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PF09904

    Table of contents
    1. 1. Topsan Members
    2. 2. Summary

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    Resources
    Pfam ID: DUF2131 PDB: 3ke2_A
    Solved by: JCSG Priority Score: 3.6
    Member of this family is in PDB.
    Member of this clan is in PDB.
    Co-occurence with annotated domain(s) (no restrictions on number of architectures).
    HMMER:
      # sequence matches: 149 # architectures: 3 # taxonomy ids:81
    FFAS:
      Top FFAS hit in PDB: "3ke2A, uncharacterized protein YP_928783.1" Top FFAS hit in Pfam: "PF04492, Bacteriophage replication protein O "
    GRDB:
      Top significant hit (PDB90): "3ke2A, structural genomics, unknown function ; crystal structure of structural genomics, unknown function (yp_928783.1) from shewanella amazonensis sb2b at 2.50 a resolution "
    PUBSERVER:
      Publications(s) found: 86
      Publications(s) meeting filtering criteria: 0
    GeneSilico Metaserver: (Login and password: Jamboree)
    PDBBLAST: PDB: 3ke2_A SCOP: predicted a.4.5.24
    FFAS: PDB: 3ke2_A SCOP: predicted a.4.5.24
    BLASTP: PDB: 3ke2_A SCOP: predicted a.4.5.24
    HHBLITS: PDB: 3ke2_A SCOP: predicted a.4.5.24
    COMA: PDB: 3ke2_A SCOP: predicted a.4.5.24
    CSBLAST: PDB: 3ke2_A SCOP: predicted a.4.5.24
    HHSEARCH: PDB: 3ke2_A SCOP: predicted a.4.5.24

    Topsan Members

    Tag pages as 'PF09904' to appear in this list.

    Name Annotation Author(s)
    3ke2
    Gene Sama_2911 from Shewanella amazonensis sb2b encodes the YP_928783 protein that belongs to the DUF2131 Pfam A class (an uncharacterized protein group conserved only in bacteria with two highly cons... haxelrod (6 edits)
    pascual (6 edits)

    Summary

    For more details see the following TOPSAN page for PDB ID 3ke2

    http://www.topsan.org/Proteins/JCSG/3ke2

    The structure is a winged-helix and most likely a transcriptional regulator. 

     

    Shown below is a multiple sequence alignment between that of pdb id 3ke2 and homologs in the non-redundant protein database that show between 30%-60% sequence identity. Alignment was generated using CONSURF after 5 rounds of a PSI-BLAST search of the nr sequence database.

    consurf_alignment.bmp

    The alignment shows that several basic amino acid sidechains on 3ke2 are conserved including Arg 20, Lys 21, Arg 46, and Arg 47. These conserved residues are on a HTH structural motif that is found in several DNA binding protein including those of transcriptional repressors.

    A DALI structural similarity search shows that 3ke2 is similar to the structure of PDBID 2h09 (DALI Z-score=8.1,rmsd=3.2 Ang, alignment length=83 residues,sequnce id=10%) a manganese transport regulatory protein from E. coli. [Ref]. Manganese transport regulatory protein (MntR) controls manganese homeostasis in B. subtilis and E. coli by repressing the transcription of genes encoding manganese uptake transporters. Tanaka et al. [Ref] proposed several residues on MntR to be positioned for close range interaction with dsDNA. Comparison of the structure of 3ke2 with that of 2h09 shows that conserved basic amino acid sidechains on 3ke2 including Arg 20, Lys 21 and Arg 47 respectively  overlap with Arg 34, Arg 77, and Lys 73 on 2h09. This structural comparison provides supporting evidence the 3ke2, along with others in DUF2131 PF09904 function as transcriptional repressors.

    A jFATCAT seach from the RCSB for the structure of 3ke2 reports that chain B, PDB ID 3hhh,  the rystal structure of transcriptional regulator, a member of PadR family, from Enterococcus faecalis V583, is the top-scoring hit (Score=188.17, rmsd=4.52 Ang, length of alignment=103,sequence id-5%).

     

    The putative DNA binding site on 3ke2 is composed of the HTH motif between helix 2(H2) below and helix 3 (H3) shown below in which the secondary structual elements of 3ke2 is shown along with the corresponding amino acid sequence. A nitrate ion from the crystallization was observed in the crystal structure of 3ke2 at the N-terminal end of H2. The positive charged sidechain of Arg 46 is positioned near the negatively-charged nitrate ion. The peptide backbond of Asn 34, Leu 35, and Leu 36 are within hydrogen bonding distance of the bound nitrate. The presence of an anion binding site suggests proteins in PF09904 could possibly be involved in anion-depedent transcriptional regulation, but more evidence is needed to confirm this hypothesis.

     

    3ke2_pdbsum.gif

     

    Current evidence indicates that proteins in the DUF2131 family can be assigned a DUF annotation level 3 (i.e. function known in Superfamily) based on the annotation scale proposed by Alex Bateman at the DUF Jamboree. Proteins in the DUF 2131 family belong to the "Winged helix" DNA-binding domain Superfamily.

     

     

     

     

     

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