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IPB Newsletter | April 2025
Understanding Plants!

The IPB Video
Molecular Signal Processing

Prof. Dr. Steffen Abel
How plants stand their ground.
Bioorganic Chemistry

Prof. Dr. Ludger Wessjohann
The chemistry of nature - basis for active compounds for human and plant health.
Biochemistry of Plant Interactions

Prof. Dr. Tina Romeis
Interactions in, of and with plants.
Cell and Metabolic Biology

Prof. Dr. Alain Tissier
Secondary but never unimportant - the biological functions of plant secondary metabolites.
Independent Junior Research Group

Dr. Mariana Schuster

New findings on OPDA: No signaling effect in the early wound response

The plant stress hormone jasmonic acid (JA) and its bioactive form jasmonoyl isoleucine (JA-Ile) play a central role in the…

The IPB has once again been recognized for its exemplary actions in terms of equal opportunity-oriented personnel and organizational policies and has received the TOTAL E-QUALITY certification for the…

The Plant Science Student Conference (PSSC) has been organised by students from the two Leibniz institutes, IPK and IPB, every year for the last 20 years. In this interview, Christina Wäsch (IPK) and…

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Synthetic Organic Chemist (m/f/d) (18/2025)

Date: 2025-08-19 Reference Number: 18/2025

PhD position in biology (m/f/d) (17/2025)

Date: 2025-08-08 Reference Number: 17/2025

PhD in Machine Learning for Enzyme Design (m/f/d)

Date: 2025-05-16 Reference Number: 11/2025

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Publications

Rausch, F.; Schicht, M.; Bräuer, L.; Paulsen, F.; Brandt, W.; Protein modeling and molecular dynamics simulation of the two novel surfactant proteins SP-G and SP-H J. Mol. Model. 20 2513 (2014) DOI: 10.1007/s00894-014-2513-0

Publications

Bräuer, L.; Brandt, W.; Wessjohann, L. A.; Modeling the E. coli 4-hydroxybenzoic acid oligoprenyltransferase (ubiA transferase) and characterization of potential active sites J. Mol. Model. 10 317-327 (2004) DOI: 10.1007/s00894-004-0197-6

4-Hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligoprenyltransferase or any structurally related enzyme is known. Knowledge of the tertiary structure and possible active sites is, however, essential for understanding the catalysis mechanism and the substrate specificity.With homology modeling techniques, secondary structure prediction tools, molecular dynamics simulations, and energy optimizations, a model with two putative active sites could be created and refined. One active site selected to be the most likely one for the docking of oligoprenyl diphosphate and 4-hydroxybenzoic acid is located near the N-terminus of the enzyme. It is widely accepted that residues forming an active site are usually evolutionary conserved within a family of enzymes. Multiple alignments of a multitude of related proteins clearly showed 100% conservation of the amino acid residues that form the first putative active site and therefore strongly support this hypothesis. However, an additional highly conserved region in the amino acid sequence of the ubiA enzyme could be detected, which also can be considered a putative (or rudimentary) active site. This site is characterized by a high sequence similarity to the aforementioned site and may give some hints regarding the evolutionary origin of the ubiA enzyme.Semiempirical quantum mechanical PM3 calculations have been performed to investigate the thermodynamics and kinetics of the catalysis mechanism. These results suggest a near SN1 mechanism for the cleavage of the diphosphate ion from the isoprenyl unit. The 4-hydroxybenzoic acid interestingly appears not to be activated as benzoate anion but rather as phenolate anion to allow attack of the isoprenyl cation to the phenolate, which appeared to be the rate limiting step of the whole process according to our quantum chemical calculations. Our models are a basis for developing inhibitors of this enzyme, which is crucial for bacterial aerobic metabolism.

IPB Newsletter | April 2025

Understanding Plants!

Molecular Signal Processing

Bioorganic Chemistry

Biochemistry of Plant Interactions

Cell and Metabolic Biology

Independent Junior Research Group

+++ News Ticker Science 183 +++ Phytohormones +++

New findings on OPDA: No signaling effect in the early wound response

IPB receives TOTAL E-QUALITY certification for the sixth time in a row

PSSC: Success for the ‘Iron Lady’

Synthetic Organic Chemist (m/f/d) (18/2025)

PhD position in biology (m/f/d) (17/2025)

PhD in Machine Learning for Enzyme Design (m/f/d)

Advanced Search