Evidence map›Paper›PMID 40864494›Full record

ArticleActa crystallographica. Section D, Structural biology2025

Crystal structures of 40- and 71-substitution variants of hydroxynitrile lyase from rubber tree.

Colin T Pierce, Panhavuth Tan, Lauren R Greenberg, Meghan E Walsh, Ke Shi, Alana H Nguyen, Elyssa L Meixner, Sharad Sarak, Hideki Aihara, Robert L Evans and 1 more

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Article in Acta crystallographica. Section D, Structural biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0cells of the map it votes in
0citing papers in PubMed
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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Colin T PierceDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Panhavuth TanDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Lauren R GreenbergDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.ORCID 0000-0001-6602-2067
Meghan E WalshDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Ke ShiDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Alana H NguyenDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Elyssa L MeixnerDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Sharad SarakDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Hideki AiharaDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.ORCID 0000-0001-7508-6230
Robert L EvansDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Romas J KazlauskasDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.ORCID 0000-0002-3570-2411

Funding

A Synchrotron Radiation Structural Biology ResourcesP30GM133894 · NIGMS · STANFORD UNIVERSITY · PI Ritimukta Sarangi · 2020 to 2026
$43.3M
User Training and OutreachP30GM124165 · NIGMS · CORNELL UNIVERSITY · PI Nozomi Ando, J Christopher Fromme · 2018 to 2026
$34.2M
Structural studies of viral replication and invasionR35GM118047 · NIGMS · UNIVERSITY OF MINNESOTA · PI Hideki Aihara · 2016 to 2026
$6.3M
Mechanism and modulation of Amyloid Precursor Protein proteolysisR35GM119483 · NIGMS · UNIVERSITY OF MINNESOTA · PI WENDY RYAN GORDON · 2016 to 2026
$4.6M
Pixel Array Detector for X-ray CrystallographyS10RR029205 · NCRR · CORNELL UNIVERSITY · PI EALICK, STEVEN E · 2010 to 2010
$1.8M
National Science Foundation, Directorate for Engineering CBET 2039039NCRR NIH HHS S10 RR029205NIGMS NIH HHS GM119483NIGMS NIH HHS P30 GM124165NIGMS NIH HHS P30 GM133894NIGMS NIH HHS R35 GM118047NIGMS NIH HHS R35-GM118047NIGMS NIH HHS R35 GM119483NIGMS NIH HHS S10 RR029205U.S. Department of Energy, Office of Science DE-AC02-06CH11357
6 · The paper itself

Abstract

Hydroxynitrile lyase from Hevea brasiliensis (HbHNL) and the esterase SABP2 from Nicotiana tabacum share the α/β-hydrolase fold, a Ser-His-Asp catalytic triad and 44% sequence identity, yet catalyze different reactions. Prior studies showed that three active-site substitutions in HbHNL conferred weak esterase activity. To investigate how regions beyond the active site influence catalytic efficiency and active-site geometry, we engineered HbHNL variants with increasing numbers of substitutions to match SABP2. Variant HNL16 has all amino acids within 6.5 Å of the active site identical to SABP2, HNL40 those within 10 Å and HNL71 those within 14 Å. HNL16 exhibited poor esterase activity, whereas both HNL40 and HNL71 showed efficient esterase catalysis, demonstrating that residues beyond the immediate active site are critical for functional conversion. X-ray structures of HNL40 and HNL71 reveal a progressive shift in backbone positions toward those of SABP2, with r.m.s.d. values of 0.51 Å (HNL40) and 0.41 Å (HNL71) over the C

Indexed as

Aldehyde-LyasesHeveaPlant ProteinsAmino Acid SequenceAmino Acid SubstitutionCatalytic DomainCrystallography, X-RayModels, MolecularProtein ConformationAldehyde-Lyasesmandelonitrile lyasePlant Proteinsengineered proteinsesteraseshydroxynitrile lyasesSABP2salicylic acid-binding protein 2α/β-hydrolase fold

Identifiers

PMID40864494
PMCPMC12400190

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.