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Crystal Structure and Comparative Sequence Analysis of GmhA from Colwellia psychrerythraea Strain 34H Provides Insight into Functional Similarity with DiaA.

Do H, Yun JS, Lee CW, Choi YJ, Kim HY, Kim YJ, Park H, Chang JH, Lee JH - Mol. Cells (2015)

Bottom Line: We also found differences in the conformations of several other catalytic residues.Extensive structural and sequence analyses reveal that CpsGmhA shows high similarity to Escherichia coli DnaA initiator-associating protein A (DiaA).Therefore, the CpsGmhA structure reported here may provide insight into the structural and functional correlations between GmhA and DiaA among specific microorganisms.

View Article: PubMed Central - PubMed

Affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea.

ABSTRACT
The psychrophilic organism Colwellia psychrerythraea strain 34H produces extracellular polysaccharide substances to tolerate cold environments. Sedoheptulose 7-phosphate isomerase (GmhA) is essential for producing d-glycero-d-mannoheptose 7-phosphate, a key mediator in the lipopolysaccharide biosynthetic pathway. We determined the crystal structure of GmhA from C. psychrerythraea strain 34H (CpsGmhA, UniProtKB code: Q47VU0) at a resolution of 2.8 Å. The tetrameric structure is similar to that of homologous GmhA structures. Interestingly, one of the catalytic residues, glutamate, which has been reported to be critical for the activity of other homologous GmhA enzymes, is replaced by a glutamine residue in the CpsGmhA protein. We also found differences in the conformations of several other catalytic residues. Extensive structural and sequence analyses reveal that CpsGmhA shows high similarity to Escherichia coli DnaA initiator-associating protein A (DiaA). Therefore, the CpsGmhA structure reported here may provide insight into the structural and functional correlations between GmhA and DiaA among specific microorganisms.

No MeSH data available.


Related in: MedlinePlus

Overall structure of CpsGmhA. (A) The overall structure of the monomeric CpsGmhA is shown as a cartoon representation. The α-helices, β-sheets, and loops are colored in green, brown, and grey, respectively. (B) Size exclusion chromatogram of CpsGmhA for the measurement of molecular weight. The estimated molecular weight is 84 kDa based on the standard (STD), whereas the calculated molecular weight of the monomer is 20.9 kDa. (C) The overall structure of tetrameric CpsGmhA viewed from the top. The four monomers are colored green, yellow, cyan, and magenta, respectively. The active sites are marked with red dotted lines. The black arrows indicate the clamp helical regions. The black dashed hexagon indicates the overall shape by interactions of the α1 helices. (D) Side view of the CpsGmhA tetramer by 90° rotation over an X-axis from Fig. 1C.
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f1-molce-38-12-1086: Overall structure of CpsGmhA. (A) The overall structure of the monomeric CpsGmhA is shown as a cartoon representation. The α-helices, β-sheets, and loops are colored in green, brown, and grey, respectively. (B) Size exclusion chromatogram of CpsGmhA for the measurement of molecular weight. The estimated molecular weight is 84 kDa based on the standard (STD), whereas the calculated molecular weight of the monomer is 20.9 kDa. (C) The overall structure of tetrameric CpsGmhA viewed from the top. The four monomers are colored green, yellow, cyan, and magenta, respectively. The active sites are marked with red dotted lines. The black arrows indicate the clamp helical regions. The black dashed hexagon indicates the overall shape by interactions of the α1 helices. (D) Side view of the CpsGmhA tetramer by 90° rotation over an X-axis from Fig. 1C.

Mentions: The GmhA from C. psychrerythraea strain 34H (CpsGmhA), including the additional serine-histidine residues located before the N-terminus as an artifact of cloning, was crystallized and the structure was determined by X-ray crystallography at a resolution of 2.8 Å. The monomeric structure is composed of five central parallel β-sheets surrounded by six α-helices (Fig. 1A). Most residues fit well in the electron density except for residues Tyr93, Gln94, Gln193, Gly194, Asp195, and Ser196. The final model was refined to R and Rfree values of 21.0% and 28.0%, respectively (Table 1). The overall topology of CpsGmhA is very similar to that of the homologous structures from various species, with an average root mean square deviation (r.m.s.d.) of 1.3 Å in monomeric Cα (Harmer, 2010; Kim and Shin, 2009; Seetharaman et al., 2006; Taylor et al., 2008). Since one molecule of CpsGmhA was observed in the asymmetric unit, we performed a size exclusion chromatographic analysis. The result indicates that CpsGmhA also exists in tetrameric form in solution, which is in agreement with the results of previous studies (Harmer, 2010; Taylor et al., 2008) (Fig. 1B).


