6NP8 image
Entry Detail
PDB ID:
6NP8
Keywords:
Title:
Xanthomonas citri Phospho-PGM in complex with mannose-6-phosphate
Biological Source:
PDB Version:
Deposition Date:
2019-01-17
Release Date:
2019-04-10
Method Details:
Experimental Method:
Resolution:
1.41 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Phosphoglucomutase
Chain IDs:A
Chain Length:468
Number of Molecules:1
Biological Source:Xanthomonas axonopodis pv. citri (strain 306)
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP A SER modified residue
Primary Citation
Structural and dynamical description of the enzymatic reaction of a phosphohexomutase.
Struct Dyn. 6 024703 024703 (2019)
PMID: 31041362 DOI: 10.1063/1.5092803

Abstact

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 Xanthomonas citri. 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) a priori 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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures