[English] 日本語
Yorodumi
- PDB-8uiu: Structure of an FMO from Bacillus niacini -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uiu
TitleStructure of an FMO from Bacillus niacini
ComponentsFlavin monooxygenase
KeywordsOXIDOREDUCTASE / flavin monooxygenase
Function / homologyChem-DR9 / FLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesNeobacillus niacini (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.14 Å
AuthorsHicks, K.A. / Perry, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1817633 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 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flavin monooxygenase
B: Flavin monooxygenase
C: Flavin monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,6297
Polymers157,6023
Non-polymers3,0274
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)359.668, 51.584, 102.669
Angle α, β, γ (deg.)90.000, 90.770, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 6 through 10 and (name N...
d_2ens_1(chain "B" and (resid 6 through 30 or (resid 31...
d_3ens_1(chain "C" and (resid 6 through 30 or (resid 31...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSASNASNAA6 - 4127 - 62
d_12GLUGLUASPASPAA51 - 42372 - 444
d_21LYSLYSASNASNBB6 - 4127 - 62
d_22GLUGLUPHEPHEBB51 - 16072 - 181
d_23GLUGLUASPASPBB167 - 423188 - 444
d_31LYSLYSASNASNCC6 - 4127 - 62
d_32GLUGLUASPASPCC51 - 42372 - 444

NCS oper:
IDCodeMatrixVector
1given(0.681865870009, -0.0178360831307, -0.731259741443), (0.00635964074677, -0.999520336487, 0.0303092711482), (-0.731449581507, -0.025317406789, -0.681425372749)87.4875841732, 52.0494110573, 199.815810503
2given(-0.504116172035, -0.00812770556225, -0.863597606235), (0.00702875942676, 0.999883986583, -0.013513323626), (0.863607249642, -0.0128823047936, -0.504000560108)245.50729022, 1.1728952398, -13.0969915229

-
Components

#1: Protein Flavin monooxygenase


Mass: 52534.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neobacillus niacini (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-DR9 / 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL / (2R)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(9E)-HEXADEC-9-ENOYLOXY]PROPYL (9E)-OCTADEC-9-ENOATE


Mass: 746.991 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H75O10P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.5 M imidazole (pH 6.2-6.5) and 10-12% PEG 3350 / PH range: 6.2-6.5

-
Data collection

DiffractionMean temperature: 183 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.14→68.09 Å / Num. obs: 33392 / % possible obs: 98.88 % / Redundancy: 13.8 % / Biso Wilson estimate: 128.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1147 / Net I/σ(I): 16.59
Reflection shellResolution: 3.14→3.252 Å / Rmerge(I) obs: 2.449 / Num. unique obs: 3261 / CC1/2: 0.377

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.14→68.09 Å / SU ML: 0.6118 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 31.0676
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.278 1657 4.97 %
Rwork0.2461 31673 -
obs0.2477 33330 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.46 Å2
Refinement stepCycle: LAST / Resolution: 3.14→68.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8641 0 206 0 8847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00949024
X-RAY DIFFRACTIONf_angle_d1.057212302
X-RAY DIFFRACTIONf_chiral_restr0.0611444
X-RAY DIFFRACTIONf_plane_restr0.00991572
X-RAY DIFFRACTIONf_dihedral_angle_d12.43872962
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.71876286628
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.793184158538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.230.46191110.45852626X-RAY DIFFRACTION97.51
3.23-3.340.39641690.37422442X-RAY DIFFRACTION95.96
3.34-3.460.35641310.28782661X-RAY DIFFRACTION99.22
3.46-3.590.32151790.26992567X-RAY DIFFRACTION99.96
3.59-3.760.31341410.26052623X-RAY DIFFRACTION99.39
3.76-3.960.33761400.27092686X-RAY DIFFRACTION99.86
3.96-4.20.281090.25022618X-RAY DIFFRACTION99.74
4.2-4.530.28941430.20832668X-RAY DIFFRACTION99.54
4.53-4.980.25091190.21552596X-RAY DIFFRACTION97.49
4.98-5.70.2711290.24282725X-RAY DIFFRACTION99.79
5.7-7.190.29151350.27672697X-RAY DIFFRACTION99.75
7.19-68.090.23351510.22172764X-RAY DIFFRACTION98.65

+
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