[English] 日本語
Yorodumi
- EMDB-18153: Beta-galactosidase from Bacillus circulans conformational state 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18153
TitleBeta-galactosidase from Bacillus circulans conformational state 1
Map data
Sample
  • Complex: Terciary complex of beta-galactosidase isoform A
    • Protein or peptide: beta-galactosidase
KeywordsGalactosidase / Transgalactosylation / Izoform A / Enzyme / HYDROLASE
Function / homology
Function and homology information


beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
: / Beta-galactosidase-like, Galactose-binding domain / Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Invasin/intimin cell-adhesion fragments ...: / Beta-galactosidase-like, Galactose-binding domain / Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesNiallia circulans subsp. circulans (bacteria) / Niallia circulans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsKascakova B / Hovorkova M / Petraskova L / Novacek J / Pinkas D / Gardian Z / Kren V / Bojarova P / Kuta Smatanova I
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic Czech Republic
CitationJournal: Structure / Year: 2024
Title: The variable structural flexibility of the Bacillus circulans β-galactosidase isoforms determines their unique functionalities.
Authors: Michaela Hovorková / Barbora Kaščáková / Lucie Petrásková / Petra Havlíčková / Jiří Nováček / Daniel Pinkas / Zdenko Gardian / Vladimír Křen / Pavla Bojarová / Ivana Kutá Smatanová /
Abstract: β-Galactosidase from Bacillus circulans ATCC 31382 (BgaD) is a biotechnologically important enzyme for the synthesis of β-galactooligosaccharides (GOS). Among its four isoforms, isoform A (BgaD-A) ...β-Galactosidase from Bacillus circulans ATCC 31382 (BgaD) is a biotechnologically important enzyme for the synthesis of β-galactooligosaccharides (GOS). Among its four isoforms, isoform A (BgaD-A) has distinct synthetic properties. Here, we present cryoelectron microscopy (cryo-EM) structures of BgaD-A and compare them with the known X-ray crystal structure of isoform D (BgaD-D), revealing substantial structural divergences between the two isoforms. In contrast to BgaD-D, BgaD-A features a flexible Big-4 domain and another enigmatic domain. The newly identified flexible region in BgaD-A is termed as "barrier domain 8," and serves as a barricade, obstructing the access of longer oligosaccharide substrates into the active site of BgaD-A. The transgalactosylation reactions catalyzed by both isoforms revealed that BgaD-A has a higher selectivity than BgaD-D in the earlier stages of the reaction and is prevailingly directed to shorter galactooligosaccharides. This study improves our understanding of the structural determinants governing β-galactosidase catalysis, with implications for tailored GOS production.
History
DepositionAug 7, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18153.png

Downloads & links

-
Map

FileDownload / File: emd_18153.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 261.76 Å		0.82 Å/pix.
x 320 pix.
= 261.76 Å		0.82 Å/pix.
x 320 pix.
= 261.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.818 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-1.1245815 - 1.8656473
Average (Standard dev.)-0.00079199334 (±0.043779712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 261.76 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18153_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18153_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18153_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Terciary complex of beta-galactosidase isoform A

EntireName: Terciary complex of beta-galactosidase isoform A
Components
  • Complex: Terciary complex of beta-galactosidase isoform A
    • Protein or peptide: beta-galactosidase

-
Supramolecule #1: Terciary complex of beta-galactosidase isoform A

SupramoleculeName: Terciary complex of beta-galactosidase isoform A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Niallia circulans subsp. circulans (bacteria)

