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The Open Protein Structure Annotation Network
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3h0n

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

    Title The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45  resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator. Acta Crystallogr.,Sect.F 66 1198-1204 2010
    Site JCSG
    PDB Id 3h0n Target Id 374450
    Molecular Characteristics
    Source Jannaschia sp. ccs1
    Alias Ids TPS1628,YP_510353.1, PF07336, 382875 Molecular Weight 20660.11 Da.
    Residues 187 Isoelectric Point 6.58
    Sequence mnldsyertglrvsldlvniatpgsrrgtphtggcviedlhdllkddpasvaqlgddhvegfvelarll htaidalsngqvataatalnhllrkhpatpelaqdpdgtwrlhhhpldaelvpmwtaicaeglareigh qnvrrfgicnahrcdrvyfdtsrngtrqycslacqnrvkaaafrerrat
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.45 Rfree 0.157
    Matthews' coefficent 2.51 Rfactor 0.140
    Waters 242 Solvent Content 50.95

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3h0n
    1. TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures
    SS Krishna, D Weekes, C Bakolitsa - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Structural classification of proteins and structural genomics: new insights into protein folding and evolution
    A Andreeva, AG Murzin - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org
     
    3. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    4. The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 A resolution reveals a new fold (the ABATE domain) and suggests its possible role as a
    C Bakolitsa, A Bateman, KK Jin, D McMullan - Section F: Structural , 2009 - scripts.iucr.org
     

    Protein Summary

    The gene Jann_2411 from Jannaschia sp. ccs1 encodes the protein YP_510353, the first structural representative of the DUF1470 (PF07336) family, that reveals a two-domain organization with the N-terminal domain presenting a new fold belonging to the DUF1470 and the C-terminal domain a treble-clef, zinc finger from the zf-CGNR group (PF11706). The structure additionally allowed a re-evaluation of the Pfam signature and the Pfam assignment and suggests a role for this family in stress-induced transcriptional regulation.
     

    SCOP classifies Jann_2411 as an unusual (new?) fold. The N-terminal domain (residues 1-142) can be visualized as two sub-domains (residues 1-55 and 56-142) sharing similar topology and secondary structure elements, namely a helix-β-hairpin-helix motif, with an additional helix in each sub-domain linking the two motifs (Fig. 1). Sequence alignment shows little residue conservation in this domain, with no strictly conserved residues observed between Jann_2411 and representative DUF1470 sequences suggesting evolutionary plasticity for this domain.



    Figure 1. Ribbon diagram of the Jann_2411 N-terminal domain. The first sub-domain is shown in green, the second sub-domain is shown in magenta. See text for more details.


    The second domain (residues 143-187) forms a treble clef zinc finger. The zinc ion is coordinated by two cysteines (Cys147, Cys152) from a loop, termed the zinc knuckle, located between the strands of the third β-hairpin, and two cysteines from the N-terminus of helix H9 (Cys168, Cys172) (Fig. 2). This placement of zinc-coordinating residues, is typical of treble clef zinc fingers (1, 2). A superposition the zinc finger in Jann_2411 and the treble clef zinc finger from yeast (PDB id: 2jmi), shows that the arrangement of the zinc ion and coordinating cysteines is shared between the two structures.

    Figure 2. The C-terminal domain of Jann_2411 forms a treble-clef zinc finger. Structural superposition of the C-terminal domain of Jann_2411 (PDB id: 2pw4, residues 144-187, in gray) and a PHD finger fragment from yeast Yng1 protein (PDB id: 2jmi, residues 38-83 in blue). Zinc ions are shown as spheres and coordinating residues are indicated.


