and is more polar than the cavity on the N-terminal domain. An unknown ligand (UNL) was observed in the ligand binding cavity on the N-terminal domain. Shown below is a representation of the bound UNL with superimposed 2fo-fc electron density.

    UNL.bmp

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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