7S3G

Structure of cofactor pyridoxal 5-phosphate bound human ornithine decarboxylase in complex with citrate at the catalytic center

Summary for 7S3G

• Entry DOI: 10.2210/pdb7s3g/pdb
• Descriptor: Ornithine decarboxylase, PYRIDOXAL-5'-PHOSPHATE, CITRIC ACID, ... (4 entities in total)
• Functional Keywords: pyridoxal 5-phosphate, human ornithine decarboxylase, citrate, lyase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 95361.76

Authors

Zhou, X.E.,Suino-Powell, K.,Schultz, C.R.,Aleiwi, B.,Brunzelle, J.S.,Lamp, J.,Vega, I.E.,Ellsworth, E.,Bachmann, A.S.,Melcher, K. (deposition date: 2021-09-06, release date: 2021-12-15, Last modification date: 2023-10-18)

Primary citation

Zhou, X.E.,Suino-Powell, K.,Schultz, C.R.,Aleiwi, B.,Brunzelle, J.S.,Lamp, J.,Vega, I.E.,Ellsworth, E.,Bachmann, A.S.,Melcher, K.
Structural basis of binding and inhibition of ornithine decarboxylase by 1-amino-oxy-3-aminopropane.
Biochem.J., 478:4137-4149, 2021

PubMed Abstract: Ornithine decarboxylase (ODC) is the rate-limiting enzyme for the synthesis of polyamines (PAs). PAs are oncometabolites that are required for proliferation, and pharmaceutical ODC inhibition is pursued for the treatment of hyperproliferative diseases, including cancer and infectious diseases. The most potent ODC inhibitor is 1-amino-oxy-3-aminopropane (APA). A previous crystal structure of an ODC-APA complex indicated that APA non-covalently binds ODC and its cofactor pyridoxal 5-phosphate (PLP) and functions by competing with the ODC substrate ornithine for binding to the catalytic site. We have revisited the mechanism of APA binding and ODC inhibition through a new crystal structure of APA-bound ODC, which we solved at 2.49 Å resolution. The structure unambiguously shows the presence of a covalent oxime between APA and PLP in the catalytic site, which we confirmed in solution by mass spectrometry. The stable oxime makes extensive interactions with ODC but cannot be catabolized, explaining APA's high potency in ODC inhibition. In addition, we solved an ODC/PLP complex structure with citrate bound at the substrate-binding pocket. These two structures provide new structural scaffolds for developing more efficient pharmaceutical ODC inhibitors.

PubMed: 34796899
DOI: 10.1042/BCJ20210647

Experimental method

X-RAY DIFFRACTION (1.66 Å)