Part:BBa_K535000

HydEF -> C. reinhardtii

HydEF is a protein from Chlamydomonas reinhardtii genome, this protein contains two unique domains that are homologous to two distinct prokaryotic proteins, HydE and HydF, which are found exclusively in organisms containing [Fe] hydrogenase.

In the C. reinhardtii genome, the HydEF gene is adjacent to another hydrogenase-related gene, HydG. All organisms with [Fe] hydrogenase and sequenced genomes contain homologues of HydE, HydF, and HydG.

HydEF and HydG genes are transcribed anaerobically in parallel with the HydA1 and HydA2 [Fe] hydrogenase genes in C. reinhardtii.

HydEF and HydG function in the assembly of [Fe] hydrogenase, they are accessory genes required for the maturation of an active [Fe] hydrogenase, thats why they are called "maturases".

The [Fe] hydrogenase (HydA1) catalytic site is known as the H-cluster and consists of a [4Fe4S] cluster connected through a bridging cysteinyl ligand to a binuclear [2Fe] center.

HydEF and HydG proteins belong to the Radical S-adenosylmethionine (designated "Radical SAM", also known as the AdoMet radical) superfamily because they contain the signature Cys-X3-Cys-X2-Cys motif that is typically found within the Radical SAM protein superfamily. This motive coordinates a redox active [4Fe4S] cluster under reducing conditions.

There is precedent for the involvement of a Radical SAM protein in the donation of iron to the catalytic metal cluster of an [Fe]-metalloenzyme, thats why its proposed that HydEF and/or HydG proteins play a similar role in the mobilization of iron for assembly of the [Fe] hydrogenase H-cluster.

The H-cluster also requires CN, CO, and the putative di(thiomethyl)amine ligand. It is conceivable that the accessory proteins HydEF and/or HydG are also responsible for the biosynthesis and assembly of these products coordinated to iron.

What makes HydEF special among other proteins from the radical SAM superfamily are two conserved sequences with the potential to coordinate metal ions. These include a E(A/G)CXH and a (I/V)HC(G/A)(G/A)C motif near the C terminus of HydF, these motifs are strictly conserved in the [Fe] hydrogenase assembly proteins, but they are absent from other Radical SAM proteins.

The N-terminal portion of the HydEF protein is homologous to a group of proteins that, to date, are only found in prokaryotes containing [Fe] hydrogenases and belongs to a previously uncharacterized subset of the Radical SAM protein superfamily.

C-terminal portion of the HydEF protein contains a domain with predicted GTPase activity. This domain is homologous to a second distinct group of prokaryotic proteins, which are also unique to organisms that contain [Fe] hydrogenases, these proteins are required for the assembly of active [Fe] hydrogenase.

It has been demostrated that mutant C. reinhardtii strains with the HydEF gene inactivated are capable of prudicing [Fe] Hydrogenase but are incapable of produce H₂, which indicates that the [Fe] Hydrogenase is not mature enough without this gene.

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  INCOMPATIBLE WITH RFC[12]

  Illegal NotI site found at 2774
  Illegal NotI site found at 3080
  
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal NgoMIV site found at 127
  Illegal NgoMIV site found at 148
  Illegal NgoMIV site found at 258
  Illegal NgoMIV site found at 931
  Illegal NgoMIV site found at 1051
  Illegal NgoMIV site found at 1114
  Illegal NgoMIV site found at 1528
  
• 1000
  INCOMPATIBLE WITH RFC[1000]

  Illegal BsaI.rc site found at 334
  Illegal BsaI.rc site found at 754
  Illegal BsaI.rc site found at 961
  Illegal BsaI.rc site found at 2764
  Illegal BsaI.rc site found at 3121