The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of conserved hypothetical protein (ZP_00837230.1) from Shewanella sp. PV-4 at 1.60 A resolution. To be published
    Site JCSG
    PDB Id 2gpi Target Id
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    Molecular Characteristics
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    Alias Ids
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    TPS1462,YP_001095851.1, PF07369, 382619
    Molecular Weight
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    Isoelectric Point
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Matthews' coefficent 2.74 Rfactor 0.151
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    Solvent Content 55.19

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    Ligand Information


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    Google Scholar output for 2gpi
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - 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. Mode of Interaction between [beta] 2GPI
    CJ Lee, A De Biasio, N Beglova - Structure, 2010 - Elsevier
    4. Advances in Implicit Models of Water Solvent to Compute Conformational Free Energy and Molecular Dynamics of Proteins at Constant pH.
    YN VOROBJEV - Computational Chemistry Methods in Structural , 2011 - books.google.com
    5. Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments
    F Pavelcik, J Vaclavik - Acta Crystallographica Section D: Biological , 2010 - scripts.iucr.org
    6. Identification of novel sweet protein for nutritional applications
    M Gnanavel, MS Peddha - Bioinformation, 2011 - ncbi.nlm.nih.gov
    7. Characterisation of the redox changes in the HIV envelope glycoprotein during cell entry
    I Azimi - 2010 - unsworks.unsw.edu.au

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    Protein Summary

    The Shew_3726 gene of Shewanella sp. PV-4 encodes the first structural representative of protein family PF07369 (DUF1488). The structure reveals a left-handed beta-sheet wrapped around a central helix that adopts a novel fold. Remote structural similarity with PX and SH2 domains suggests a possible role in signaling through interaction with a phosphorylated ligand such as phosphotyrosine or a nucleotide-based second messenger, while remote sequence homology with transcription factors suggests possible interactions with RNA. The electrostatic surface of Shew_3726 reveals a basic patch formed by main-chain nitrogens that could serve as a binding site, while the genome context of this family suggests a involvement in shikimate biosynthesis.


    Overall structure

    Shew_3726 comprises a single α+β domain characterized by a three-helix insertion between the last two strands of a mixed beta sheet (Fig. 1). The helices are all located on one side of the sheet that twists around them along the longest axis of the protein. The structure is classified in SCOP as a new fold (http://scop.mrc-lmb.cam.ac.uk/scop/d...bcf.b.b.b.html).




    Figure 1: Crystal structure of Shew_3726 from Shewanella loihica. (A) Stereo ribbon diagram of the Shew_3726 monomer color-coded from N-terminus (blue) to C-terminus (red). Helices H1–H3 and β-strands (β1−β4) are indicated. (B) Diagram showing the secondary structure elements of Shew_3726 superimposed on its primary sequence. The labeling of secondary structure elements is in accord with PDBsum (http://www.ebi.ac.uk/pdbsum), where α-helices are labeled H1, H2, H3 etc., β-strands are assigned to the β-sheets to which they belong  and labeled A,B, etc., β-turns and γ-turns are designated by their respective Greek letters (β, γ), and red loops indicate β-hairpins. For Shew_3726, the α-helices (H1-H3), β-strands in the β-sheet (A), β-turns (β) and γ-turn (γ) are indicated.


    Similarity to other structures

    A search with DALI {Holm, 1995 #22} reveals similarities of Shew_3726 with the SH2 and PX domains (Fig. 2). However, these similarities are weak (top hits have Z-score 4-4.3, main-chain rmsd 3.5-4.4 Å over 68-74 residues, sequence identity 1-8%) with superposition covering only the three-stranded beta sheet characteristic of the SH2 fold but missing both the extra strands found in Shew_3726 and the bidirectional flanking of the sheet by helices that characterizes SH2 domains (Fig. 2A). Shew_3726 is closest to PX domains, although it has additional C-terminal β-strand and misses several helices observed in PX domains (Fig. 2B).

    Src homology 2 (SH2) domains constitute the most prevalent phosphotyrosine-recognising module and are involved in regulating protein tyrosine kinase signaling (Machida & Mayer, 2005). Phox homology (PX) domains are implicated in a variety of cell-signaling processes, such as cell-polarity and membrane targeting, through phosphoinositide-binding (DiNitto et al., 2003). Both SH2 and PX domains are eykaryotic specific signaling modules. Although phosphoinositide-based signaling is absent from bacteria, prokaryotic signal transduction involves phosphorylation (Zhang et al., 1998) and nucleotide-based second messengers (Pesavento & Hengge, 2009).




    Figure 2: Shew_3726 exhibits structural similarity to PX and SH2-like folds. Stereo ribbon diagram showing the superposition of Shew_3726 (PDB id: 2gpi, residues 1-90, in blue) and (A) the SH2 domain from human haematopoietic cell kinase (PDB id 2hck, residues 142-244, in magenta), (B) the human p47 (phox) PX domain (PDB 1o7k, residues 4-123, in gray).


    The DUF1488 protein family
    The DUF1488 family as defined by the Pfam database contains over 140 homologous proteins from a variety of alpha, beta and gamma proteobacteria. The E. coli member of this family is called YrdB. Nearly all members of this family are composed solely of this domain and are less than 100 amino acids in length.  However there are a few exceptions that have an extended N-terminus, for example Q3JFS8 and Q2T4Y2 from burkholderia species.


