Genetic analyses of the functions of [NiFe]-hydrogenase maturation endopeptidases in the hyperthermophilic archaeon Thermococcus kodakarensis

Kanai, Tamotsu; Yasukochi, Ayako; Simons, Jan-Robert; Scott, Joseph W.; Fukuda, Wakao; Imanaka, Tadayuki; Atomi, Haruyuki

doi:10.1007/s00792-016-0875-1

Cited by 9 publications

(5 citation statements)

References 38 publications

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“…This work presents the first demonstration of cross-species complementation by hydrogenase maturation endopeptidases, highlighting the close evolutionary relationship between group 4 [NiFe]-hydrogenases and demonstrating the critical importance of the HycI-type protease in the biosynthesis of these enzymes. These data are in line with studies showing a endopeptidase for a group 1D hydrogenase was able to activate a different group 1D enzyme within the same organism (Salmonella enterica) [34], and one endopeptidase was able to activate both a group 3B hydrogenase and group 4D hydrogenase within the same organism (Thermococcus kodakarensis) [35].…”

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confidence: 90%

Activation of a [NiFe]-hydrogenase-4 isoenzyme by maturation proteases

et al. 2020

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Maturation of [NiFe]-hydrogenases often involves specific proteases responsible for cleavage of the catalytic subunits. Escherichia coli HycI is the protease dedicated to maturation of the Hydrogenase-3 isoenzyme, a component of formate hydrogenlyase-1. In this work, it is demonstrated that a Pectobacterium atrosepticum HycI homologue, HyfK, is required for hydrogenase-4 activity, a component of formate hydrogenlyase-2, in that bacterium. The P. atrosepticum ΔhyfK mutant phenotype could be rescued by either P. atrosepticum hyfK or E. coli hycI on a plasmid. Conversely, an E. coli ΔhycI mutant was complemented by either E. coli hycI or P. atrosepticum hyfK in trans. E. coli is a rare example of a bacterium containing both hydrogenase-3 and hydrogenase-4, however the operon encoding hydrogenase-4 has no maturation protease gene. This work suggests HycI should be sufficient for maturation of both E. coli formate hydrogenlyases, however no formate hydrogenlyase-2 activity was detected in any E. coli strains tested here.

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confidence: 90%

Activation of a [NiFe]-hydrogenase-4 isoenzyme by maturation proteases

et al. 2020

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“…The structure of immature HyhL reveals that the Cterminal extension of immature HyhL interacts with its β2 strand, adopting a β-strand conformation (the β11 strand). It has been reported that the His424 residue of HyhL at the C-terminal region is a recognition residue for the C-terminal cleavage by its maturation protease HybD (17). The His424 residue is also located in the β11 strand of immature HyhL.…”

Section: Discussionmentioning

confidence: 99%

Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA

Kwon

Watanabe

Nishitani

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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Ni-Fe clusters are inserted into the large subunit of [NiFe] hydrogenases by maturation proteins such as the Ni chaperone HypA via an unknown mechanism. We determined crystal structures of an immature large subunit HyhL complexed with HypA from Structure analysis revealed that the N-terminal region of HyhL extends outwards and interacts with the Ni-binding domain of HypA. Intriguingly, the C-terminal extension of immature HyhL, which is cleaved in the mature form, adopts a β-strand adjacent to its N-terminal β-strands. The position of the C-terminal extension corresponds to that of the N-terminal extension of a mature large subunit, preventing the access of endopeptidases to the cleavage site of HyhL. These findings suggest that Ni insertion into the active site induces spatial rearrangement of both the N- and C-terminal tails of HyhL, which function as a key checkpoint for the completion of the Ni-Fe cluster assembly.

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“…It was reported that the specific endopeptidase T . kodakarensis HybD cleaves immature HyhL at His424 in the C-terminal extension, which is also located in the β11 strand in the immature HyhL. In the immature state, the recognition site at the C-terminal extension is sterically protected from the endopeptidase by formation of the β11 strand.…”

Section: Recognition Of the Immature Large Subunit Hyhl By Hypamentioning

confidence: 99%

“…Our structures of the HypA-HyhL complex provide a clear understanding of how specific endopeptidases can cleave the C-terminal extension of the large subunit only after the [NiFe] incorporation. It was reported that the specific endopeptidase T. kodakarensis HybD cleaves immature HyhL at His424 in the C-terminal extension, 54 which is also located in the β11 strand in the immature HyhL. In the immature state, the recognition site at the C-terminal extension is sterically protected from the endopeptidase by formation of the β11 strand.…”

Section: ■ Introductionmentioning

confidence: 99%

Structural Insight into [NiFe] Hydrogenase Maturation by Transient Complexes between Hyp Proteins

2020

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Conspectus [NiFe] hydrogenases catalyze reversible hydrogen production/consumption. The core unit of [NiFe] hydrogenase consists of a large and a small subunit. The active site of the large subunit of [NiFe] hydrogenases contains a NiFe(CN)2CO cluster. The biosynthesis/maturation of these hydrogenases is a complex and dynamic process catalyzed primarily by six Hyp proteins (HypABCDEF), which play central roles in the maturation process. HypA and HypB are involved in the Ni insertion, whereas HypC, D, E, and F are required for the biosynthesis, assembly, and insertion of the Fe(CN)2CO group. HypE and HypF catalyze the synthesis of the CN group through the carbamoylation and cyanation of the C-terminus cysteine of HypE. HypC and HypD form a scaffold for the assembly of the Fe(CN)2CO moiety. Over the last decades, a large number of biochemical studies on maturation proteins have been performed, revealing basic functions of each Hyp protein and the overall framework of the maturation pathway. However, it is only in the last 10 years that structural insight has been gained, and our group has made significant contributions to the structural biology of hydrogenase maturation proteins. Since our first publication, where crystal structures of three Hyp proteins have been determined, we have performed a series of structural studies of all six Hyp proteins from a hyperthermophilic archaeon Thermococcus kodakarensis, providing molecular details of each Hyp protein. We have also determined the crystal structures of transient complexes between Hyp proteins that are formed during the maturation process to sequentially incorporate the components of the NiFe(CN)2CO cluster to immature large subunits of [NiFe] hydrogenases. Such complexes, whose crystal structures are determined, include HypA-HypB, HypA-HyhL (hydrogenase large subunit), HypC-HypD, and HypC-HypD-HypE. The structures of the HypC-HypD, and HypCDE complexes reveal a sophisticated process of transient formation of the HypCDE complex, providing insight into the molecular basis of Fe atom cyanation. The high-resolution structures of the carbamoylated and cyanated forms of HypE reveal a structural basis for the biological conversion of primary amide to nitrile. The structure of the HypA-HypB complex elucidates nucleotide-dependent transient complex formation between these two proteins and the molecular basis of acquisition and release of labile Ni. Furthermore, our recent structure analysis of a complex between HypA and immature HyhL reveals that spatial rearrangement of both the N- and C-terminal tails of HyhL will occur upon the [NiFe] cluster insertion, which function as a key checkpoint for the maturation completion. This Account will focus on recent advances in structural studies of the Hyp proteins and on mechanistic insights into the [NiFe] hydrogenase maturation.

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Genetic analyses of the functions of [NiFe]-hydrogenase maturation endopeptidases in the hyperthermophilic archaeon Thermococcus kodakarensis

Cited by 9 publications

References 38 publications

Activation of a [NiFe]-hydrogenase-4 isoenzyme by maturation proteases

Activation of a [NiFe]-hydrogenase-4 isoenzyme by maturation proteases

Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA

Structural Insight into [NiFe] Hydrogenase Maturation by Transient Complexes between Hyp Proteins

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