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The Open Protein Structure Annotation Network
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3k8r

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

    Title Crystal structure of protein of unknown function (YP_427503.1) from Rhodospirillum rubrum ATCC 11170 at 2.75 A resolution. To be published
    Site JCSG
    PDB Id 3k8r Target Id 391960
    Molecular Characteristics
    Source Rhodospirillum rubrum atcc 11170
    Alias Ids TPS27705,YP_427503.1, 325793 Molecular Weight 13205.13 Da.
    Residues 123 Isoelectric Point 5.07
    Sequence madltdalidaalergrsahanepraakarydrssarvivdlengctfafpprlaqglegasddqlcav eilgqgyglhwetldvdlslpglmagifgtkawmakraepppsaakdawsnlpr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.75 Rfree 0.235
    Matthews' coefficent 2.66 Rfactor 0.213
    Waters 4 Solvent Content 53.72

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3k8r
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

    Protein Summary

    Pfam update: This protein is part of DUF3532. It is the first structure for the family so will be very interesting. The most conserved feature is a DXD motif at the C-terminal end of the domain, which looks to be functionally important. It is intresting that some members of the family have a 50 amino acid insert just before this motif. There is also a protein that contains a duplication of this domain: A8YGB5_MICAE from Microcystis aeruginosa. Let me know if you would like some help writing this one up. The structure you have found similarity to is part of DUF2442. One of the sequences belonging to the this DUF is the second highest scoring insignificant match. DUF2442 is annotated as: "This family of bacterial and fungal proteins has several members annotated as being putative molybdopterin-guanine dinucleotide biosynthesis protein A; however this could not be verified. Hence the function is not known." The highest scoring insignificant match is to a sequence belonging to PF00345.

     

    Gene Rru_A2416 from Rhodospirillum rubrum atcc 11170 encodes the YP_427503 protein of unknown function that belongs to Pfam DUF3532. It shows sequence similarity to many other hypothetical proteins by PSI-BLAST. A weak PSI-BLAST hit is to a putative integron gene cassette protein (NCBI GI: 164515077, Ref1, e-value=2e-16, 27% sequence identity, 2 rounds of PSI-BLAST, UniProt id B0BG20_9BACT). STRING analysis of the Rru_A2416 gene vicinity shows a co-ocurrence hit scored at 0.7 with Rru_A3015, a twin-arginine translocation pathway signal protein (YP_428097).

    There are no significant hits with FFAS although there is a weak similarity (FFAS score -8.6) to a hypothetical/putative DNA binding protein (PDB id 2auw). HHpred and 3D-blast corroborate weak hit. This similarity maps onto the most conserved regions of our protein and there is reasonable topological similarities.

    A search for other proteins of similar structure using DALI also returns 2auw as the top hit (Z-score 7.1, 2.4A rmsd over 69 aligned Ca atoms, 13% sequence identity; the next hit, 2de6, is at Z-score 4.2 with 3.2A rmsd over 61 Ca). The FATCAT server also shows that 2auw is the most significant hit in terms of structural similarity (P-value 7.59e-05 vs. the next hit, 2jo6, at 6.60e-04). A search for other proteins of similar structure using SSM returns a single low scoring hit with a biphenyl dioxygenase BphA (Q-score=0.22, Z-score 4.2, rmsd=2.57A over 59 Ca atoms, 15% sequence identity, SSE 60%) with PDB id 2e4p.

    The protein is present as a dimer in the 3k8r crystal structure:

    Fig1.png

    The 3k8r structure reveals a structural motif of 3 anti-parallel beta strands followed by an alpha-helix (residues 22-69). This motif is then repeated in residues 70-103:

     

    Fig2.png

    3k8r (purple) superimposes with the N-terminal domain of 2auw (cyan; the C-terminal domain of 2auw belongs to the SCOP family of lambda repressor-like DNA binding domain). The N-terminal domain of 2auw has been classified into a new SCOP fold, NE0471 N-terminal domain-like.

    Fig3.png

    and the structure-based sequence alignment (DALI Lite) shows the residue conservation:

     

     

     

     

    DSSP  ..LLLEEEEEEELllLEEEEEELLLLEEEELHHHLL....LLLL.LLHHHHLLLEEELLL
    Query ..EPRAAKARYDRssARVIVDLENGCTFAFPPRLAQ....GLEG.ASDDQLCAVEILGQG 53
    ident    |            |       |                |           | |
    Sbjct yfFPKLTAVEALA.pYRLRTTWSTGEVLEVDVGDILrkipDLAPiLDPEAFARVHIAEWE 59
    DSSP  llLLLEEEEEELL.lLEEEEEELLLLEEEEELHHHHhhlhHHHHhHLHHHHLLLEELLLL


    DSSP  LEEEELllLEEEEHHHHHHL........................................
    Query YGLHWEtlDVDLSLPGLXAG........................................ 73
    ident     |   |         |
    Sbjct GSVEWF..DTEFGRDNVYAWakeqagevshexfgdwxhrnnlslttaaealgisrrxvsy 117
    DSSP LLEELL..LLLLLHHHHHHHhhhhlllllhhhhhhhhhhllllhhhhhhhhlllhhhhhh


    DSSP  ......................llllhhhhhlll
    Query ......................ifgtkawxakra 85
    ident
    Sbjct yrtahkiiprtiwlaclgweatrpetktlprtlp 151
    DSSP  hhlllllllhhhhhhhhhhhhlllllllllllll

     

    It should be noted that the structure of 3k8r here is ~70% complete at 2.7A. So it is possible that the remaining portion of the protein may have more structural features similar to 2auw.

    However, it is more likely that this is a like an integron gene cassette protein of unknown function.

    Further structure-putative function analysis will be presented later.

     

    References:

    1. Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments.Koenig, JE, et. al. Environ Microbiol. 2008 Apr;10(4):1024-38. Epub 2008 Jan 7. 

    Ligand Summary

    Reviews

    References

     

    No references found.

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