8DQV

The 1.52 angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - catalytic dimer (Huc2S2L)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history. 


Literature

Structural basis for bacterial energy extraction from atmospheric hydrogen.

Grinter, R., Kropp, A., Venugopal, H., Senger, M., Badley, J., Cabotaje, P.R., Jia, R., Duan, Z., Huang, P., Stripp, S.T., Barlow, C.K., Belousoff, M., Shafaat, H.S., Cook, G.M., Schittenhelm, R.B., Vincent, K.A., Khalid, S., Berggren, G., Greening, C.

(2023) Nature 

  • DOI: 10.1038/s41586-023-05781-7
  • Primary Citation of Related Structures:  
    7UTD, 7UUR, 7UUS, 8DQV

  • PubMed Abstract: 

    • Diverse aerobic bacteria use atmospheric H 2 as an energy source for growth and survival 1 . This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments 2,3 ...

    Diverse aerobic bacteria use atmospheric H 2 as an energy source for growth and survival 1 . This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments 2,3 . Atmospheric H 2 oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily 4,5 . However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H 2 amid ambient levels of the catalytic poison O 2 and how the derived electrons are transferred to the respiratory chain 1 . Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H 2 to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H 2 at the expense of O 2 , and 3 [3Fe-4S] clusters modulate the properties of the enzyme so that atmospheric H 2 oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H 2 oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H 2 in ambient air.

    Organizational Affiliation: 

    ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, Victoria, Australia. chris.greening@monash.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogenase-2, large subunitA, C513Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: hybC, MSMEG_2263
EC: 1.12.99.6
UniProt
Find proteins for A0QUM7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QUM7 
Go to UniProtKB:  A0QUM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QUM7
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogenase-2, small subunitB, D322Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEI_2206
EC: 1.12.99.6
UniProt
Find proteins for I7G634 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore I7G634 
Go to UniProtKB:  I7G634
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7G634
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F3S (Subject of Investigation/LOI)
Query on F3S
Download Ideal Coordinates CCD File 
J [auth B],
K [auth B],
L [auth B],
R [auth D],
S [auth D],
J [auth B],
K [auth B],
L [auth B],
R [auth D],
S [auth D],
T [auth D]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW		 Ligand Interaction
VK3 (Subject of Investigation/LOI)
Query on VK3
Download Ideal Coordinates CCD File 
I [auth B],
Q [auth D]		MENADIONE
C11 H8 O2
MJVAVZPDRWSRRC-UHFFFAOYSA-N		 Ligand Interaction
FCO (Subject of Investigation/LOI)
Query on FCO
Download Ideal Coordinates CCD File 
G [auth A],
O [auth C]		CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N		 Ligand Interaction
3NI (Subject of Investigation/LOI)
Query on 3NI
Download Ideal Coordinates CCD File 
H [auth A],
P [auth C]		NICKEL (III) ION
Ni
JDRCAGKFDGHRNQ-UHFFFAOYSA-N		 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
F [auth A],
N [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
O (Subject of Investigation/LOI)
Query on O
Download Ideal Coordinates CCD File 
E [auth A],
M [auth C]		OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20
MODEL REFINEMENTCoot0.92
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP200103074
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1197376

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-04
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2023-03-08
    Changes: Database references
  • Version 1.3: 2023-03-22
    Changes: Database references