[English] 日本語
Yorodumi
- EMDB-18607: Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18607
TitleMycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) ATP-bound form, compressed
Map dataLocScale filtered map
Sample
  • Complex: Octameric assembly of inosine monophosphate dehydrogenase in complex with ATP
    • Protein or peptide: Inosine-5'-monophosphate dehydrogenase
KeywordsOctamer / ATP complex / Purine metabolism / IMPDH / OXIDOREDUCTASE
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsBulvas O / Kouba T / Pichova I
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: Nat Commun / Year: 2024
Title: Deciphering the allosteric regulation of mycobacterial inosine-5'-monophosphate dehydrogenase.
Authors: Ondřej Bulvas / Zdeněk Knejzlík / Jakub Sýs / Anatolij Filimoněnko / Monika Čížková / Kamila Clarová / Dominik Rejman / Tomáš Kouba / Iva Pichová /
Abstract: Allosteric regulation of inosine 5'-monophosphate dehydrogenase (IMPDH), an essential enzyme of purine metabolism, contributes to the homeostasis of adenine and guanine nucleotides. However, the ...Allosteric regulation of inosine 5'-monophosphate dehydrogenase (IMPDH), an essential enzyme of purine metabolism, contributes to the homeostasis of adenine and guanine nucleotides. However, the precise molecular mechanism of IMPDH regulation in bacteria remains unclear. Using biochemical and cryo-EM approaches, we reveal the intricate molecular mechanism of the IMPDH allosteric regulation in mycobacteria. The enzyme is inhibited by both GTP and (p)ppGpp, which bind to the regulatory CBS domains and, via interactions with basic residues in hinge regions, lock the catalytic core domains in a compressed conformation. This results in occlusion of inosine monophosphate (IMP) substrate binding to the active site and, ultimately, inhibition of the enzyme. The GTP and (p)ppGpp allosteric effectors bind to their dedicated sites but stabilize the compressed octamer by a common mechanism. Inhibition is relieved by the competitive displacement of GTP or (p)ppGpp by ATP allowing IMP-induced enzyme expansion. The structural knowledge and mechanistic understanding presented here open up new possibilities for the development of allosteric inhibitors with antibacterial potential.
History
DepositionOct 6, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18607.png

Downloads & links

-
Map

FileDownload / File: emd_18607.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocScale filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 380 pix.
= 316.768 Å		0.83 Å/pix.
x 380 pix.
= 316.768 Å		0.83 Å/pix.
x 380 pix.
= 316.768 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.22326134 - 0.62002325
Average (Standard dev.)0.0017143888 (±0.018967642)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 316.768 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18607_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RELION post-processed map

Fileemd_18607_additional_1.map
AnnotationRELION post-processed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18607_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18607_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Octameric assembly of inosine monophosphate dehydrogenase in comp...

EntireName: Octameric assembly of inosine monophosphate dehydrogenase in complex with ATP
Components
  • Complex: Octameric assembly of inosine monophosphate dehydrogenase in complex with ATP
    • Protein or peptide: Inosine-5'-monophosphate dehydrogenase

-
Supramolecule #1: Octameric assembly of inosine monophosphate dehydrogenase in comp...

SupramoleculeName: Octameric assembly of inosine monophosphate dehydrogenase in complex with ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 426.658 KDa

-
Macromolecule #1: Inosine-5'-monophosphate dehydrogenase

MacromoleculeName: Inosine-5'-monophosphate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: IMP dehydrogenase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155
Molecular weightTheoretical: 53.388988 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSIAESSVPI AVPVPTGGDD PTKVAMLGLT FDDVLLLPAA SDVVPATADT SSQLTKRIRL RVPLVSSAMD TVTESRMAIA MARAGGMGV LHRNLPVAEQ AGQVETVKRS EAGMVTDPVT CSPDNTLAEV DAMCARFRIS GLPVVDDTGE LVGIITNRDM R FEVDQSKP ...String:
MSIAESSVPI AVPVPTGGDD PTKVAMLGLT FDDVLLLPAA SDVVPATADT SSQLTKRIRL RVPLVSSAMD TVTESRMAIA MARAGGMGV LHRNLPVAEQ AGQVETVKRS EAGMVTDPVT CSPDNTLAEV DAMCARFRIS GLPVVDDTGE LVGIITNRDM R FEVDQSKP VSEVMTKAPL ITAKEGVSAE AALGLLRRHK IEKLPIVDGH GKLTGLITVK DFVKTEQFPL STKDSDGRLL VG AAVGVGD DAWTRAMTLV DAGVDVLIVD TAHAHNRGVL DMVSRLKQAV GERVDVVGGN VATRAAAAAL VEAGADAVKV GVG PGSICT TRVVAGVGAP QITAILEAVA ACKPYGVPVI ADGGLQYSGD IAKALAAGAS TAMLGSLLAG TAESPGELIF VNGK QFKSY RGMGSLGAMQ GRGAAKSYSK DRYFQDDVLS EDKLVPEGIE GRVPFRGPLG TVIHQLTGGL RAAMGYTGSA TIEQL QQAQ FVQITAAGLK ESHPHDITMT VEAPNYYTR

UniProtKB: Inosine-5'-monophosphate dehydrogenase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPES2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid
500.0 mMKClPotassium chloride
5.0 mMDTTDithiothreitol
4.0 mMMgCl2Magnesium chloride
2.0 mMATPAdenosine triphosphate
1.0 mMIMPInosine monophosphate

Details: 50 mM HEPES (pH 7.5), 200 mM KCl, 5 mM DTT, 4 mM MgCl2 Ligand: 2 mM ATP + 1 mM IMP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 11232 / Average exposure time: 2.0 sec. / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 7395061
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ahl

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69863
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

qsu3


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial fitting was done in UCSF ChimeraX. Model refinement was done by iterative cycles of manual fitting with Coot and ISOLDE and automated fitting with phenix.real_space_refine.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 50.2 / Target criteria: CC coefficient
Output model

PDB-8qqw:
Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) ATP-bound form, compressed

+
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