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- EMDB-56607: CryoEM structure of guanidinase from Nitrospira inopinata -

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Basic information

Entry
Database: EMDB / ID: EMD-56607
TitleCryoEM structure of guanidinase from Nitrospira inopinata
Map data
Sample
  • Complex: Guanidinase (homo 6-mer)
    • Protein or peptide: Putative agmatinase 2
KeywordsHomo 6-mer / hydrolase / guanidine / comammox / METAL BINDING PROTEIN
Function / homology
Function and homology information


agmatinase / agmatinase activity / metal ion binding
Similarity search - Function
Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
Putative agmatinase 2
Similarity search - Component
Biological speciesCandidatus Nitrospira inopinata (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsProkhorova I / Lecomte L / Papp G / Schreiner C / Djinovic-Carugo K
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission945405European Union
CitationJournal: Nature / Year: 2024
Title: Growth of complete ammonia oxidizers on guanidine.
Authors: Marton Palatinszky / Craig W Herbold / Christopher J Sedlacek / Dominic Pühringer / Katharina Kitzinger / Andrew T Giguere / Kenneth Wasmund / Per H Nielsen / Morten K D Dueholm / Nico ...Authors: Marton Palatinszky / Craig W Herbold / Christopher J Sedlacek / Dominic Pühringer / Katharina Kitzinger / Andrew T Giguere / Kenneth Wasmund / Per H Nielsen / Morten K D Dueholm / Nico Jehmlich / Richard Gruseck / Anton Legin / Julius Kostan / Nesrete Krasnici / Claudia Schreiner / Johanna Palmetzhofer / Thilo Hofmann / Michael Zumstein / Kristina Djinović-Carugo / Holger Daims / Michael Wagner /
Abstract: Guanidine is a chemically stable nitrogen compound that is excreted in human urine and is widely used in manufacturing of plastics, as a flame retardant and as a component of propellants, and is well ...Guanidine is a chemically stable nitrogen compound that is excreted in human urine and is widely used in manufacturing of plastics, as a flame retardant and as a component of propellants, and is well known as a protein denaturant in biochemistry. Guanidine occurs widely in nature and is used by several microorganisms as a nitrogen source, but microorganisms growing on guanidine as the only substrate have not yet been identified. Here we show that the complete ammonia oxidizer (comammox) Nitrospira inopinata and probably most other comammox microorganisms can grow on guanidine as the sole source of energy, reductant and nitrogen. Proteomics, enzyme kinetics and the crystal structure of a N. inopinata guanidinase homologue demonstrated that it is a bona fide guanidinase. Incubation experiments with comammox-containing agricultural soil and wastewater treatment plant microbiomes suggested that guanidine serves as substrate for nitrification in the environment. The identification of guanidine as a growth substrate for comammox shows an unexpected niche of these globally important nitrifiers and offers opportunities for their isolation.
History
DepositionFeb 6, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56607.png

Downloads & links

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Map

FileDownload / File: emd_56607.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 224 pix.
= 196.672 Å		0.88 Å/pix.
x 224 pix.
= 196.672 Å		0.88 Å/pix.
x 224 pix.
= 196.672 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0939
Minimum - Maximum-0.16576098 - 0.27647737
Average (Standard dev.)-0.0005558023 (±0.01802814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 196.672 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_56607_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56607_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Guanidinase (homo 6-mer)

EntireName: Guanidinase (homo 6-mer)
Components
  • Complex: Guanidinase (homo 6-mer)
    • Protein or peptide: Putative agmatinase 2

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Supramolecule #1: Guanidinase (homo 6-mer)

SupramoleculeName: Guanidinase (homo 6-mer) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candidatus Nitrospira inopinata (bacteria)
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Putative agmatinase 2

MacromoleculeName: Putative agmatinase 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Nitrospira inopinata (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPMAKKRTYQ GKVPLHDNYG PEAKYAVEAE ALLPTTKFEE EIARGLELGL PGADSIKDRR IPTFSRGELP HFAGINTFIK APYVEDVRKC GQYDVAILGA PFDGGTTYRA GTRFGPQGIR KISALYGTYS FELGVDLRES VSICDVGDIF TIPGNIEKTF DQVSKGVGHV ...String:
GPMAKKRTYQ GKVPLHDNYG PEAKYAVEAE ALLPTTKFEE EIARGLELGL PGADSIKDRR IPTFSRGELP HFAGINTFIK APYVEDVRKC GQYDVAILGA PFDGGTTYRA GTRFGPQGIR KISALYGTYS FELGVDLRES VSICDVGDIF TIPGNIEKTF DQVSKGVGHV FASGAFPVVL GGDHSLGFAT VRGVAQHLNG KKLGILHFDR HVDTQDTDLD ERMHTTPWFH ATNIPNVPAK NLVQIGIGGW QAPRPGVKAG RERQTTIMTV TDCVEMGIEN AAKQALEVAF DGVDAVWLSF DVDCLDAAFV PGTGWPEPGG FLPREVLKFL QIIADTKPLA GMEIVECAPP YDAAEITSLM ATRVICDVLA CQVRSGHLGN RKKR

UniProtKB: Putative agmatinase 2

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHepes
150.0 mMNaClsodium chloride
0.357 %C3H8O3Glycerol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: AIR / Details: Passing several times in front of plasma torch
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 280 K
Details: Prepared with EasyGrid2 device by vitrification in ethane jet..
DetailsMonodisperse, high purity

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 549 / Average exposure time: 4.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 398821
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 119931
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final 3D classificationNumber classes: 2 / Avg.num./class: 114000 / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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