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Filling out the structural map of the NTF2-like superfamily.

(2013) BMC Bioinformatics 14

PubMed: 24246060 | PubMedCentral: PMC3924330 | DOI: 10.1186/1471-2105-14-327

jejuni serotype O:2 (strain NCTC 11168) [PDB:3K7C], rumgna_01855) and RUMGNA_01855 from Ruminococcus gnavus (strain ATCC 29149) [PDB:4HYZ] have been solved by X-ray crystallography.

Comparison of these three structures showed that they are significantly similar to each other, especially for [PDB:3K7C] and [PDB:4HYZ].

Data collection and refinement statistics (PDB 4hyz).

The structure of [PDB:3K7C] differs from that of [PDB:3KZT] and [PDB:4HYZ] in that it lacks the edge strands in the beta-sheet but has a longer helix on the opposite side.

[PDB:4HYZ] is a member of DUF3887, [PDB:3K7C] is a member of DUF4878 and [PDB:3KZT] is a member of DUF3828.

X-ray diffraction data were collected from a single crystal at wavelengths corresponding to the inflection (λ 1 ), high energy remote (λ 2 ), and peak (λ 3 ) [PDB:3K7C]; the peak(λ 1 ), inflection (λ 2 ), and high energy remote (λ 3 ) [PDB: 4HYZ]; or the inflection (λ 1 ) and high energy remote (λ 2 ) [PDB:3KZT], of a multi-wavelength or a two-wavelength selenium multi-wavelength anomalous diffraction (MAD).

It is significantly less similar to [PDB:3K7C] (maximum Z-score of 6.4 when compared to chain A), and [PDB:4HYZ] (maximum Z-score of 6.8 when compared to chain B).

Model completion was performed using the interactive computer-graphics program COOT [ 42 ] and MAD-phase-restrained refinement was accomplished using the program REFMAC ver 5.5.0102 [PDB:3K7C], ver 5.5.0053 [PDB:3KZT] [ 43 ] or BUSTER ver 2.10.0 [ 44 ] [PDB:4HYZ].

Here we describe the first crystal structures of three Pfam families with NTF2-like folds: DUF3828 [PDB:3KZT] [Pfam:PF12883], DUF3887 [PDB:4HYZ] [Pfam:PF13026] and DUF4878 [PDB:3K7C] [Pfam:PF12870].

FATCAT results showed that the structures of [PDB:3KZT] and [PDB:4HYZ] are significantly similar with P-value of 1.53e- 03 and the structure alignment has 85 equivalent positions with an RMSD of 1.72 Å; the structures of [PDB:3KZT] and [PDB:3K7C] are significantly similar with P-value of 2.57e- 03 and the structure alignment has 95 equivalent positions with an RMSD of 2.53 Å; the structures of [PDB:4HYZ] and [PDB:3K7C] are significantly similar with P-value of 1.55e- 06 and the structure alignment has 95 equivalent positions with an RMSD of 2.99 Å [ 19 ].

[PDB:4HYZ] has a cavity of a similar size in a similar position with weakly positive electrostatic potential.

The data were integrated and scaled using the XDS and XSCALE programs respectively [ 32 , 33 ] [PDB:3K7C] or the MOSFLM [ 34 ] and SCALA [ 35 ] programs [PDB:3KZT][PDB:4HYZ].

Sequence conservation in the region of the cavities in [PDB:3K7C] and in [PDB:4HYZ] is poor.

Table 1 Percentage identity of the three proteins for which structure has been determined, calculated using DALI [ 24 ] PDB ID 3KZT 3K7C 4HYZ 3KZT   11% 14% 3K7C 11%   10% 4HYZ 14% 10%   DALI [ 24 ] searches revealed that [PDB:3KZC] and [PDB:4HYZ] are more similar to each other than they are to most other members of the NTF2-like superfamily (Z-score 9.8), however [PDB:3KZT] is more distantly related.

Atomic coordinates and experimental structure factors have been deposited in the PDB and are accessible under the codes [PDB:3KZT], [PDB:3K7C] and [PDB:4HYZ].

The crystal structure of a DUF3887 protein, the hypothetical protein Rumgna_01855 [UniProtKB:A7B2S7] from Ruminococcus gnavus (strain ATCC 29149), was determined to 2.25 Å resolution by MAD method and was deposited to PDB as [PDB:4HYZ].

The three structures ([PDB:3K7C], [PDB:3KZT] and [PDB:4HYZ]) all possess NTF2-like folds, despite being dissimilar in sequence (Figures  6 and 7 , Table  1 ).

[PDB:4HYZ] and [PDB:3K7C] are most similar to members of the SnoAL_3 family [Pfam:PF13474] including [PDB:3GWR] (Z-score 10.1 when compared to [PDB:3K7C]), and the SnoAL_2 family [Pfam:PF12860] including [PDB:3D9R] (Z-score 9.5 when compared to [PDB:3K7C]).

Iterative automated model building was performed with RESOLVE [ 38 ] at a resolution of 2.00 Å [PDB:3K7C] or Arp/Warp [ 39 ] at a resolution of 2.15 Å [PDB:3KZT] or with Buccaneer [ 40 , 41 ] at a resolution of 2.25 Å [PDB:4HYZ] from density-modified electron density.

Publication Year: 2013