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- EMDB-71280: HmuS heme dechelatase: disordered domain 1, heme free. -

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Basic information

Entry
Database: EMDB / ID: EMD-71280
TitleHmuS heme dechelatase: disordered domain 1, heme free.
Map dataHmuS disordered head domain, no heme at site 1
Sample
  • Complex: HmuS in complex with heme
    • Protein or peptide: HmuS heme dechelatase
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsIron / Microbiome / Heme / METAL TRANSPORT
Function / homologycobaltochelatase activity / CobN/magnesium chelatase / CobN/Magnesium Chelatase / membrane / Cobaltochelatase subunit CobN
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsGauvin CC / Nath AK / Rodrigues da Silva R / Akpoto E / Dubois JL / Lawrence CM
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Science Foundation (NSF, United States)DBI-1828765 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM140963 United States
CitationJournal: EMBO J / Year: 2025
Title: Commensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.
Authors: Arnab Kumar Nath / Ronivaldo Rodrigues da Silva / Colin C Gauvin / Emmanuel Akpoto / Mensur Dlakić / C Martin Lawrence / Jennifer L DuBois /
Abstract: Iron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu ...Iron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu operon, primarily found in Bacteroidota and ubiquitous in gastrointestinal tract metagenomes of healthy humans, encodes proteins involved in heme acquisition. Here, we provide direct physiological, biochemical, and structural evidence for the anaerobic removal of iron from heme by HmuS, a membrane-bound, NADH-dependent de-chelatase that deconstructs heme to protoporphyrin IX (PPIX) and Fe(II). Heme can serve as the sole iron source for the model gastrointestinal bacterium Bacteroidetes thetaiotaomicron, when active HmuS is present. Heterologously expressed HmuS was isolated with bound heme molecules under saturating conditions. Its cryo-EM structure at 2.6 Å resolution revealed binding of heme and a pair of cations at distant sites. These sites are conserved across the HmuS family and chelatase superfamily, respectively. The proposed structure-based mechanism for iron removal by HmuS is chemically analogous to the chelatases in both unrelated heme biosynthetic pathways and homologous enzymes in the biosynthetic pathways for chlorophyll and vitamin B12, although the reaction proceeds in the opposite direction. Taken together, our study identifies a widespread mechanism via which anaerobic bacteria can extract nutritional iron from heme.
History
DepositionJun 17, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71280.png

Downloads & links

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Map

FileDownload / File: emd_71280.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHmuS disordered head domain, no heme at site 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 320 pix.
= 289.92 Å		0.91 Å/pix.
x 320 pix.
= 289.92 Å		0.91 Å/pix.
x 320 pix.
= 289.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.906 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.09066388 - 0.26066428
Average (Standard dev.)0.00007903569 (±0.005441104)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 289.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71280_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_71280_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_71280_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : HmuS in complex with heme

EntireName: HmuS in complex with heme
Components
  • Complex: HmuS in complex with heme
    • Protein or peptide: HmuS heme dechelatase
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: HmuS in complex with heme

SupramoleculeName: HmuS in complex with heme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 153.058 KDa

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Macromolecule #1: HmuS heme dechelatase

MacromoleculeName: HmuS heme dechelatase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Molecular weightTheoretical: 162.423281 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKKSKIILG GCIVVAALIG LSVWNTWFSA TKIAFVNFQT IQQGSISKAN DNSFIKLSEV SLDNLDRLTS YDMVFINGMG LRIVEEQRQ QIQQAADKGI PVYTSMATNP ANNICNLDSI QQNLIRGYLS NGGKTNYRNM LNYIRKAIDG KASAVPEVED P IERPSDML ...String:
MKKKSKIILG GCIVVAALIG LSVWNTWFSA TKIAFVNFQT IQQGSISKAN DNSFIKLSEV SLDNLDRLTS YDMVFINGMG LRIVEEQRQ QIQQAADKGI PVYTSMATNP ANNICNLDSI QQNLIRGYLS NGGKTNYRNM LNYIRKAIDG KASAVPEVED P IERPSDML YHAGISNPDD EQEFLTVADY EKFMQENNLY KEGARKIMIT GQMADATDLI KALENAGYNV YPVQSMTRFM SF IEEVQPD AVINMAHGRM GDKMVDYLKA RNILLFAPLT INSLVDEWEN DPMGMSGGFM SQSIVTPEID GAIRPFALFA QYE DKEGLR HSYAVPERLK TFVSTIDNYL NLKTKPNFEK KVAIYYYKGP GQNALTAAGM EVVPSLYNLL LRMKQEGYNI SGLP ANAQE LGKMIQAQGA VFNAYAEGAF NDFMQNGHPE LITKEQYESW VKESLRPEKY QEVVDAFGEF PGNYMVTPDG KLGIA RLQF GNVVLLPQNA AGSGDNSFQV VHGTDMAPPH TYIASYLWMQ HGFKADALIH FGTHGSLEFT PRKQVALCSN DWPDRL VGA VPHYYLYSIG NVGEGMMAKR RSYATLQSYL TPPFLESSVR GIYRELMEKI KIYNNSQKAN KDQESLAVKT LTVKMGI HR DLGLDSMANK PYTEDEIARV ENFAEELATE KITGQLYTMG VPYEPERITS SVYAMATEPI AYSLFALDKQ RGKATESA E KHRSVFTQQY LMPARLLVER LMANPSLATD ELICHTAGIT PQELAKARQI EAERNAPKGM MAMMMAAAAK KDQADNEPS GNGHPASAKM EKGPHGKMPA GMKEAMKKMG ANMDPEKAME MAKSMGASPE ALKKMEASMK ANKDTSTDAS GKPAMAGKTE KPQGMSAMM AAMGKAPKEY SKEEVEFALA VAEVERTIKN VGNYKNALLT SPEEELSSLM NALKGGYTAP TPGGDPIANP N TLPTGRNM YAINAEATPT ESAWEKGIAL AKQTIDRYKQ RHNDSIPRKV SYTLWSSEFI ETGGATIAQV LYMLGVEPVR DA FGRVSDL KLIPSTELGR PRIDVVVQTS GQLRDLAASR LFLINRAVEM AAAAKDDKYE NQVASSVIEA ERVLTEKGLS PKD AREIST FRVFGGANGM YGTGIQEMVE SGDRWENESE IADTYLNNMG AYYGSEKNWE VFQKFAFEAA LTRTDVVVQP RQSN TWGAL SLDHVYEFMG GMNLAVRNVT GKDPDAYLSD YRNRNHMKMQ ELKEAVGVES RTTILNPTYI KEKMKGGASS ASEFA EVIT NTYGWNVMKP AAIDKELWDN IYNVYVKDEL NLGVKQYFEQ QNPAALEEMT AVMLESARKG LWQASEEQVA ELSKLH TEI VNTYRPSCSG FVCDNAKLRD FIASKADAQT ATQYKENISK IREAKASGSN KGVVMKKEEM NQTAENQTNT LSNVAVG IA VIIVILALIL FVRKRRKSSQ M

UniProtKB: Cobaltochelatase subunit CobN

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 95 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1.5 mg/mL
BufferpH: 7.1
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3ClTris-Cl
250.0 mMNaClSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 100.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12602 / Average exposure time: 3.06 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 55187 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 18955798 / Details: Blob picked, then particles washed to give
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 3795134
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-9p4s:
HmuS heme dechelatase: disordered domain 1, heme free.

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