Crystal Structure and Comparative Sequence Analysis of GmhA from Colwellia psychrerythraea Strain 34H Provides Insight into Functional Similarity with DiaA.

Do H, Yun JS, Lee CW, Choi YJ, Kim HY, Kim YJ, Park H, Chang JH, Lee JH - Mol. Cells (2015)

Overall structure of CpsGmhA. (A) The overall structure of the monomeric CpsGmhA is shown as a cartoon representation. The α-helices, β-sheets, and loops are colored in green, brown, and grey, respectively. (B) Size exclusion chromatogram of CpsGmhA for the measurement of molecular weight. The estimated molecular weight is 84 kDa based on the standard (STD), whereas the calculated molecular weight of the monomer is 20.9 kDa. (C) The overall structure of tetrameric CpsGmhA viewed from the top. The four monomers are colored green, yellow, cyan, and magenta, respectively. The active sites are marked with red dotted lines. The black arrows indicate the clamp helical regions. The black dashed hexagon indicates the overall shape by interactions of the α1 helices. (D) Side view of the CpsGmhA tetramer by 90° rotation over an X-axis from Fig. 1C.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4697000&req=5

f1-molce-38-12-1086: Overall structure of CpsGmhA. (A) The overall structure of the monomeric CpsGmhA is shown as a cartoon representation. The α-helices, β-sheets, and loops are colored in green, brown, and grey, respectively. (B) Size exclusion chromatogram of CpsGmhA for the measurement of molecular weight. The estimated molecular weight is 84 kDa based on the standard (STD), whereas the calculated molecular weight of the monomer is 20.9 kDa. (C) The overall structure of tetrameric CpsGmhA viewed from the top. The four monomers are colored green, yellow, cyan, and magenta, respectively. The active sites are marked with red dotted lines. The black arrows indicate the clamp helical regions. The black dashed hexagon indicates the overall shape by interactions of the α1 helices. (D) Side view of the CpsGmhA tetramer by 90° rotation over an X-axis from Fig. 1C.
Mentions: The GmhA from C. psychrerythraea strain 34H (CpsGmhA), including the additional serine-histidine residues located before the N-terminus as an artifact of cloning, was crystallized and the structure was determined by X-ray crystallography at a resolution of 2.8 Å. The monomeric structure is composed of five central parallel β-sheets surrounded by six α-helices (Fig. 1A). Most residues fit well in the electron density except for residues Tyr93, Gln94, Gln193, Gly194, Asp195, and Ser196. The final model was refined to R and Rfree values of 21.0% and 28.0%, respectively (Table 1). The overall topology of CpsGmhA is very similar to that of the homologous structures from various species, with an average root mean square deviation (r.m.s.d.) of 1.3 Å in monomeric Cα (Harmer, 2010; Kim and Shin, 2009; Seetharaman et al., 2006; Taylor et al., 2008). Since one molecule of CpsGmhA was observed in the asymmetric unit, we performed a size exclusion chromatographic analysis. The result indicates that CpsGmhA also exists in tetrameric form in solution, which is in agreement with the results of previous studies (Harmer, 2010; Taylor et al., 2008) (Fig. 1B).

Bottom Line: We also found differences in the conformations of several other catalytic residues.Extensive structural and sequence analyses reveal that CpsGmhA shows high similarity to Escherichia coli DnaA initiator-associating protein A (DiaA).Therefore, the CpsGmhA structure reported here may provide insight into the structural and functional correlations between GmhA and DiaA among specific microorganisms.

View Article: PubMed Central - PubMed

Affiliation: Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea.

ABSTRACT
The psychrophilic organism Colwellia psychrerythraea strain 34H produces extracellular polysaccharide substances to tolerate cold environments. Sedoheptulose 7-phosphate isomerase (GmhA) is essential for producing d-glycero-d-mannoheptose 7-phosphate, a key mediator in the lipopolysaccharide biosynthetic pathway. We determined the crystal structure of GmhA from C. psychrerythraea strain 34H (CpsGmhA, UniProtKB code: Q47VU0) at a resolution of 2.8 Å. The tetrameric structure is similar to that of homologous GmhA structures. Interestingly, one of the catalytic residues, glutamate, which has been reported to be critical for the activity of other homologous GmhA enzymes, is replaced by a glutamine residue in the CpsGmhA protein. We also found differences in the conformations of several other catalytic residues. Extensive structural and sequence analyses reveal that CpsGmhA shows high similarity to Escherichia coli DnaA initiator-associating protein A (DiaA). Therefore, the CpsGmhA structure reported here may provide insight into the structural and functional correlations between GmhA and DiaA among specific microorganisms.

No MeSH data available.


Related in: MedlinePlus