6NQF

Xanthomonas citri PGM Apo-Phospho at room temperature

Summary for 6NQF

• Entry DOI: 10.2210/pdb6nqf/pdb
• Related: 6NN1 6NN2 6NNN 6NNO 6NNP 6NNS 6NNT 6NNU 6NOL 6NOQ 6NP8 6NPX
• Descriptor: Phosphoglucomutase, CALCIUM ION (3 entities in total)
• Functional Keywords: phosphoglucomutase, isomerase
• Biological source: Xanthomonas axonopodis pv. citri (strain 306)
• Total number of polymer chains: 1
• Total formula weight: 51471.70

Authors

Stiers, K.M.,Beamer, L.J. (deposition date: 2019-01-21, release date: 2019-04-10, Last modification date: 2024-10-16)

Primary citation

Stiers, K.M.,Graham, A.C.,Zhu, J.S.,Jakeman, D.L.,Nix, J.C.,Beamer, L.J.
Structural and dynamical description of the enzymatic reaction of a phosphohexomutase.
Struct Dyn., 6:024703-024703, 2019

PubMed Abstract: Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium . The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes. Key residues in ligand recognition and regions undergoing conformational change are identified and correlated with the various steps of the catalytic reaction. In addition, we use principal component analysis to examine various subsets of these structures with two goals: (1) identifying sites of conformational heterogeneity through a comparison of room temperature and cryogenic structures of the apo-enzyme and (2) clustering of the enzyme-ligand complexes into functionally related groups, showing sensitivity of this method to structural features difficult to detect by traditional methods. This study captures, in a single system, the structural basis of diverse substrate recognition, the subtle impact of covalent modification, and the role of ligand-induced conformational change in this representative enzyme of the α-D-phosphohexomutase superfamily.

PubMed: 31041362
DOI: 10.1063/1.5092803

Experimental method

X-RAY DIFFRACTION (1.9 Å)