8QPD image
Deposition Date 2023-10-01
Release Date 2024-02-14
Last Version Date 2024-03-27
Entry Detail
PDB ID:
8QPD
Keywords:
Title:
Structure of thioredoxin m from pea
Biological Source:
Source Organism:
Pisum sativum (Taxon ID: 3888)
Method Details:
Experimental Method:
Conformers Calculated:
300
Conformers Submitted:
20
Selection Criteria:
target function
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Thioredoxin M-type, chloroplastic
Chain IDs:A
Chain Length:108
Number of Molecules:1
Biological Source:Pisum sativum
Ligand Molecules
Primary Citation
Three-dimensional solution structure, dynamics and binding of thioredoxin m from Pisum sativum.
Int.J.Biol.Macromol. 262 129781 129781 (2024)
PMID: 38296131 DOI: 10.1016/j.ijbiomac.2024.129781

Abstact

Thioredoxins (TRXs) are ubiquitous small, globular proteins involved in cell redox processes. In this work, we report the solution structure of TRX m from Pisum sativum (pea), which has been determined on the basis of 1444 nuclear Overhauser effect- (NOE-) derived distance constraints. The average pairwise root-mean-square deviation (RMSD) for the 20 best structures for the backbone residues (Val7-Glu102) was 1.42 ± 0.15 Å, and 1.97 ± 0.15 Å when all heavy atoms were considered. The structure corresponds to the typical fold of TRXs, with a central five-stranded β-sheet flanked by four α-helices. Some residues had an important exchange dynamic contribution: those around the active site; at the C terminus of β-strand 3; and in the loop preceding α-helix 4. Smaller NOE values were observed at the N and C-terminal residues forming the elements of the secondary structure or, alternatively, in the residues belonging to the loops between those elements. A peptide derived from pea fructose-1,6-biphosphatase (FBPase), comprising the preceding region to the regulatory sequence of FBPase (residues Glu152 to Gln179), was bound to TRX m with an affinity in the low micromolar range, as measured by fluorescence and NMR titration experiments. Upon peptide addition, the intensities of the cross-peaks of all the residues of TRX m were affected, as shown by NMR. The value of the dissociation constant of the peptide from TRX m was larger than that of the intact FBPase, indicating that there are additional factors in other regions of the polypeptide chain of the latter protein affecting the binding to thioredoxin.

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