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Title: Structural studies on putative essential gene products from Bacillus subtilis and Burkholderia pseudomallei
Author: Newman, Joseph
ISNI:       0000 0001 3443 8586
Awarding Body: University of Sheffield
Current Institution: University of Sheffield
Date of Award: 2007
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In an effort to combat the emerging threat of multiplely antibiotic resistant microbes, a pilot scale structural genomics programme specifically targeting essential or putative essential genes from B. pseudomallei and B. subtilis has been initiated. This thesis describes a contribution,to these programmes and more specifically describes the structure determination of the product of the thiD gene of B. subtilis and the queF gene product from B. pseudomallei to 2.8 and 1.6A respectively. B. subtilis thiD gene was initially identified as a HMPP kinase owing to its sequence similarity with the E. coli enzyme. More recently it has been shown to encode a pyridoxal kinase. In this thesis the crystal structure of the B. subtilis thiD gene product has been solved by the molecular replacement method in complex with ADP. Pyridoxal kinase is an enzyme which catalyses the phosphorylation of pyridoxal, pyridoxine and pyridoxamine to their 5' phosphates and plays an important role in the pyridoxal ?' phosphate salvage pathway. Analysis of the structure suggests that binding of the nucleotide induces the ordering of two loops, which operate independently to close a flap on the active site. Comparisons with other enzymes in the ribokinase superfamily reveal that B. subtilis pyridoxal kinase is more closely related in both sequence and structure to the family of HMPP kinases than to other pyridoxal / kinases, suggesting that this structure represents the first member of a novel family of 'HMPP kinase-like' pyridoxal kinases. Moreover this further suggests that the enzyme activity has evolved independently on multiple occasions from within the ribokinase superfamily. The B. pseudomallei ORF BPSL0632 is currently assigned in the genome database as encoding a 'putative GTP cyclohydrolase I'. However recent data on E. coli yqcD whose sequence is closely related to BPSL0632 indicate that this enzyme is a NADPH dependant nitrile oxidoreductase involved in the queuosine biosynthetic pathway. The discovery of nitrile reductase activity in this enzyme generates considerable interest both biologically and as an industrial biocatalyst in the pharmicutical industry. The structure of B. psuedomallei QueF has been determined by the seleno methionine MAD technique and analysis of the structure has allowed the identification of QueF as a unique member of the T fold structural superfamily. Analysis of sequence conservation patterns and comparisons with other enzyme structures have allowed the determination of the putative active site cleft that appears to contain a Zinc ion co-ordinated in an unusual fashion by a backbone peptide nitrogen that is presumed to be deprotonated. A model has been constructed for the mode of binding PreQo and NADPH to this enzyme and possible mechanisms of catalysis are discussed.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available