Dataset Information

Structural insight into ?-Clamp and its interaction with DNA Ligase in Helicobacter pylori.

ABSTRACT: Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of antimicrobial drugs. Here, we report 2Å structure of ?-clamp from H. pylori (Hp?-clamp), which is one of the critical components of DNA polymerase III. Despite of similarity in the overall fold of eubacterial ?-clamp structures, some distinct features in DNA interacting loops exists that have not been reported previously. The in silico prediction identified the potential binders of ?-clamp such as alpha subunit of DNA pol III and DNA ligase with identification of ?-clamp binding regions in them and validated by SPR studies. Hp?-clamp interacts with DNA ligase in micromolar binding affinity. Moreover, we have successfully determined the co-crystal structure of ?-clamp with peptide from DNA ligase (not reported earlier in prokaryotes) revealing the region from ligase that interacts with ?-clamp.

SUBMITTER: Pandey P

PROVIDER: S-EPMC4976356 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Structural insight into β-Clamp and its interaction with DNA Ligase in Helicobacter pylori.

Pandey Preeti P Tarique Khaja Faisal KF Mazumder Mohit M Rehman Syed Arif Abdul SA Kumari Nilima N Gourinath Samudrala S

Scientific reports 20160808

Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of antimicrobial drugs. Here, we report 2Å structure of β-clamp from H. pylori (Hpβ-clamp), which is one of the critical components of DNA polymerase III. Despite of similarity in the overall fold of eubacterial β-clamp structures, some distinct feature ...[more]

PMID: 27499105

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Project description:Serine hydroxymethyltransferase (SHMT), encoded by the glyA gene, is a ubiquitous pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the formation of glycine from serine. The thereby generated 5,10-methylene tetrahydrofolate (MTHF) is a major source of cellular one-carbon units and a key intermediate in thymidylate biosynthesis. While in virtually all eukaryotic and many bacterial systems thymidylate synthase ThyA, SHMT and dihydrofolate reductase (DHFR) are part of the thymidylate/folate cycle, the situation is different in organisms using flavin-dependent thymidylate synthase ThyX. Here the distinct catalytic reaction directly produces tetrahydrofolate (THF) and consequently in most ThyX-containing organisms, DHFR is absent. While the resulting influence on the folate metabolism of ThyX-containing bacteria is not fully understood, the presence of ThyX may provide growth benefits under conditions where the level of reduced folate derivatives is compromised. Interestingly, the third key enzyme implicated in generation of MTHF, serine hydroxymethyltransferase (SHMT), has a universal phylogenetic distribution, but remains understudied in ThyX-containg bacteria. To obtain functional insight into these ThyX-dependent thymidylate/folate cycles, we characterized the predicted SHMT from the ThyX-containing bacterium Helicobacter pylori. Serine hydroxymethyltransferase activity was confirmed by functional genetic complementation of a glyA-inactivated E. coli strain. A H. pylori ΔglyA strain was obtained, but exhibited markedly slowed growth and had lost the virulence factor CagA. Biochemical and spectroscopic evidence indicated formation of a characteristic enzyme-PLP-glycine-folate complex and revealed unexpectedly weak binding affinity of PLP. The three-dimensional structure of the H. pylori SHMT apoprotein was determined at 2.8Ǻ resolution, suggesting a structural basis for the low affinity of the enzyme for its cofactor. Stabilization of the proposed inactive configuration using small molecules has potential to provide a specific way for inhibiting HpSHMT.

Dataset Information

Structural insight into ?-Clamp and its interaction with DNA Ligase in Helicobacter pylori.

Publications

Structural insight into β-Clamp and its interaction with DNA Ligase in Helicobacter pylori.

Similar Datasets

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