9NH3

Helicobacter pylori strain SS1 KatA

Summary for 9NH3

• Entry DOI: 10.2210/pdb9nh3/pdb
• Related: 1qwl 1qwm 2a9e 2iqf
• Descriptor: Catalase, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL, ... (6 entities in total)
• Functional Keywords: catalase, oxidative stress, oxidoreductase
• Biological source: Helicobacter pylori SS1
• Total number of polymer chains: 2
• Total formula weight: 119068.69

Authors

Baylink, A. (deposition date: 2025-02-23, release date: 2025-07-23)

Primary citation

Baylink, A.
AlphaFold 3 accurately models natural variants of Helicobacter pylori catalase KatA.
Biorxiv, 2025

PubMed Abstract: Subtle changes in protein sequence can equate to large changes in function, such as enabling pathogens to evade the immune system, hindering antibody recognition of antigens, or conferring antibiotic resistance. Even single amino acid substitutions may alter ligand binding affinity, enzymatic activity, and protein stability. Yet, due to limitations in time and resources, proteins closely related in sequence to those already characterized often remain unexamined. AlphaFold has emerged as a promising tool for protein structure prediction, though its utility in modeling single amino acid substitutions remains uncertain. In this study, we assessed AlphaFold 3's accuracy in modeling natural variants of the catalase KatA by comparing its predictions to a novel high-resolution crystal structure of KatA from strain SS1. This variant contains key substitutions at residues 234, 237, 255, and 421 relative to the well-characterized strain 26695. AlphaFold 3 models accurately reproduced the global structure and local conformations of most variant residues, with high fidelity in conservative substitutions but variable accuracy in more flexible or interface-exposed sites. We further explored how user inputs, such as incorrect oligomeric states or sequence modifications, influence prediction quality. While AlphaFold 3 consistently produced high-quality models, deviations at variant sites occurred when incorrect oligomeric states were specified. Our findings highlight both the strengths and limitations of AlphaFold 3 in modeling natural protein variants and underscore the importance of accurate user input for reliable structural predictions.

PubMed: 40501634
DOI: 10.1101/2025.06.02.657526

Experimental method

X-RAY DIFFRACTION (1.87 Å)