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oai:www.ideals.illinois.edu:2142/14751 2023-07-10 col_2142_5131 col_2142_14795 com_2142_5130 com_2142_14794 com_2142_14793 com_2142_8903

Gerlt, John A. Gerlt, John A. Martinis, Susan A. Morrissey, James H. Nair, Satish K. Lukk, Tiit 2010-01-06T17:49:18Z 2010-01-06T17:49:18Z 2012-01-07T11:00:12Z 2010-01-06T17:49:18Z In the genomic era, advanced sequencing techniques have enabled an exponential growth of the protein sequence databases. Although the abundance of genomic sequences is valuable, the correctness of the gene annotations poses a problem--approximately one- half of the deposited sequences are incorrectly annotated. We are using the enolase superfamily as a model system to try to solve that problem. To date, >4000 members have been identified in the enolase superfamily, of which ~50% have unknown functions. The muconate lactonizing enzyme (MLE) subgroup contains a family of enzymes that catalyze the epimerization of dipeptide substrates. Identification of function of unknown members of the MLE subgroup, based on sequence information and homology modeling, has been successful. A novel D-Ala-D/L-Ala and a unique L-Ala-D/L-Glu epimerase (AEE) were identified and kinetically characterized from Cytophaga hutchinsonii (kcat/KM of 5.5 x 104 M-1s-1) and Bacteroides thetaiotaomicron (kcat/KM of 5.8 x 104 M-1s-1), respectively. Computational predictions, provided by Prof. Matthew Jacobson’s laboratory at UCSF, were proven correct for both enzymes. In collaboration with Prof. Steven Almo’s laboratory at Albert Einstein College of Medicine, an X-ray crystal structure was solved at 1.6 Å resolution for the B. thetaiotaomicron AEE, establishing the correctness of the predicted homology model. Many enzymes in the mandelate racemase (MR) subgroup catalyze dehydration of various acid-sugar substrates. Attempts were made to elucidate the biochemical function of previously uncharacterized MR subgroup members from Agrobacterium tumefaciens, Mesorhizobium loti, Polaromonas sp., Silicibacter sp. and Sinorhizobium meliloti. The glucarate degradation operon in Escherichia coli encodes two enolase superfamily members: D-glucarate dehydratase (GlucD) and its catalytically impaired close homologue, GlucD related protein (GlucDRP). However, the function of GlucDRP is unclear. New biochemical evidence suggests that GlucD and GlucDRP are interaction partners in vivo. The role of several residues in catalysis and substrate recognition from the capping domain loops were investigated via a mutagenesis study of GlucD. Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2009-11-20T14:30:29Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Lukk_Tiit.pdf: 5789330 bytes, checksum: d02fc7072ed84a31d0e1be08d67ea294 (MD5) Made available in DSpace on 2010-01-06T17:49:18Z (GMT). No. of bitstreams: 3 license.txt: 4057 bytes, checksum: dbc60f30debc00a74dde5811dcac4079 (MD5) Lukk_Tiit.pdf: 5789330 bytes, checksum: d02fc7072ed84a31d0e1be08d67ea294 (MD5) 1_Lukk_Tiit.pdf: 7047512 bytes, checksum: a43689593c81edb118c11f1b4ddf9437 (MD5) Item marked as restricted to the 'Administrator' Group (id=1) by William Ingram (wingram2@illinois.edu) on 2010-01-06T17:49:46Z Item is restricted until 2012-01-06T17:49:44Z Item reinstated by Sarah Shreeves (sshreeve@illinois.edu) on 2012-01-07T11:00:11Z Item was in collections: University of Illinois Dissertations and Theses (ID: 204) Dissertations and Theses - Biochemistry (ID: 679) No. of bitstreams: 4 1_Lukk_Tiit.pdf.txt: 239528 bytes, checksum: db05d0f04ee32135574b7fd73d0442df (MD5) license.txt: 4057 bytes, checksum: dbc60f30debc00a74dde5811dcac4079 (MD5) Lukk_Tiit.pdf: 5789330 bytes, checksum: d02fc7072ed84a31d0e1be08d67ea294 (MD5) 1_Lukk_Tiit.pdf: 7047512 bytes, checksum: a43689593c81edb118c11f1b4ddf9437 (MD5) Item released from any restrictions by Sarah Shreeves (sshreeve@illinois.edu) on 2012-01-07T11:00:12Z http://hdl.handle.net/2142/14751 en Copyright 2009 Tiit Lukk enolase superfamily discovery of function dipeptide epimerase glucarate dehydratase acid sugar dehydratase x-ray crystal structure novel function Discovery of function in the enolase superfamily 2009-12 Biochemistry 1438 Biochemistry 0318 University of Illinois at Urbana-Champaign Dissertation Ph.D. PHD:Biochemistry -UIUC 10KS0318PHD