The Heme -Copper Oxidoreductase Superfamily: Genomics and Structural Analyses
Hemp, James
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https://hdl.handle.net/2142/87910
Description
Title
The Heme -Copper Oxidoreductase Superfamily: Genomics and Structural Analyses
Author(s)
Hemp, James
Issue Date
2007
Doctoral Committee Chair(s)
Martinez, Todd J.
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biology, Microbiology
Language
eng
Abstract
In this work we characterize the sequence diversity of the heme-copper oxidoreductase superfamily by analyzing over 1100 microbial genomes (Bacteria and Archaea) and nine microbial environmental metagenomic datasets. Over 2000 new putative members were found which we classify into eight oxygen reductase families (A-, B-, C-, D-, E-, F-, G-, and H-families) and five nitric oxide reductase families (cNOR, qNOR, sNOR, eNOR and gNOR) based on enzymatic, structural, genomic, and phylogenetic information. Molecular modeling was then used to characterize the structural properties of the individual families. We predict that the C-type oxygen reductases contain a histidine-tyrosine crosslinked cofactor analogous to that found in the A- and B-families However in the C-family the tyrosine participating in the crosslink is found to originate within a different transmembrane helix than in the A- and B-families. We then use mass spectrometry to verify that the predicted histidine-tyrosine crosslinked cofactor is formed in the active site of the C-type oxygen reductases. This is the first known example of the evolutionary migration of a post-translationally modified active-site residue. It also verifies the presence of a unique crosslinked cofactor in the A-, B-, and C-families of proton pumping respiratory oxidases, demonstrating that these enzymes likely share a common reaction mechanism. Finally we predict the properties of proton channels within the C-family. Modeling and sequence analysis suggests that the C-family has only one conserved proton channel. Site-directed mutagenesis was used to verify that the C-family has a proton channel which is spatially analogous to the K-channel in the A-family. This conserved channel is used for the delivery of protons for both chemistry and pumping.
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