The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase

Acta Crystallographica. Section D, Biological Crystallography
Markus AlahuhtaVladimir V Lunin

Abstract

The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase (PL3) enzyme has been thoroughly characterized using a series of point mutations, X-ray crystallography, pK(a) calculations and biochemical assays. The X-ray structures of seven PL3 active-site mutants, five of them in complex with intact trigalacturonic acid, were solved and characterized structurally, biochemically and computationally. The results confirmed that Lys108 is the catalytic base, but there is no clear candidate for the catalytic acid. However, the reaction mechanism can also be explained by an antiperiplanar trans-elimination reaction, in which Lys108 abstracts a proton from the C5 atom without the help of simultaneous proton donation by an acidic residue. An acidified water molecule completes the anti β-elimination reaction by protonating the O4 atom of the substrate. Both the C5 hydrogen and C4 hydroxyl groups of the substrate must be orientated in axial configurations, as for galacturonic acid, for this to be possible. The wild-type C. bescii PL3 displays a pH optimum that is lower than that of Bacillus subtilis PL1 according to activity measurements, indicating that C. bescii PL3 has acquired a lower pH optimum by utilizing lysine...Continue Reading

References

Oct 1, 1994·Nature Structural Biology·R PickersgillJ Robert-Baudouy
Apr 1, 1997·Nature Structural Biology·K Diederichs, P A Karplus
Jun 15, 1999·The Plant Cell·R D ScavettaF Jurnak
Sep 14, 2000·Proceedings of the National Academy of Sciences of the United States of America·B Kuhlman, D Baker
Aug 11, 2001·Cellular and Molecular Life Sciences : CMLS·V Pancholi
Apr 1, 1997·Scientific American·M T Madigan, B L Marrs
Sep 27, 2002·Journal of Experimental Botany·M Celia Marín-RodríguezGraham B Seymour
Jan 24, 2003·The Journal of Biological Chemistry·Steven R HerronFrances Jurnak
Dec 13, 2003·The Journal of Biological Chemistry·John JenkinsRichard W Pickersgill
Jun 28, 2005·Nucleic Acids Research·John C GordonAlexey Onufriev
Dec 22, 2005·Acta Crystallographica. Section D, Biological Crystallography·Philip Evans
Apr 24, 2008·The Journal of Biological Chemistry·Christophe CrezePatrice Gouet
Nov 20, 2008·Acta Crystallographica. Section D, Biological Crystallography·S Michael SoltisGuenter Wolf
Oct 6, 2009·International Journal of Systematic and Evolutionary Microbiology·Sung-Jae YangMichael W W Adams
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Alexei Vagin, Alexei Teplyakov
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Wolfgang Kabsch
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Wolfgang Kabsch
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
Sep 21, 2010·The Journal of Biological Chemistry·D Wade AbbottAlisdair B Boraston
Jan 29, 2011·BMC Structural Biology·Michał RostkowskiJan H Jensen
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Martyn D WinnKeith S Wilson
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Garib N MurshudovAlexei A Vagin
Dec 6, 2011·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Markus AlahuhtaVladimir V Lunin
Mar 23, 2013·Acta Crystallographica. Section D, Biological Crystallography·Markus AlahuhtaVladimir V Lunin
Jun 26, 2013·Acta Crystallographica. Section D, Biological Crystallography·Philip R Evans, Garib N Murshudov
Jul 12, 2011·Journal of Chemical Theory and Computation·Chresten R SøndergaardJan H Jensen

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Acta Crystallographica. Section D, Biological Crystallography
Markus AlahuhtaVladimir V Lunin
Acta Crystallographica. Section F, Structural Biology and Crystallization Communications
Md Mominul HoqueAkio Takénaka
Biochemical and Biophysical Research Communications
Takafumi ItohKousaku Murata
Acta Crystallographica. Section D, Biological Crystallography
Federico RuizAlberto Podjarny
© 2021 Meta ULC. All rights reserved