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2re3

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

    Title Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction. Acta Crystallogr.,Sect.F 66 1218-1225 2010
    Site JCSG
    PDB Id 2re3 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1631,YP_165412.1, PF06938, 285601
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 3.00 Rfactor 0.215
    Waters
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    Solvent Content 59.02

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 2re3
    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. Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain
    Q Xu, A Bateman, RD Finn, P Abdubek - Journal of molecular , 2010 - Elsevier
     
    4. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal
    GW Han, C Bakolitsa, MD Miller, A Kumar - Section F: Structural , 2010 - scripts.iucr.org
     
    5. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

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    Protein Summary

    The SPO0140 gene from Silicibacter pomeroyi encodes the YP_165412 protein, a member of the protein family PF06938 (DUF1285), which is an uncharacterized family of bacterial proteins (COG3816). SPO0140 (PDB id: 2re3) and Sbal_2486 (PDB id: 2ra9) provide the first structural representatives of this family. SPO0140 genomic context (SPO0025, hypothetical hydrolase from the NUDIX family and SPO0026, a polyA polymerase family protein) indicates functional association (score 0.63) with nucleic acid processing enzymes.

      

    The 2re3 structure reveals a PH-like domain with some structural similarity to proteins that bind DNA or RNA (1prk, 1l3a, 2gia) or negatively charged oligosaccharides  (PDB:1plf). SPO0140 is an a/b protein comprising two domains (Fig. 1) both characterized by short helix-β-meander motifs. Each β-meander is composed of three anti-parallel β-strands linked by hairpins to form a small sheet, while the intervening helices are oriented at right angles to one another. The N-terminal domain (residues 1-93) consists of two helix-meander motifs with the two β-meanders aligning along their edge to form a twisted mixed sheet. This arrangement is repeated in the C-terminal domain (residues 94-193) with an additional β-sheet packing up against one end of the six-stranded twisted mixed sheet to form a β-sandwich (Fig. 1).

         

    2re3_topFig1 (1).png

     

    Figure 1. Ribbon diagram of SPO0140. Rainbow color coding is from blue (N-terminus) to red (C-terminus) showing the N-terminal (right) and C-terminal (left) domains. Secondary structure elements are indicated.

     

    SPO0140 crystallized as a dimer with 2-fold symmetry. The dimer buries ~810 Å^2 of solvent-accessible surface per monomer and involves mainly helix H1, strand β1 and the H3-β4 loop from the N-terminal domain, helix H4 and strands β14-β15 from the C-terminal domain. Packing analysis (PISA) indicates that a dimer is the likely biologically relevant form.

         

    [Look at conservation of residues implicated in dimerization interface]

         

    A structural superposition of SPO0140 with Sbal_2486 (PDB id: 2ra9), another member of the DUF1285 family, shows an r.m.s.d of 2.4 Å over 146 residues with a sequence identity of 25% (Dali Z-scr=14). Structural elements missing from Sbal_2486 involve SPO0140 helices H1 and H2 and part of strand β1, as well as the C-terminal β-meander and helix H6 (Fig. 2A). Sbal_2486 crystallized as a monomer, suggesting that the missing regions could be necessary for dimer formation.

         

    [In addition to dimerization, the missing elements are also involved in the formation of the likely binding cavities (see below)].

         

    A search with FATCAT using both domains of SPO0140 revealed weak similarity to a small number of structures with diverse functions, perhaps sharing in common binding to a negatively-charged ligand (sugar-binding platelet activation factor, transcriptional regulator, serine/threonine kinase, mitochondrial RNA binding protein). The closest similarity occurs with PA2021 from Pseudomonas aeruginosa (PDB id: 1ywy) over the C-terminal domain of SPO0140 with an r.m.s.d. of 3.4 Å over 67 residues and a sequence identity of 12% (Fig. 2B). Pre-SCOP classifies PA2021 as having a PH domain-like barrel capped by an alpha helix.

     

    A search using the N-terminal domain of SPO0140 returned a single weak hit with the RNA-recognition motif of polyadenylation element protein 3 (PDB id: 2dnl) with an r.m.s.d. of 3.1 Å over 47 residues and a sequence identity of 14%.

         

    (A) 

    2re3_topsan_2A.png

    (B) 

    2re3_topsan_2B.png

         

    Figure 2. Stereo ribbon diagrams showing the structural superposition of structures exhibiting similarity to SPO0140. (A) Superposition of SPO0140 (residues 10-192, PDB id: 2re3, in gray) with Sbal_2486 (residues 29-155, PDB id: 2ra9, in blue), another member of the DUF1285 family. (B) Superposition of the C-terminal domain of SPO0140 (residues 94-193, PDB id 2re3, in gray) with a member of the UPF0051 family (residues 23-96, PDB id 1ywy, in blue).

     

    In addition to a similarity with the UPF0051 family (PDB id: 1ywy), structural comparisons of the C-terminal domain indicate an involvement with the cytoskeleton. Top hits include the EVH1 domain from a mouse ENA/VASP-like protein (PDB id: 1qc6, r.m.s.d. 3.6 Å over 65 residues, 3% sequence identity), the human EVH1 domain from VASP (PDB id: 1egx, r.m.s.d. 3.5 Å over 64 residues, 7% sequence identity), the human EVH1 domain from mena (PDB id: 2iyb, r.m.s.d. 3.5 Å over 63 residues, 5% sequence identity). Except for sequence identity, these superposition values are very similar to the ones obtained for 1ywy. A superposition of the structures is shown in Fig. 3.


     

    [MoxR genetic context, repeated through DUF1285 family members, also has functional associations with metal binding and chaperones] 

         

    HMM          akkGlPPVhlWNPpFCGDlDmrIaaDGTWFYlGTPIGRkpLVRLFSTvLRrDgDgyTfLVTPVEKVGIrVdDAPFiAVemdvqGEgeeqVLrFrTNVgDvVeAGAdhpLRfeidpetgelkPYihVRgrLEALVaRaVfYdLVelGeerevDGqemfGVrSgGafFPiap
    MATCH        + kG++PVhlWNPpF GD+DmrIa+DGTWFY+GTPI R ++VRLFS++L+r++D   +LVTPVEKVGIrVdDAPF+AV ++v G g +qVL+F T VgD + AG ++p+R + dp tge++PY+hVR++LEAL+ R  fY L +lGe     ++++fG +S G fFP++    
    SPO0140      KSKGPAPVHLWNPPFNGDIDMRIARDGTWFYQGTPINRPAMVRLFSSILKREEDRF-YLVTPVEKVGIRVDDAPFVAVDVEVAGQGRKQVLTFTTHVGDSAVAGEGNPIRMAQDPATGEPAPYVHVRAGLEALIDRKSFYRLMDLGEI----EDGWFGLWSSGSFFPLMT    186  

         

     N-terminal domain cavity (775 Å^3) residues:

         

         

         

    C-terminal domain cavity residues:

         

    Interdomain cavity residues:

         

    Dimer cavity residues:

         

     

     

    A search with CastP reveals two cavities, one in each domain. The N-terminal domain cavity (~775 Å^3) is hydrophobic

    [check electrostatics plot]


    and contains a number of solvent-exposed aromatics (W50, F51, Y52, F66) - also hydrophobic (L14, A20, I21, I40, I44, I57, V83, V86, I88) residues.

         

    [check conservation/alignments]

         

    The  C-terminal domain cavity (~675 Å^3) is of similar nature, containing a number of solvent-exposed hydrophobic and aromatic residues (P140, P142, F159, Y160, L162, W172, F173, L175, L184, L190).

         

    [FY motifs? Are the domains formed by gene duplication? Cavities are not found in 2ra9.]

         

    The largest cavity (~ 1590 Å^3) occurs along the two-fold symmetric dimerization interface (P26, A27, P28, V29, H30, S68, L70, R72, D119, S120, A121, V122, G124, G126, N127, H145, V146, R147, A148, G149, L150).

         

    [significance?] 

         

    The domain architecture of one DUF1285 homolog includes a member of the phosphoglycerate mutase family (PF00300) suggesting an involvement in carbohydrate metabolism.

     

    The genome context (STRING) of  DUF1285 members supports a role in (...). SPO0140 shows a high degree of confidence in a functional association with a member of the MoxR family of ATPases (SPO0139), proteins that have been suggested to act as molecular chaperones (Snider 2006)

     

     

    Ligand Summary



    References

    Reviews

    References

     

    No references found.

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