7XQM image
Entry Detail
PDB ID:
7XQM
Title:
InDel-mutant short chain Dehydrogenase bound to SAH
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2022-05-08
Release Date:
2022-12-21
Method Details:
Experimental Method:
Resolution:
2.71 Å
R-Value Free:
0.18
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Dehydrogenase
Chain IDs:A, B, C, D
Chain Length:253
Number of Molecules:4
Biological Source:Thermus thermophilus HB27
Ligand Molecules
Primary Citation
Insertions and deletions mediated functional divergence of Rossmann fold enzymes.
Proc.Natl.Acad.Sci.USA 119 e2207965119 e2207965119 (2022)
PMID: 36417431 DOI: 10.1073/pnas.2207965119

Abstact

Nucleobase-containing coenzymes are hypothesized to be relics of an early RNA-based world that preceded the emergence of proteins. Despite the importance of coenzyme-protein synergisms, their emergence and evolution remain understudied. An excellent target to address this issue is the Rossmann fold, the most catalytically diverse and abundant protein architecture in nature. We investigated two main Rossmann lineages: the nicotinamide adenine dinucleotide phosphate (NAD(P)) and the S-adenosyl methionine (SAM)- binding superfamilies. To identify the evolutionary changes that lead to a coenzyme specificity switch on these superfamilies, we performed structural and sequence-based Hidden Markov model analysis to systematically search for key motifs in their coenzyme-binding pockets. Our analyses revealed that through insertions and deletions (InDels) and a residue substitution, the ancient β1-loop-α1 coenzyme-binding structure of NAD(P) could be reshaped into the SAM-binding β1-loop-α1 structure. To experimentally prove this obsevation, we removed three amino acids from the NAD(P)-binding pocket and solved the structure of the resulting mutant, revealing the characteristic loop features of the SAM-binding pocket. To confirm the binding to SAM, we performed isothermal titration calorimetry measurements. Molecular dynamics simulations also corroborated the role of InDels in abolishing NAD binding and acquiring SAM binding. Our results uncovered how nature may have utilized insertions and deletions to optimize the different coenzyme-binding pockets and the distinct functionalities observed for Rossmann superfamilies. This work also proposes a general mechanism by which protein templates could have been recycled through the course of evolution to adopt different coenzymes and confer distinct chemistries.

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