4AXX

The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP 3-phosphoglycerate and beryllium trifluoride

Summary for 4AXX

• Entry DOI: 10.2210/pdb4axx/pdb
• Related: 2WZB 2WZC 2WZD 2X13 2X14 2X15 2XE6 2XE7 2XE8 2Y3I 2YBE
• Descriptor: PHOSPHOGLYCERATE KINASE 1, MAGNESIUM ION, CHLORIDE ION, ... (7 entities in total)
• Functional Keywords: ground state analogue, hereditary hemolytic anemia, phosphoprotein, glycolysis, transferase, phosphoryl transfer, nucleotide-binding
• Biological source: HOMO SAPIENS (HUMAN)
• Cellular location: Cytoplasm: P00558
• Total number of polymer chains: 1
• Total formula weight: 45425.67

Authors

Bowler, M.W. (deposition date: 2012-06-15, release date: 2013-06-26, Last modification date: 2024-08-21)

Primary citation

Pellegrini, E.,Juyoux, P.,von Velsen, J.,Baxter, N.J.,Dannatt, H.R.W.,Jin, Y.,Cliff, M.J.,Waltho, J.P.,Bowler, M.W.
Metal fluorides-multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide.
Structure, 2024

PubMed Abstract: Enzymes facilitating the transfer of phosphate groups constitute the most extensive protein families across all kingdoms of life. They make up approximately 10% of the proteins found in the human genome. Understanding the mechanisms by which enzymes catalyze these reactions is essential in characterizing the processes they regulate. Metal fluorides can be used as multifunctional tools to study these enzymes. These ionic species bear the same charge as phosphate and the transferring phosphoryl group and, in addition, allow the enzyme to be trapped in catalytically important states with spectroscopically sensitive atoms interacting directly with active site residues. The ionic nature of these phosphate surrogates also allows their removal and replacement with other analogs. Here, we describe the best practices to obtain these complexes, their use in NMR, X-ray crystallography, cryo-EM, and SAXS and describe a new metal fluoride, scandium tetrafluoride, which has significant anomalous signal using soft X-rays.

PubMed: 39106858
DOI: 10.1016/j.str.2024.07.007

Experimental method

X-RAY DIFFRACTION (1.74 Å)