    Treble clef zinc fingers are usually incorporated in larger structures and are found in proteins with a wide range of functions, many of which involve transcriptional regulation (1, 2). Of note, the Jann_2411 zinc finger domain harbors several positively charged residues that are conserved across the majority of members of this family. In the Jann_2411 dimer, the likely quaternary form of the protein, these residues (Arg143, Arg161, Arg165, Arg 175, Lys 177, Arg 182 and Arg184) are clustered on one face of the zinc-finger domain and could plausibly present a nucleic acid binding site (Fig. 3). In the same region, a high degree of conservation is seen in Jann_2411 sequence position 146 (hydrophobic residue) and 167 (aromatic residue), residues that could allow for specific stacking between DNA bases.



    Figure 3. Conservation of positive charge in the Jann_2411 dimer. Conserved residues are depicted as spheres and labeled along one of the interacting monomers.

     

    We have named the  N-terminal the ABATE domain, that represents the Alpha-Beta-hairpin-Alpha TandEm motif. Based on the most conserved motif found in the C-terminal α-helix in this family of proteins, we have named this domain the CGNR zinc finger (Cys-Gly-asN-aRg). The actual sequence in Jann_2411 is CQNR (Fig. 4). These findings led to the reevaluation of the Pfam DUF1470 family which,  as a result of our study,  will now be split into two entries in the next Pfam release (n.b. the current release is Pfam 23.0, July 2008). The original DUF1470 entry was truncated and renamed to represent the ABATE domain, while a new Pfam family was created for the C-terminal CGNR zinc finger domain called zf-CGNR (Pfam accession: PF11706).

     

    DUF1470_Pfam.png

     

    Figure 4. Multiple sequence alignment of Jann_2411 and representative ABATE family sequences from related species. Sequences were chosen from the DUF1470 Pfam seed alignment. The alignment was derived from the Pfam full alignment. UniProt abbreviations are as follows: Q28PN4_JANSC, gene locus Jann_2411 from Jannaschia sp. (strain CSS1); Q92QX7_RHIME, gene locus R01166 from Rhizobium meliloti; Q98CF3_RHILO, gene locus mlr5173 from Rhizobium loti; Q9L267_STRCO, gene locus SCO1542 from Streptomyces coelicolor; Q8UGB4_AGRT5, gene locus Atu1124 from Agrobacterium tumefaciens; Q8XT11_RALSO, gene locus RSp0306 from Ralstonia solonacearum; Q9RJT3_STRO, gene locus SCO0403 from Streptomyces coelicolor; Q89FX4_BRAJA, gene locus bII6575 Bradyrhizobium japonicum; Q93J49_STRCO, gene locus SCO3054 from Streptomyces coelicolor.


    Genes predicted (http://string.embl.de) to have functional associations with Jann_2411 include the transcriptional regulator Jann_2412, a member of the Asr gene family. Most Asr genes are upregulated under a range of environmental stress conditions and their products are thought to function as transcriptional regulators (3). Other members of the DUF1470 protein family are found in plant symbionts (Rhizobium, Bradyrhizobium) and plant pathogens (Streptomyces, Ralstonia, Agrobacterium), all of which are around 180 residues in length. Genome location analysis of representative DUF1470 sequences shows co-occurrence with putative DNA-binding proteins and transcriptional regulators. In Streptomyces, several of the DNA-binding proteins co-occurring with DUF1470 homologs, are suggested to play a role in the regulation of methylenomycin production. Production of this antibiotic is known to be triggered by environmental signals such as growth-rate-limiting conditions and acidic shock (4). In this context, the weakly conserved N-terminal domain could provide functional versatility by acting as a transcription response modifier.

     The YP_510353.1 gene from M. jannaschi domain encodes a protein comprising two domains. The N-terminal presents an unusual fold and shows little sequence conservation among Jann_2411 homologs (DUF1470/PF07336). The C-terminal domain folds into a highly conserved treble-clef zinc finger. Structural and genomic analysis of this protein family suggests a role as a bacterial transcription regulator, possibly activated under conditions of environmental stress.

    Ligand Summary

    C-terminal domain contains a strictly conserved zinc-binding site

    References

    Reviews

    References

     

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