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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

Comparison of GmhA homologous structures. (A) Overlay of the apo and M7P product-bound GmhA structures from P. aeruginosa. The PaGmhA-M7P complex (PDB id: 1X92) and apo PaGmhA (PDB id: 3BJZ) are shown in pink and grey, respectively. The M7P molecules are shown in black with the phosphorous and oxygen atoms in yellow and red, respectively. (B) Overlay of the apo and M7P product-bound GmhA structures from B. pseudomallei. The BpGmhA-M7P complex (PDB id: 2XBL) and apo BpGmhA (PDB id: 2X3Y) are shown in blue and grey, respectively. (C) Overlay of the apo and substrate S7P-bound GmhA structures from E. coli. The EcGmhA-S7P complex (PDB id: 2I22) and apo EcGmhA (PDB id: 2I2W) are shown in orange and grey, respectively. The S7P molecules are shown in blue. (D) Overlay of the apo structures of CpsGmhA (green), PaGmhA (pink) and EcGmhA (orange). The tilted α2 and α6 helices of EcGmhA are presented in the black squares.
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f3-molce-38-12-1086: Comparison of GmhA homologous structures. (A) Overlay of the apo and M7P product-bound GmhA structures from P. aeruginosa. The PaGmhA-M7P complex (PDB id: 1X92) and apo PaGmhA (PDB id: 3BJZ) are shown in pink and grey, respectively. The M7P molecules are shown in black with the phosphorous and oxygen atoms in yellow and red, respectively. (B) Overlay of the apo and M7P product-bound GmhA structures from B. pseudomallei. The BpGmhA-M7P complex (PDB id: 2XBL) and apo BpGmhA (PDB id: 2X3Y) are shown in blue and grey, respectively. (C) Overlay of the apo and substrate S7P-bound GmhA structures from E. coli. The EcGmhA-S7P complex (PDB id: 2I22) and apo EcGmhA (PDB id: 2I2W) are shown in orange and grey, respectively. The S7P molecules are shown in blue. (D) Overlay of the apo structures of CpsGmhA (green), PaGmhA (pink) and EcGmhA (orange). The tilted α2 and α6 helices of EcGmhA are presented in the black squares.

Mentions: Conformational differences between the open and closed may be because of the binding of the product to the active site. For example, the open-conformation structure of PaGmhA is converted to a closed structure by M7P binding (Taylor et al., 2008) (Fig. 3A). M7P binding drives the α4 helix to move away from the central cavity, resulting in a disordered α3 helix as a result of its interaction with the α2 of the other subunit. However, the B. pseudomallei and E. coli GmhA structures are not changed upon product or substrate binding (Harmer, 2010; Taylor et al., 2008) (Figs. 3B and 3C). In addition, the open conformations of EcGmhA and PaGmhA are slightly different in that the α2 and α6 helices in EcGmhA are tilted outwards at 25° and 15°, respectively (Fig. 3D). Therefore, the two pairs of subunits in EcGmhA are not symmetric, and the three different GmhA structures exist in two open states and one closed state (Fig. 3D). Taken together, no correlations are currently evident between the open and closed conformation and the structures.


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)

Comparison of GmhA homologous structures. (A) Overlay of the apo and M7P product-bound GmhA structures from P. aeruginosa. The PaGmhA-M7P complex (PDB id: 1X92) and apo PaGmhA (PDB id: 3BJZ) are shown in pink and grey, respectively. The M7P molecules are shown in black with the phosphorous and oxygen atoms in yellow and red, respectively. (B) Overlay of the apo and M7P product-bound GmhA structures from B. pseudomallei. The BpGmhA-M7P complex (PDB id: 2XBL) and apo BpGmhA (PDB id: 2X3Y) are shown in blue and grey, respectively. (C) Overlay of the apo and substrate S7P-bound GmhA structures from E. coli. The EcGmhA-S7P complex (PDB id: 2I22) and apo EcGmhA (PDB id: 2I2W) are shown in orange and grey, respectively. The S7P molecules are shown in blue. (D) Overlay of the apo structures of CpsGmhA (green), PaGmhA (pink) and EcGmhA (orange). The tilted α2 and α6 helices of EcGmhA are presented in the black squares.
© Copyright Policy
Related In: Results  -  Collection

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

f3-molce-38-12-1086: Comparison of GmhA homologous structures. (A) Overlay of the apo and M7P product-bound GmhA structures from P. aeruginosa. The PaGmhA-M7P complex (PDB id: 1X92) and apo PaGmhA (PDB id: 3BJZ) are shown in pink and grey, respectively. The M7P molecules are shown in black with the phosphorous and oxygen atoms in yellow and red, respectively. (B) Overlay of the apo and M7P product-bound GmhA structures from B. pseudomallei. The BpGmhA-M7P complex (PDB id: 2XBL) and apo BpGmhA (PDB id: 2X3Y) are shown in blue and grey, respectively. (C) Overlay of the apo and substrate S7P-bound GmhA structures from E. coli. The EcGmhA-S7P complex (PDB id: 2I22) and apo EcGmhA (PDB id: 2I2W) are shown in orange and grey, respectively. The S7P molecules are shown in blue. (D) Overlay of the apo structures of CpsGmhA (green), PaGmhA (pink) and EcGmhA (orange). The tilted α2 and α6 helices of EcGmhA are presented in the black squares.
Mentions: Conformational differences between the open and closed may be because of the binding of the product to the active site. For example, the open-conformation structure of PaGmhA is converted to a closed structure by M7P binding (Taylor et al., 2008) (Fig. 3A). M7P binding drives the α4 helix to move away from the central cavity, resulting in a disordered α3 helix as a result of its interaction with the α2 of the other subunit. However, the B. pseudomallei and E. coli GmhA structures are not changed upon product or substrate binding (Harmer, 2010; Taylor et al., 2008) (Figs. 3B and 3C). In addition, the open conformations of EcGmhA and PaGmhA are slightly different in that the α2 and α6 helices in EcGmhA are tilted outwards at 25° and 15°, respectively (Fig. 3D). Therefore, the two pairs of subunits in EcGmhA are not symmetric, and the three different GmhA structures exist in two open states and one closed state (Fig. 3D). Taken together, no correlations are currently evident between the open and closed conformation and the structures.

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