[English] 日本語
Yorodumi
- EMDB-42489: Bacillus niacini flavin monooxygenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42489
TitleBacillus niacini flavin monooxygenase
Map dataHomologous refinement map filtered by estimated local resolution
Sample
  • Complex: Flavin monooxygenase trimer
    • Protein or peptide: Flavin monooxygenase
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL
KeywordsMonooxygenase / flavin binding / CYTOSOLIC PROTEIN
Biological speciesNeobacillus niacini (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsRichardson BC / French JB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124898 United States
CitationJournal: Biochemistry / Year: 2024
Title: Structural and Functional Characterization of a Novel Class A Flavin Monooxygenase from .
Authors: Brian C Richardson / Zachary R Turlington / Sofia Vaz Ferreira de Macedo / Sara K Phillips / Kay Perry / Savannah G Brancato / Emmalee W Cooke / Jonathan R Gwilt / Morgan A Dasovich / Andrew ...Authors: Brian C Richardson / Zachary R Turlington / Sofia Vaz Ferreira de Macedo / Sara K Phillips / Kay Perry / Savannah G Brancato / Emmalee W Cooke / Jonathan R Gwilt / Morgan A Dasovich / Andrew J Roering / Francis M Rossi / Mark J Snider / Jarrod B French / Katherine A Hicks /
Abstract: A gene cluster responsible for the degradation of nicotinic acid (NA) in has recently been identified, and the structures and functions of the resulting enzymes are currently being evaluated to ...A gene cluster responsible for the degradation of nicotinic acid (NA) in has recently been identified, and the structures and functions of the resulting enzymes are currently being evaluated to establish pathway intermediates. One of the genes within this cluster encodes a flavin monooxygenase (BnFMO) that is hypothesized to catalyze a hydroxylation reaction. Kinetic analyses of the recombinantly purified BnFMO suggest that this enzyme catalyzes the hydroxylation of 2,6-dihydroxynicotinic acid (2,6-DHNA) or 2,6-dihydroxypyridine (2,6-DHP), which is formed spontaneously by the decarboxylation of 2,6-DHNA. To understand the details of this hydroxylation reaction, we determined the structure of BnFMO using a multimodel approach combining protein X-ray crystallography and cryo-electron microscopy (cryo-EM). A liganded BnFMO cryo-EM structure was obtained in the presence of 2,6-DHP, allowing us to make predictions about potential catalytic residues. The structural data demonstrate that BnFMO is trimeric, which is unusual for Class A flavin monooxygenases. In both the electron density and coulomb potential maps, a region at the trimeric interface was observed that was consistent with and modeled as lipid molecules. High-resolution mass spectral analysis suggests that there is a mixture of phosphatidylethanolamine and phosphatidylglycerol lipids present. Together, these data provide insights into the molecular details of the central hydroxylation reaction unique to the aerobic degradation of NA in .
History
DepositionOct 25, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42489.png

Downloads & links

-
Map

FileDownload / File: emd_42489.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHomologous refinement map filtered by estimated local resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 352 pix.
= 229.22 Å		0.65 Å/pix.
x 352 pix.
= 229.22 Å		0.65 Å/pix.
x 352 pix.
= 229.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65119 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.142
Minimum - Maximum-2.9861577 - 4.320865
Average (Standard dev.)0.0034011044 (±0.09255731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 229.22 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Flavin monooxygenase trimer

EntireName: Flavin monooxygenase trimer
Components
  • Complex: Flavin monooxygenase trimer
    • Protein or peptide: Flavin monooxygenase
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL

-
Supramolecule #1: Flavin monooxygenase trimer

SupramoleculeName: Flavin monooxygenase trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Neobacillus niacini (bacteria)
Molecular weightTheoretical: 165 KDa

-
Macromolecule #1: Flavin monooxygenase

MacromoleculeName: Flavin monooxygenase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Neobacillus niacini (bacteria)
Molecular weightTheoretical: 52.534094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: (MSE)GSSHHHHHH SSGENLYFQG H(MSE)EELIKEVQ SDVCIVGAGP AG(MSE)LLGLLLA KQGLEVIVLE QNGDFHRE Y RGEITQPRFV QL(MSE)KQLNLLD YIESNSHVKI PEVNVFHNNV KI(MSE)QLAFNTL IDEESYCARL TQPTLLSALL D KAKKYPNF ...String:
(MSE)GSSHHHHHH SSGENLYFQG H(MSE)EELIKEVQ SDVCIVGAGP AG(MSE)LLGLLLA KQGLEVIVLE QNGDFHRE Y RGEITQPRFV QL(MSE)KQLNLLD YIESNSHVKI PEVNVFHNNV KI(MSE)QLAFNTL IDEESYCARL TQPTLLSALL D KAKKYPNF KLLFNTKVRD LLREDGKVTG VYAVAKPGEQ INFTEDEVFE GNLNIKSRVT VGVDGRNST(MSE) EKLGNFEL E LDYYDNDLLW FSFEKPESWD YNIYHFYFQK NYNYLFLPKL GGYIQCGISL TKGEYQKIKK EGIESFKEKI LED(MSE)P ILKQ HFDTVTDFKS FVQLLCR(MSE)RY IKDWAKEEGC (MSE)LIGDAAHCV TPWGAVGSTL A(MSE)GTAVIAAD VIYK GFKNN DLSLETLKQV QSRRKEEVK(MSE) IQNLQLTIEK FLTREPIKKE IAPL(MSE)FSIAT K(MSE)PDITNLYK KLF TREFPL DIDESFIFHD ELVEAN

-
Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 3 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

-
Macromolecule #3: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL

MacromoleculeName: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL
type: ligand / ID: 3 / Number of copies: 3 / Formula: DR9
Molecular weightTheoretical: 746.991 Da
Chemical component information

ChemComp-DR9:
1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
50.0 mMsodium chlorideNaCl
1.0 mMdithiothreitol
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 4176 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3395411 / Details: Template based picking
Startup modelType of model: OTHER / Details: Crystal structure determined in same publication
Final reconstructionNumber classes used: 26 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 432941
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 50 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8urc:
Bacillus niacini flavin monooxygenase

+
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