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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 and DiaA structures. (A) Multiple sequence alignment of CpsGmhA, CpsDiaA, EcGmhA, EcDiaA, and HpHobA. Conserved residues are presented in either orange or yellow background according to the degree of conservation. The catalytic residues are indicated in red. The residues known to be involved in DnaA binding are presented in blue. (B) Overlay of the catalytic residues of CpsGmhA (green), EcGmhA (yellow), and EcDiaA (pink). Each of the residue numbers are indicated by their corresponding colors. (C) Overlay of the overall structures of CpsGmhA and EcDiaA. CpsGmhA and EcDiaA are shown in green and pink, respectively.
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f4-molce-38-12-1086: Comparison of GmhA and DiaA structures. (A) Multiple sequence alignment of CpsGmhA, CpsDiaA, EcGmhA, EcDiaA, and HpHobA. Conserved residues are presented in either orange or yellow background according to the degree of conservation. The catalytic residues are indicated in red. The residues known to be involved in DnaA binding are presented in blue. (B) Overlay of the catalytic residues of CpsGmhA (green), EcGmhA (yellow), and EcDiaA (pink). Each of the residue numbers are indicated by their corresponding colors. (C) Overlay of the overall structures of CpsGmhA and EcDiaA. CpsGmhA and EcDiaA are shown in green and pink, respectively.

Mentions: We searched for structural homologs of CpsGmhA using the DALI server system and found that DiaA from E. coil (EcDiaA) has high similarity to GmhA, with a Z-score of 32.7 (Holm and Rosenstrom, 2010). DiaA is essential for the accurate initiation and precise timing of chromosomal replication during the cell cycle (Ishida et al., 2004). Thus, DiaA directly and specifically interacts with DnaA independent of nucleotides or DNA (Ishida et al., 2004; Keyamura et al., 2007). Moreover, the structure of DiaA shows similarity with the DnaA-binding protein HobA from Helicobacter pylori (HpHobA) (Natrajan et al., 2007). Based on this structural information, we compared the protein sequences and found that the catalytic glutamate residues are variable, with Gln (CpsGmhA), Ser (EcDiaA), and Asn (HpHobA) being observed at catalytic sites (Fig. 4A). In addition, the other catalytic residues are varied and HobA has no identical residues. Given the difference in the catalytic residues of HpHobA, we compared the conformations of the catalytic residues among CpsGmhA, EcGmhA, and EcDiaA (Fig. 4B). The conformation of the catalytic residues between CpsGmhA and EcDiaA is much more similar than that of other pairs of compared proteins because the two residues Glu65 and Gln172 are differently oriented. This result indicates that CpsGmhA and EcDiaA are closely related.


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 and DiaA structures. (A) Multiple sequence alignment of CpsGmhA, CpsDiaA, EcGmhA, EcDiaA, and HpHobA. Conserved residues are presented in either orange or yellow background according to the degree of conservation. The catalytic residues are indicated in red. The residues known to be involved in DnaA binding are presented in blue. (B) Overlay of the catalytic residues of CpsGmhA (green), EcGmhA (yellow), and EcDiaA (pink). Each of the residue numbers are indicated by their corresponding colors. (C) Overlay of the overall structures of CpsGmhA and EcDiaA. CpsGmhA and EcDiaA are shown in green and pink, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

f4-molce-38-12-1086: Comparison of GmhA and DiaA structures. (A) Multiple sequence alignment of CpsGmhA, CpsDiaA, EcGmhA, EcDiaA, and HpHobA. Conserved residues are presented in either orange or yellow background according to the degree of conservation. The catalytic residues are indicated in red. The residues known to be involved in DnaA binding are presented in blue. (B) Overlay of the catalytic residues of CpsGmhA (green), EcGmhA (yellow), and EcDiaA (pink). Each of the residue numbers are indicated by their corresponding colors. (C) Overlay of the overall structures of CpsGmhA and EcDiaA. CpsGmhA and EcDiaA are shown in green and pink, respectively.
Mentions: We searched for structural homologs of CpsGmhA using the DALI server system and found that DiaA from E. coil (EcDiaA) has high similarity to GmhA, with a Z-score of 32.7 (Holm and Rosenstrom, 2010). DiaA is essential for the accurate initiation and precise timing of chromosomal replication during the cell cycle (Ishida et al., 2004). Thus, DiaA directly and specifically interacts with DnaA independent of nucleotides or DNA (Ishida et al., 2004; Keyamura et al., 2007). Moreover, the structure of DiaA shows similarity with the DnaA-binding protein HobA from Helicobacter pylori (HpHobA) (Natrajan et al., 2007). Based on this structural information, we compared the protein sequences and found that the catalytic glutamate residues are variable, with Gln (CpsGmhA), Ser (EcDiaA), and Asn (HpHobA) being observed at catalytic sites (Fig. 4A). In addition, the other catalytic residues are varied and HobA has no identical residues. Given the difference in the catalytic residues of HpHobA, we compared the conformations of the catalytic residues among CpsGmhA, EcGmhA, and EcDiaA (Fig. 4B). The conformation of the catalytic residues between CpsGmhA and EcDiaA is much more similar than that of other pairs of compared proteins because the two residues Glu65 and Gln172 are differently oriented. This result indicates that CpsGmhA and EcDiaA are closely related.

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