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TitleStructural basis for bacterial energy extraction from atmospheric hydrogen.
Journal, issue, pagesNature, Vol. 615, Issue 7952, Page 541-547, Year 2023
Publish dateMar 8, 2023
AuthorsRhys Grinter / Ashleigh Kropp / Hari Venugopal / Moritz Senger / Jack Badley / Princess R Cabotaje / Ruyu Jia / Zehui Duan / Ping Huang / Sven T Stripp / Christopher K Barlow / Matthew Belousoff / Hannah S Shafaat / Gregory M Cook / Ralf B Schittenhelm / Kylie A Vincent / Syma Khalid / Gustav Berggren / Chris Greening /
PubMed AbstractDiverse aerobic bacteria use atmospheric H as an energy source for growth and survival. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and ...Diverse aerobic bacteria use atmospheric H as an energy source for growth and survival. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments. Atmospheric H oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily. However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H amid ambient levels of the catalytic poison O and how the derived electrons are transferred to the respiratory chain. 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 to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H at the expense of O, and 3 [3Fe-4S] clusters modulate the properties of the enzyme so that atmospheric H 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 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 in ambient air.
External linksNature / PubMed:36890228 / PubMed Central
MethodsEM (single particle)
Resolution1.52 - 8.0 Å
Structure data

26767

7utd

EMDB-26767, PDB-7utd:
The 2.19-angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - Complex minus stalk
Method: EM (single particle) / Resolution: 2.19 Å

26801

7uur

EMDB-26801, PDB-7uur:
The 1.67 Angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - catalytic dimer (Huc2S2L)
Method: EM (single particle) / Resolution: 1.67 Å

26802

7uus

EMDB-26802, PDB-7uus:
The CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - Full complex focused refinement of stalk
Method: EM (single particle) / Resolution: 8.0 Å

27661

8dqv

EMDB-27661, PDB-8dqv:
The 1.52 angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - catalytic dimer (Huc2S2L)
Method: EM (single particle) / Resolution: 1.52 Å

Chemicals

ChemComp-3NI:
NICKEL (III) ION / Nickel

ChemComp-FCO:
CARBONMONOXIDE-(DICYANO) IRON

ChemComp-MG:
Unknown entry

ChemComp-MQ9:
MENAQUINONE-9 / Vitamin K2

ChemComp-F3S:
FE3-S4 CLUSTER / Iron–sulfur cluster

ChemComp-OH:
HYDROXIDE ION / Hydroxide

ChemComp-VK3:
MENADIONE / Menadione

ChemComp-HOH:
WATER / Water

ChemComp-O:
OXYGEN ATOM / Oxygen

Source
  • mycolicibacterium smegmatis (bacteria)
  • mycolicibacterium smegmatis mc2 155 (bacteria)
KeywordsOXIDOREDUCTASE / [NiFe] Hydrogenase / Membrane associated / Complex / Quinone Transport / ELECTRON TRANSPORT / OXIDOREDUCTASE (EC 1.12.99.6) / [NiFe]-Hydrogenase / Membrane-associated

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