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- EMDB-49363: Cryo-EM map of the inactive conformation of a glycoside hydrolase... -

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Basic information

Entry
Database: EMDB / ID: EMD-49363
TitleCryo-EM map of the inactive conformation of a glycoside hydrolase (CapGH2b) from the GH2 family
Map data
Sample
  • Complex: CapGH2b
    • Other: Glycosyl hydrolase from GH2 family
Keywordsredox-regulation / glycosyl hydrolase / mannosidase / redox-switch / metagenome / disulfide bond / HYDROLASE
Biological speciesmetagenome (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsMartins MP / Dolce LG / Santos CR / Murakami MT
Funding support Brazil, 2 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/04891-3 Brazil
Sao Paulo Research Foundation (FAPESP)2021/09793-0 Brazil
CitationJournal: Nat Commun / Year: 2026
Title: A disulfide redox switch mechanism regulates glycoside hydrolase function.
Authors: Marcele Pandeló Martins / Gustavo Henrique Martins / Felipe Jun Fuzita / João Paulo Menezes Spadeto / Renan Yuji Miyamoto / Felippe Mariano Colombari / Fabiane Stoffel / Luciano Graciani ...Authors: Marcele Pandeló Martins / Gustavo Henrique Martins / Felipe Jun Fuzita / João Paulo Menezes Spadeto / Renan Yuji Miyamoto / Felippe Mariano Colombari / Fabiane Stoffel / Luciano Graciani Dolce / Camila Ramos Dos Santos / Rodrigo Silva Araujo Streit / Antônio Carlos Borges / Rafael Henrique Galinari / Yoshihisa Yoshimi / Paul Dupree / Gabriela Felix Persinoti / Mariana Abrahão Bueno Morais / Mario Tyago Murakami /
Abstract: Disulfide bonds are a key post-translational modification involved in protein folding, structural stability, and functional regulation. Here, we demonstrate that a glycoside hydrolase from the GH2 ...Disulfide bonds are a key post-translational modification involved in protein folding, structural stability, and functional regulation. Here, we demonstrate that a glycoside hydrolase from the GH2 family undergoes reversible redox regulation through an intramolecular disulfide bond. The enzyme is inactive in its oxidized state and becomes active when reduced through a fully reversible process. Under oxidative conditions, multiple crystallographic and cryo-EM structures revealed a pronounced structural disorder in the active site, most prominent in the regulatory and catalytic loops, which disrupts the substrate binding site and, remarkably, the configuration of the acidic catalytic residues. Conversely, a high-resolution cryo-EM structure of the active (reduced) state unveiled a well-ordered active site with catalytic residues properly positioned for a classical Koshland retaining mechanism. This reversible order-disorder process based on a disulfide switch provides a mechanism for redox-dependent control of glycoside hydrolase activity, with potential implications for carbohydrate metabolism, microbial adaptation and biotechnological applications.
History
DepositionFeb 21, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49363.png

Downloads & links

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Map

FileDownload / File: emd_49363.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 500 pix.
= 335. Å		0.67 Å/pix.
x 500 pix.
= 335. Å		0.67 Å/pix.
x 500 pix.
= 335. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.40780836 - 1.1377645
Average (Standard dev.)0.00042900915 (±0.030856993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 335.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49363_msk_1.map
Projections & Slices
AxesZYX

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Additional map: DeepEMhancer sharpening

Fileemd_49363_additional_1.map
AnnotationDeepEMhancer sharpening
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Half map: #1

Fileemd_49363_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_49363_half_map_2.map
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Sample components

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Entire : CapGH2b

EntireName: CapGH2b
Components
  • Complex: CapGH2b
    • Other: Glycosyl hydrolase from GH2 family

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Supramolecule #1: CapGH2b

SupramoleculeName: CapGH2b / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: metagenome (others)

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Macromolecule #1: Glycosyl hydrolase from GH2 family

MacromoleculeName: Glycosyl hydrolase from GH2 family / type: other / ID: 1 / Classification: other
Source (natural)Organism: metagenome (others)
SequenceString: MGSSHHHHHH SSGLVPRGSH MFVSEQSLNG RWTLKFFPQP AVPVMTIEGA EAANGIVVDA VVPGNVEIDM EAAGLVEDPM VGNNIYKLRP YEGYQWYYSR TFAAPVVTEG QRLVLHFGGI DTFAEVYVNG IKVGSADNML IEHDYDITSV VKEGENRLDV IIRSSVMEAQ ...String:
MGSSHHHHHH SSGLVPRGSH MFVSEQSLNG RWTLKFFPQP AVPVMTIEGA EAANGIVVDA VVPGNVEIDM EAAGLVEDPM VGNNIYKLRP YEGYQWYYSR TFAAPVVTEG QRLVLHFGGI DTFAEVYVNG IKVGSADNML IEHDYDITSV VKEGENRLDV IIRSSVMEAQ NHFLGTLSIG NFSNEESAPV RRAPSTYGWD IMPRLVSAGL WRDVTLRVEN PVTIVDANWV TLSVNPKARE ASESLYLQTR LPFEMHDKVK AVITISRDGR QILRKEALMR KFANLFTLNL SGVDAWWPRG YGEPALYTAE VSLVDVTSGK IYDTKTSKIG FRTVKLELDE VNLPGQPGQF QFIINGEPVF AKGTNWVPLD ALHSRDASHV EEAVQLMVEM NCNIVRCWGG NVYEDTHFFE LCDKYGIMVW QDFAMGCGNY SQRDNFAAAL EKEAISVVVK LRNHPSLILW SGNNEDDQSL VFGRLAPFKA NPNNDRVSRQ VLSRVIYEFD PTRPYLPSSP YYGPKVCEVG VRDEVLPENH LWGPRGYYKD PFYTENPSQF VSEIGYHGCP NRETLERMFS PDSVNPWQNG VVGMWNDEWQ TKANRIYDDK FQGGRNDLMT NQVRIIFGEV PADLDDFIFA SQSVQAEAMK FFVELWRGRR PYRTGIIWWN IRDGWPLLSD AISDYWGGKK QAFYYMQNVH HDVCCLINPA ANGYMLKVDN NTLKDFEGVV EVKDVASGKQ VFKGKFVSKA NQMSEIATLP MQKGQGMLVI SYRIEGNEYF NHYLYGEPPY KLDQYRKWVK KCGIYELE
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139826
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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