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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

Active site of CpsGmhA. (A) Structure-based multiple sequence alignment of CpsGmhA with other homologs. Conserved residues are presented in either orange or yellow backgrounds depending on their degree of conservation. The residues composed of the active site are indicated with red rectangles under the sequences. The catalytic residues are marked with open circles. The secondary structure was generated based on the structure of CpsGmhA. Sequences were aligned using Clustal X 2.1 (Chenna et al., 2003) and photographs were generated using the program ESPript (Gouet et al., 1999). (B) Overlay of the catalytic residues of CpsGmhA with those of BpGmhA (PDB id: 2X3Y) and CjGmhA (PDB id: 1TK9). The colors of CpsGmhA are the same as those described for Fig. 1C. BpGmhA and CjGmhA are colored in yellow and grey, respectively. The yellow sphere indicates the zinc ion present in the BpGmhA structure. Oxygen and nitrogen atoms are shown in red and blue, respectively. (C) Overlay of the catalytic residues of CpsGmhA with EcGmhA (PDB id: 2I2W), which is shown in grey.
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f2-molce-38-12-1086: Active site of CpsGmhA. (A) Structure-based multiple sequence alignment of CpsGmhA with other homologs. Conserved residues are presented in either orange or yellow backgrounds depending on their degree of conservation. The residues composed of the active site are indicated with red rectangles under the sequences. The catalytic residues are marked with open circles. The secondary structure was generated based on the structure of CpsGmhA. Sequences were aligned using Clustal X 2.1 (Chenna et al., 2003) and photographs were generated using the program ESPript (Gouet et al., 1999). (B) Overlay of the catalytic residues of CpsGmhA with those of BpGmhA (PDB id: 2X3Y) and CjGmhA (PDB id: 1TK9). The colors of CpsGmhA are the same as those described for Fig. 1C. BpGmhA and CjGmhA are colored in yellow and grey, respectively. The yellow sphere indicates the zinc ion present in the BpGmhA structure. Oxygen and nitrogen atoms are shown in red and blue, respectively. (C) Overlay of the catalytic residues of CpsGmhA with EcGmhA (PDB id: 2I2W), which is shown in grey.

Mentions: The active site of GmhA is mainly composed of four α-helices, which are each composed of two equivalent helices (α2–α6 and α2′–α6′) from two subunits. In addition, the conserved residues on the α3 helix and the three loops (β1–α2, α2–β2, and β3–α5) support the conformation of the active site (Fig. 2A). The E-Q-H residues, which are located at the α2, α6′, and α6 helices, respectively, are strongly involved in catalytic reactions. The E-QH residues are highly conserved in the GmhA family; however, the glutamate residue is replaced by glutamine at the equivalent position in CpsGmhA (Fig. 2A). Previous mutagenesis studies have shown no GmhA activity in EQ mutants (Harmer, 2010; Taylor et al., 2008), suggesting that CpsGmhA might be more closely related to DiaA this inference is supported by the bioinformatic analysis (see below).


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)

Active site of CpsGmhA. (A) Structure-based multiple sequence alignment of CpsGmhA with other homologs. Conserved residues are presented in either orange or yellow backgrounds depending on their degree of conservation. The residues composed of the active site are indicated with red rectangles under the sequences. The catalytic residues are marked with open circles. The secondary structure was generated based on the structure of CpsGmhA. Sequences were aligned using Clustal X 2.1 (Chenna et al., 2003) and photographs were generated using the program ESPript (Gouet et al., 1999). (B) Overlay of the catalytic residues of CpsGmhA with those of BpGmhA (PDB id: 2X3Y) and CjGmhA (PDB id: 1TK9). The colors of CpsGmhA are the same as those described for Fig. 1C. BpGmhA and CjGmhA are colored in yellow and grey, respectively. The yellow sphere indicates the zinc ion present in the BpGmhA structure. Oxygen and nitrogen atoms are shown in red and blue, respectively. (C) Overlay of the catalytic residues of CpsGmhA with EcGmhA (PDB id: 2I2W), which is shown in grey.
© Copyright Policy
Related In: Results  -  Collection

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

f2-molce-38-12-1086: Active site of CpsGmhA. (A) Structure-based multiple sequence alignment of CpsGmhA with other homologs. Conserved residues are presented in either orange or yellow backgrounds depending on their degree of conservation. The residues composed of the active site are indicated with red rectangles under the sequences. The catalytic residues are marked with open circles. The secondary structure was generated based on the structure of CpsGmhA. Sequences were aligned using Clustal X 2.1 (Chenna et al., 2003) and photographs were generated using the program ESPript (Gouet et al., 1999). (B) Overlay of the catalytic residues of CpsGmhA with those of BpGmhA (PDB id: 2X3Y) and CjGmhA (PDB id: 1TK9). The colors of CpsGmhA are the same as those described for Fig. 1C. BpGmhA and CjGmhA are colored in yellow and grey, respectively. The yellow sphere indicates the zinc ion present in the BpGmhA structure. Oxygen and nitrogen atoms are shown in red and blue, respectively. (C) Overlay of the catalytic residues of CpsGmhA with EcGmhA (PDB id: 2I2W), which is shown in grey.
Mentions: The active site of GmhA is mainly composed of four α-helices, which are each composed of two equivalent helices (α2–α6 and α2′–α6′) from two subunits. In addition, the conserved residues on the α3 helix and the three loops (β1–α2, α2–β2, and β3–α5) support the conformation of the active site (Fig. 2A). The E-Q-H residues, which are located at the α2, α6′, and α6 helices, respectively, are strongly involved in catalytic reactions. The E-QH residues are highly conserved in the GmhA family; however, the glutamate residue is replaced by glutamine at the equivalent position in CpsGmhA (Fig. 2A). Previous mutagenesis studies have shown no GmhA activity in EQ mutants (Harmer, 2010; Taylor et al., 2008), suggesting that CpsGmhA might be more closely related to DiaA this inference is supported by the bioinformatic analysis (see below).

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