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The Open Protein Structure Annotation Network
PDB Keyword
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3byq

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

    Title Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism. Acta Crystallogr.,Sect.F 66 1182-1189 2010
    Site JCSG
    PDB Id 3byq Target Id 381697
    Molecular Characteristics
    Source Bordetella bronchiseptica rb50
    Alias Ids TPS1758,NP_889209.1, PF06684, 89071 Molecular Weight 20898.10 Da.
    Residues 192 Isoelectric Point 7.11
    Sequence mslieirkrtlivettyhengpapaqplklaascavirnpyagryepdlmpfmaelrslgtllatelvd tlgkdnievyskaaivgvdgemehgavwheaggwamrsvlgepkamvpavkavatagyrmmvpvhyiha syvrshfnsieigiqdaprpreilfalvmgtgarvharlggltkeavsvhdgqr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 1.70 Rfree 0.169
    Matthews' coefficent 2.32 Rfactor 0.138
    Waters 566 Solvent Content 46.87

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3byq
    1. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-
    C Bakolitsa, A Kumar, KK Jin, D McMullan - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    The DUF1185 (PF06684) protein family  contains more than 200 sequence homologs found mostly in proteobacteria, but found also in Firmicutes and uncultured bacteria from ocean, soil, and human microbiomes, all of which are around 180 residues in length. Members of the DUF1185 family are also present in several human and animal pathogens from the Burkholderia and Bordetella, as well as Clostridia, groups, where their genome location on virulence islands suggests a possible role in pathogenesis ([Ref]).

    The BB2672 gene of Bordetella bronchiseptica encodes the highly conserved NP_889209 protein, a member of the DUF1185 (PF06684) protein family. BB2672 structure, 3byq, belongs to the class of α+β proteins with a mainly antiparallel sheet and segregated α and β regions. 3byq forms a single domain composed of seven β-strands, three α-helices and three 310-helices (Fig. 1), and shows significant structural similarity to proteins from the Bacillus chorismate mutase (BCM)-like fold, a variant by "circular permutation" of the thioredoxin-like fold (2). 


    Figure 1. Crystal structure of BB2672 from Bordetella bronchiseptica. Ribbon diagram of the 3byq monomer rainbow color-coded from N-terminus (blue) to C-terminus (red). Helices H1-H6 and β-strands (β1-β7) are indicated.

     

    A structural superposition (Fig. 2) of 3byq with the chorismate mutase from Bacillus subtilis (PDB accession code: 2cht) reveals a similar overall fold in both structures (backbone RMSD 2.5 Å with 10% sequence identity over 86 aligned residues; DALI Z-score=6) with the exception of strands β1, β5 and β6, and the region C-terminal of strand β7 which are absent in 2cht. These additional structural elements appear to be involved in promoting a distinct oligomerization state in 3byq (see below), namely formation of a hexamer (trimer of dimers) as opposed to a trimer in 2cht.



    2cht3byq.png

    Figure 2. Stereo ribbon diagram showing the structural superposition of BB2672 (PDB id: 3byq, in magenta) and chorismate mutase from Bacillus subtilis (PDB id: 2cht, in cyan).

    Analysis of the crystallographic packing of 3byq using the PISA server  indicates that a hexamer is the likely quaternary form, consistent with results from analytical size exclusion chromatography in combination with static light scattering. The 3byq hexamer is formed by a 180° rotation of each consecutive monomer along the central axis of the molecule, with the helices positioned on the outside and the β-strands layering the inner core (Fig. 3). This arrangement creates two types of dimerization interface, one along the N-terminal β-strand and one along the C-terminal region. The hexamer thus contains three N-terminal and three C-terminal type interfaces. The C-terminal type interface is more extensive (1960 Å^2 of buried solvent-accessible surface per monomer versus 950 Å^2 for the N-terminal type interface) and highly conserved among BB2672 homologs, suggesting a conserved evolutionary purpose.

