6XMR

X-ray crystallographic structure model of Lactococcus lactis prolidase mutant H38S

Summary for 6XMR

• Entry DOI: 10.2210/pdb6xmr/pdb
• Related: 4ZNG
• Descriptor: Aminopeptidase P family protein, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: proline-specific, allosteric behaviour, substrate inhibition, dipeptidase, lactic acid bacteria, debittering of fermented foods, hydrolase
• Biological source: Lactococcus lactis
• Total number of polymer chains: 2
• Total formula weight: 80144.21

Authors

Xu, S.,Grochulski, P.,Tanaka, T. (deposition date: 2020-06-30, release date: 2020-07-15, Last modification date: 2023-10-18)

Primary citation

Kgosisejo, O.,Chen, J.A.,Grochulski, P.,Tanaka, T.
Crystallographic structure of recombinant Lactococcus lactis prolidase to support proposed structure-function relationships.
Biochim Biophys Acta Proteins Proteom, 1865:473-480, 2017

PubMed Abstract: Lactococcus lactis prolidase (Xaa-Pro dipeptidase; EC.3.4.13.9) is unique from other prolidases by showing allosteric behaviour, substrate inhibition, and metal-dependent substrate specificity. We have previously shown several critical residues for these characteristics using site-directed mutagenesis and amino acid sequence-based models. In this present study, the three-dimensional structure of recombinant L. lactis prolidase was determined by X-ray crystallography at 2.25Å resolution in order to provide evidences of the proposed mechanism. Three molecules are located in the crystal asymmetric unit where molecule A forms a dimer with molecule B, while molecule C forms a dimer with molecule C' in the adjacent asymmetric unit. Of all the three molecules, molecule C is less defined and incomplete. While this fact compromises the overall quality of the refined model, the functional interpretation of the structure is not compromised since the biologically-functional homodimeric configuration of L. lactis prolidase is represented by well-defined molecules A and B. The refined model confirmed that there is a twelve-residue (residues 32-43) loop structure from one subunit over the active site of the other subunit, proving the existence of the putative loop structure in our previous study. This loop is three amino acids longer than the loops of prolidases of Pyrococcus furious (1pv9) and Pyrococcus horikoshii OT3 (1wy2). The crystal structure shows the loop structure can form two states ("open" and "closed" states) through interaction between the loop and active site proximity. It supports the proposed formation of allosteric site by the loop and Arg 293.

PubMed: 28179139
DOI: 10.1016/j.bbapap.2017.02.004

Experimental method

X-RAY DIFFRACTION (1.7 Å)