-
Macromolecule #1: beta-galactosidase

MacromoleculeName: beta-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Niallia circulans (bacteria)
Molecular weightTheoretical: 192.584391 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKAISCVFL ISALILSSFQ VPVQGQAMSK TTSAAGNSVS YDGERRVNFN ENWRFQRETN GSIAGAQNPG FDDSSWRKLN LPHDWSIEL DFNKNSLATH EGGYLDGGIG WYRKTFTIPE SMKGKRISLD FDGVYMNSTT YLNGEVLGTY PFGYNAFSYD I SDKLYKDG ...String:
MKKAISCVFL ISALILSSFQ VPVQGQAMSK TTSAAGNSVS YDGERRVNFN ENWRFQRETN GSIAGAQNPG FDDSSWRKLN LPHDWSIEL DFNKNSLATH EGGYLDGGIG WYRKTFTIPE SMKGKRISLD FDGVYMNSTT YLNGEVLGTY PFGYNAFSYD I SDKLYKDG RANVLVVKVN NTQPSSRWYS GSGIYRNVYL TVTDPIHVAR YGTFVTTPNL EKSIKEDRAD VNIKTKISND AA EAKQVKI KSTIYDGAGN TVQTVETEEK TAAAGTVTPF EQNTVIKQPK LWSIDKPYRY NLVTEVIVGG QTVDTYETKF GVR YFKFDE NEGFSLNGEY MKLHGVSMHH DLGALGAATN ARGVERQMQI MKDMGVNAIR VTHNPASPEL LEAANKLGLF IIEE AFDSW AQSKKPYDYG RFFNAWAEHD IKEMVDRGKN EPAIIMWSIG NEIYDTTNAA GVETARNLVG WVKEIDTTRP TTIGE DKTR GDKVNVTPIN SYIKEIFNIV DVVGLNYSEN NYDGYHKQNP SWKLYGSETS SATRSRGVYT HPYQYNQSTK YADLQQ SSY DNDYVGWGRT AEDAWKYDRD LKHIAGQFIW TGFDYIGEPT PYYNSYPAKS SYFGAVDTAG FPKDIFYYYQ SQWKKEP MV HLLPHWNWKE GEKVRVLAYT NASKVELVLN GESLGEKNYD NKQTSWGAPY KETKDGKTYL EWAVPFKPGK LEAVAKDE N GKVIARDQVV TAGEPASVRL TADRKVVKAD GTDLSFITAD IVDSKGIVVP DADHLITFNV TGQGELAGVD NGNASSVER YKDNKRKAFS GKALAIVQSS KLSGKITVHA SVAGLSSDST SVFTVTPADH DKKIVAGIDD VNLTVDVNEA PKLPSEIKVY YSDESAAAK NVTWDEVDPK QYSTVGEFTV EGSVEGTSLK AKAFVIVKGI VAVKPYSTAT KVGVQPVLPE KATLLYSDGT T KGATVTWD EIPEDKLAKE GRFTVEGSVE GTDLKANVYV RVTNEVKSVN IMLQEQGSAY PKLEATFTNP ADNLQHLNDG IK SYTNNPV NRWTNWTRTP RDAGDSITVN FGKKHVINNL DLFVFTDSGT VVPEKAEVQY WDGTAWKDVE NLTQPSPYVV EKN ELTFDA VATEKLKFHL TPSVKGKFLA LTEAEVYADQ IVMGETAKLQ SITVNGKALE GFDHAKKNYE LVLPYGSELP KIEA AAADN ATVTILPAFS YPGTAKLFVT SEDGKVTTEY SIGVSTEEPK LVSAELSADK TNVMEDDIID LKVIGLFESK EKIDV TDSQ PTYEFDQQII KIEGNKLYAL ETGNVKVKVT VTYKGVSVTT PALEFTIAKN PAPKYITSLE PVTVVVKKGE APELPA TVV AHYNRGIPRD VKVKWERINP SKYQQLGEFT VSGMVEGTDI KAQAKVIVKG AVAVEDIRMA VLLKQMPQLP GKVTVYY SD GAEEQRAVKW EEIPQEELEN VGEFKVKGDV NGVKLKATAT IRVTDEVGGE QNISRAKNGY EYPKAEASFT NNGPGSSD R IEAINDDVIS YEANPHNRWT NWQPVPRAGD WVSITFGDYE PTEYDVDSME IHWFADHGTS YPERFQIEYK SGDSWKEVT SLKSDPASPA LGKANVYSFD RVKTSAIRVK MTAQAGKSLA ITELKVFSKW PKAGTEPEVT DIKVGGKSIL EDFEQKGDHY EVTIDAGDA NVMPKINVKA KDQTSITIVP AVTSPSTAKV IAKSEDGKKV KVYSIHYK

UniProtKB: Beta galactosidase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.18 mg/mL
BufferpH: 6 / Component - Concentration: 2.0 mg/ml / Component - Name: sodium phosphate / Details: 50 mM sodium phosphate buffer pH 6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 5.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 265100
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more