    Both types of interface involve strictly conserved intermolecular salt bridges which, in the case of the C-terminal type interface (Glu90-Arg176, Glu92-Arg172), are almost entirely shielded from solvent upon oligomerization, making them exceptionally strong in nature. The β1 strand (N-terminal type interface) and the region C-terminal of strand β7 (implicated in C-terminal type interface), regions absent in classic BCM folds in which monomers are arranged in parallel to each other to form trimers (3), could thus be implicated in the formation of two distinct types of interface observed in 3byq and the creation of a trimer of dimers, since an anti-parallel orientation is required to ensure the ionic complementarity necessary for salt-bridge formation.





    Figure 3. Ribbon diagram of the 3byq hexamer showing the anti-parallel arrangement of consecutive subunits (top view). Monomers with the N-terminus pointing out of the page are shown in gray. Monomers with the N-terminus pointing towards the back of the page are shown in blue.

    Analysis of the 3byq hexamer structure using the CastP server revealed a large cavity (~1,000 Å^3) that occurs along the C-terminal dimer interface and includes residues from helix H4, the H4–β4 loop, β5, the β5–H5 loop, the 310-helix H5, and the region C-terminal of β7. Within this cavity, a highly conserved cluster of 4 histidines, His93, His98, His144, His174, is located within interacting distance of residues involved in the formation of intermolecular salt bridges (Fig. 4). All four histidines are located in flexible regions of the molecule: His144 and His174 in loops, and His87 and His98 at the beginning of helices H3 and H4 respectively. The presence of histidines in flexible regions along this interface and in the proximity of salt bridges implicated in oligomerization indicates activity modulated by pH or metal binding.




    Figure 4. Close-up view of 3byq at the C-terminal type dimer interface. Conserved histidines and salt bridges are indicated.

    In bacteria, fungi and higher plants, chorismate mutase (EC 5.4.99.5) catalyzes the isomerization of chorismate to prephenate, in the first committed step in the biosynthesis of the aromatic amino acids Phe and Tyr. In the chorismate mutase from Bacillus subtilis (PDB accession code: 2cht), the active sites are located at each of the three subunit interfaces and the reaction involves stabilization of the charged transition state of chorismate via formation of ionic bonds with a number of acidic and basic side chains in BCM (4). A number of studies have established that these electrostatic effects provide the main drive in catalysis (5). Electrostatic catalysis can additionally be mediated by metal ions and histidine proton shuttling (6). Despite differences in the oligomerization states between BCM and BB2672, as well as a lack of sequence similarity between the two proteins, conservation of charged residues and histidines along protomer-interacting interfaces, support the idea that BB2672 might be involved in an isomerization reaction employing a similar catalytic mechanism to that observed in BCM although likely implicating a different ligand.


    The protein structure of another member of the same DUF1185 family was deposited with PDB code 2qtp. According to the annotation of a similar protein (YP_333612.1), the DUFF1185 family could function as a peptide synthase. The genomic neighborhood of BB2672 and its orthologs, includes transcriptional regulators implicated in pathogenesis and multiple antibiotic resistance, proteins involved in branched-chain amino acid (BCAA) metabolism and proteins implicated in ABC-type branched-chain amino acid transport, suggesting that the principal products may be secreted.


    In some pathogenic bacteria, a subclass of chorismate mutases are secreted (7), a step that is believed to correlate with pathogenicity (8).  In other pathogens, one of the modes of BCAA transportation is thought to be sensitive to stress induced by changes in osmolarity, pH, or temperature (9). In this context, BB2672 and its homologs might  present attractive drug targets, since like chorismate mutases, BB2672 homologs are not found in mammals. Alternatively, the BB2672 family could act as environmental sensors, enabling bacterial adaptation and survival under a range of conditions. 

    Ligand Summary

     

    References

    Reviews

    References

     

    1. Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC, Davidsen TD, Deboy RT, Dimitrov G, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Khouri H, Kolonay JF, Madupu R, Mohammoud Y, Nelson WC, Radune D, Romero CM, Sarria S, Selengut J, Shamblin C, Sullivan SA, White O, Yu Y, Zafar N, Zhou L, and Fraser CM Structural flexibility in the Burkholderia mallei genome. Proc Natl Acad Sci U S A. 2004 Sep 28; 101(39):14246-51 PubMed HubMed doi:10.1073/pnas.0403306101 pmid:15377793.

       


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