A residue-50 crystallographic B-factor scalar tracks catalytic-efficiency ordering across HG Kemp eliminase evolution
- 1founder, GreenFelix Innovations Pvt. Ltd., balco nagar , Korba, Chhattisgarh, India
- 2internal medicine , BALCO Hospital, balco nagar ,korba, Korba, Chhattisgarh, India
Abstract
Active-site pre-organisation is a well-characterised contributor to enzyme catalysis, and progressive rigidification of catalytic residues during HG-series Kemp eliminase evolution — including decreasing structure-normalised B-factor Z-scores at the position-50 residue — has already been reported directly from room-temperature crystallography (Broom et al., 2020). The contribution here is therefore not that observation, but a bounded quantitative test of how completely a single compact scalar recovers catalytic-efficiency ordering within an HG Kemp eliminase series, together with an explicit account of where that scalar fails to transfer. In the primary HG dataset — five room-temperature structures from the directed-evolution series plus the separately engineered variant HG4 — the residue-50 side-chain scalar correlated with log10(kcat/KM) at r = −0.9899 (p = 1.52 × 10-4) and reproduced the catalytic-efficiency ordering of the archived scalar values exactly (Spearman ρ = −1.000; exact two-sided permutation p = 0.0028). Restricting the analysis to the five evolutionary-series variants gave r = −0.9893. The association is robust to the choice of published kinetic dataset. In four independently designed HG variants the multi-residue active-site scalar was directionally negative (r = −0.7759) but weak on a rank basis (ρ = −0.400; exact two-sided p = 0.75) and is treated as neither replication nor support of comparable weight. Application of the same extraction logic to an independent KE07 scaffold failed a pre-committed robustness criterion and is reported as a negative transfer result. Two distinct sensitivities are separated there: a normalization correction, and an additional dependence on which deposited structure represents each variant across all 48 pre-declared combinations. We do not claim that the specificity of the primary single-residue scalar has been established: the archived negative controls were computed on a four-residue active-site average, not on the primary scalar, and their generating workflow is not fully archived. B-factors are treated throughout as operational crystallographic observables rather than as measurements of solution dynamics. The result is a narrowly scoped, reproducible descriptive reanalysis of public data with a clearly documented limit on transfer — not a causal mechanism, a specificity demonstration, or a generalisation to other reaction classes.
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BibTeX
@misc{sodalagunta2026residue50,
title = {{A residue-50 crystallographic B-factor scalar tracks catalytic-efficiency ordering across HG Kemp eliminase evolution}},
author = {Mahesh babu Sodalagunta},
howpublished = {ChemRxiv},
year = {2026},
month = sep,
doi = {10.26434/chemrxiv.15008941/v1},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008941/v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A residue-50 crystallographic B-factor scalar tracks catalytic-efficiency ordering across HG Kemp eliminase evolution
AU - Mahesh babu Sodalagunta
PY - 2026
DA - 2026/09/16
PB - ChemRxiv
DO - 10.26434/chemrxiv.15008941/v1
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008941/v1
AB - Active-site pre-organisation is a well-characterised contributor to enzyme catalysis, and progressive rigidification of catalytic residues during HG-series Kemp eliminase evolution — including decreasing structure-normalised B-factor Z-scores at the position-50 residue — has already been reported directly from room-temperature crystallography (Broom et al., 2020). The contribution here is therefore not that observation, but a bounded quantitative test of how completely a single compact scalar recovers catalytic-efficiency ordering within an HG Kemp eliminase series, together with an explicit account of where that scalar fails to transfer. In the primary HG dataset — five room-temperature structures from the directed-evolution series plus the separately engineered variant HG4 — the residue-50 side-chain scalar correlated with log10(kcat/KM) at r = −0.9899 (p = 1.52 × 10-4) and reproduced the catalytic-efficiency ordering of the archived scalar values exactly (Spearman ρ = −1.000; exact two-sided permutation p = 0.0028). Restricting the analysis to the five evolutionary-series variants gave r = −0.9893. The association is robust to the choice of published kinetic dataset. In four independently designed HG variants the multi-residue active-site scalar was directionally negative (r = −0.7759) but weak on a rank basis (ρ = −0.400; exact two-sided p = 0.75) and is treated as neither replication nor support of comparable weight. Application of the same extraction logic to an independent KE07 scaffold failed a pre-committed robustness criterion and is reported as a negative transfer result. Two distinct sensitivities are separated there: a normalization correction, and an additional dependence on which deposited structure represents each variant across all 48 pre-declared combinations. We do not claim that the specificity of the primary single-residue scalar has been established: the archived negative controls were computed on a four-residue active-site average, not on the primary scalar, and their generating workflow is not fully archived. B-factors are treated throughout as operational crystallographic observables rather than as measurements of solution dynamics. The result is a narrowly scoped, reproducible descriptive reanalysis of public data with a clearly documented limit on transfer — not a causal mechanism, a specificity demonstration, or a generalisation to other reaction classes.
ER -