    Shew_3726 has two adjacent clusters of conserved residues - cluster A: Phe-7, Glu-9, Phe-22 (buried), Cys-33 (buried), Leu-40, Phe-58 (buried), Arg-62, and Glu-66; cluster B: Asn-2, Gln-3, Ile-5, Ile-73. Two conserved glycines (Gly-28, Gly-82) may play important role in protein folding.


    Sequence similarity to other protein families.
    Weak sequence similarity to protein serine/threonine phosphatases 2C (PP2C, cd00143) is not located on the equivalent structural fragments, so this similarity is irrelevant.

    A weak match (score 41.3) was identified to the GRAS transcription factor family (PF03514) with the SCOOP software, but this similarity did not appear to be backed up by further sequence analysis.

    A search with HHPred {Soding, 2005 #111} showed a weak similarity (P-value 0.0057) to PF06421(LepA_C, ex DUF1012), the C-terminal domain of LepA (EF4), over almost the entire length of the protein (residues 5-68).



    LepA has been shown to be implicated in the back-translocation of tRNAs on the ribosome during the elongation cycle (Qin 2006). Although the near-universal presence of LepA in bacteria implies a central role, LepA knockout strains are viable, suggesting that LepA is essential under certain growth conditions (e.g. in Helicobacter pylori, LepA is essential to sustain growth at low pH (Bijlsma 2000)). The C-terminal domain (CTD) of LepA is unique to LepA (other domains show homology fo EF-G domain) and is thought to form a new fold (Evans 2008). The E. coli CTD is very basic and has been proposed to serve a primary role in back translocation by providing additional binding interactions with a back-translocated tRNA.


    Figure 3: Shew_3726 exhibits weak sequence and structural similarity to the C-terminal domain of LepA (EF4). Ribbon diagram of the C-terminal domain of LepA (PDB id: 2ywg, residues 484-551).


    Shew_3726 does not share the large basic surfaces characteristic of PX, SH2 and LepA CTD domains, and is in fact overall a highly acidic protein. It does, however, contain a localized basic patch in the groove formed between helix H1, and strands β4 and β5 (Fig. 4). There is no strong residue conservation in this area of the protein with the main contributions in forming the basic patch coming for the most part from main-chain nitrogens (Gln36, Gln85, Val86). This suggests that formation of this basic cavity is due to the fold itself, rather than the chemical character of individual residues. This notion is supported by the presence of two strictly conserved glycines (Gly28, Gly82) located at the beginning of strands β4 and β5 respectively that could play an important role in maintaining the protein fold.

    Involvement of main-chain nitrogens and carbonyl oxygens in phosphate binding been previously reported (Shi 2000) (Gonzalez-Segura 2009), including recognition of phosphotyrosine (Sarmiento 2000).



    Figure 4. A potential binding site formed by the fold of Shew_3726. (A) Electrostatic surface potential representation of Shew_3726 calculated with the program APBS (Baker et al., 2001). Positive potential is in blue (+10kTe-1), negative is in red (-10kTe-1). (B) Ribbon representation of Shew_3726 in the same orientation as in (A). Conserved glycines and main-chain nitrogens involved in formation of the basic patch are in ball-and-stick and labeled.


    [NB - Basic patch does not match sequence conservation pattern. Explore fold similarities further - is there a common structural core/overlap between SH2, PX and 2gpi families?]

    Genomic context.
    In Shewanella sp. PV-4 and over 20 other genomes, Shew_3726 gene is downstream of AroE (shikimate 5-dehydrogenase or dehydroshikimate reductase), indicating an important correlation between both genes. Other functional correlations involve DNA topoisomerase type I, yrdD (topoisomerase DNA-binding), hbiA (HtH luxR-type DNA-binding domain protein), DNA protecting protein DprA (Tadesse 2007), rimN (ribosome maturation factor, required for maturation of 16S rRNA, may keep an rRNA structure needed for proper processing of 16S rRNA), iraP (anti-adapter protein, involved in regulation of cellular stress, namely phosphate starvation (Bougdour 2007)).


    The shikimate pathway plays a pivotal role in the production of precursors of aromatic compounds in microorganisms and plants. The pathway is absent from mammals and presents an attractive target for herbicides and antimicrobial agents development. Phosphate sensing would be a natural step of regulating this pathway since condensation of two phosphate-containing compounds, phosphoenolpyruvate and erythrose-4-phosphate, forms the first step (Fig. 5).


    We therefore propose that Shew_3726 homologs are implicated in transcriptional regulation of the shikimate pathway, likely under conditions of environmental stress, such as phosphate starvation. This regulation could take the form of binding to a phosphorylated compound  (e.g. phosphotyrosine or phosphoinositide, by analogy with SH2 and PX domains respectively) in the basic cavity formed by this novel fold or by interaction with nucleic acids during transcription (e.g. RNA, by analogy with the CTD of LepA).



     Figure 5. The shikimate pathway in higher plants. Reproduced from Herrmann and Weaver, 1999.


    To do - confirm functional prediction: 2gpi can transfer Tyrosyl-tRNA to shikimate 5-dehydrogenase? Possible ligands: Tyrosyl-tRNA or ssDNA/RNA or phosphatidylinositol 3-phosphate, or peptide with phosphotyrosine.

    Ligand Summary





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