STIC2 selectively binds ribosome-nascent chain complexes in the cotranslational sorting of Arabidopsis thylakoid proteins.

Chloroplast-encoded multi-span thylakoid membrane proteins are crucial for photosynthetic complexes, yet the coordination of their biogenesis remains poorly understood. To identify factors that specifically support the cotranslational biogenesis of the reaction center protein D1 of photosystem (PS) II, we generated and affinity-purified stalled ribosome-nascent chain complexes (RNCs) bearing D1 nascent chains. Stalled RNCs translating the soluble ribosomal subunit uS2c were used for comparison. Quantitative tandem-mass spectrometry of the purified RNCs identified around 140 proteins specifically associated with D1 RNCs, mainly involved in protein and cofactor biogenesis, including chlorophyll biosynthesis, and other metabolic pathways. Functional analysis of STIC2, a newly identified D1 RNC interactor, revealed its cooperation with chloroplast protein SRP54 in the de novo biogenesis and repair of D1, and potentially other cotranslationally-targeted reaction center subunits of PSII and PSI. The primary binding interface between STIC2 and the thylakoid insertase Alb3 and its homolog Alb4 was mapped to STIC2's ß-sheet region, and the conserved Motif III in the C-terminal regions of Alb3/4.

On the evolution of the plant phytochrome chromophore biosynthesis.

Phytochromes are biliprotein photoreceptors present in plants, algae, certain bacteria, and fungi. Land plant phytochromes use phytochromobilin (PΦB) as the bilin chromophore. Phytochromes of streptophyte algae, the clade within which land plants evolved, employ phycocyanobilin (PCB), leading to a more blue-shifted absorption spectrum. Both chromophores are synthesized by ferredoxin-dependent bilin reductases (FDBRs) starting from biliverdin IXα (BV). In cyanobacteria and chlorophyta, BV is reduced to PCB by the FDBR phycocyanobilin:ferredoxin oxidoreductase (PcyA), whereas, in land plants, BV is reduced to PФB by phytochromobilin synthase (HY2). However, phylogenetic studies suggested the absence of any ortholog of PcyA in streptophyte algae and the presence of only PФB biosynthesis-related genes (HY2). The HY2 of the streptophyte alga Klebsormidium nitens (formerly Klebsormidium flaccidum) has already indirectly been indicated to participate in PCB biosynthesis. Here, we overexpressed and purified a His6-tagged variant of K. nitens HY2 (KflaHY2) in Escherichia coli. Employing anaerobic bilin reductase activity assays and coupled phytochrome assembly assays, we confirmed the product and identified intermediates of the reaction. Site-directed mutagenesis revealed 2 aspartate residues critical for catalysis. While it was not possible to convert KflaHY2 into a PΦB-producing enzyme by simply exchanging the catalytic pair, the biochemical investigation of 2 additional members of the HY2 lineage enabled us to define 2 distinct clades, the PCB-HY2 and the PΦB-HY2 clade. Overall, our study gives insight into the evolution of the HY2 lineage of FDBRs.

Insights into the Molecular Mechanism of Formaldehyde Inhibition of [FeFe]-Hydrogenases.

[FeFe]-hydrogenases are efficient H2 converting biocatalysts that are inhibited by formaldehyde (HCHO). The molecular mechanism of this inhibition has so far not been experimentally solved. Here, we obtained high-resolution crystal structures of the HCHO-treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum, showing HCHO reacts with the secondary amine base of the catalytic cofactor and the cysteine C299 of the proton transfer pathway which both are very important for catalytic turnover. Kinetic assays via protein film electrochemistry show the CpI variant C299D is significantly less inhibited by HCHO, corroborating the structural results. By combining our data from protein crystallography, site-directed mutagenesis and protein film electrochemistry, a reaction mechanism involving the cofactor's amine base, the thiol group of C299 and HCHO can be deduced. In addition to the specific case of [FeFe]-hydrogenases, our study provides additional insights into the reactions between HCHO and protein molecules.

ATP binding and ATP hydrolysis in full-length MsbA monitored via time-resolved Fourier transform infrared spectroscopy.

The essential Escherichia coli ATPase MsbA is a lipid flippase that serves as a prototype for multi drug resistant ABC transporters. Its physiological function is the transport of lipopolisaccharides to build up the outer membranes of Gram-negative bacteria. Although several structural and biochemical studies of MsbA have been conducted previously, a detailed picture of the dynamic processes that link ATP hydrolysis to allocrit transport remains elusive. We report here for the first time time-resolved Fourier transform infrared (FTIR) spectroscopic measurements of the ATP binding and ATP hydrolysis reaction of full-length MsbA and determined reaction rates at 288 K of k 1 = 0.49 ± 0.28 s-1 and k 2 = 0.014 ± 0.003 s-1, respectively. We further verified these rates with photocaged NPEcgAppNHp where only nucleotide binding was observable and the negative mutant MsbA-H537A that showed slow hydrolysis (k 2 < 2 × 10-4 s-1). Besides single turnover kinetics, FTIR measurements also deliver IR signatures of all educts, products and the protein. ADP remains protein-bound after ATP hydrolysis. In addition, the spectral changes observed for the two variants MsbA-S378A and MsbA-S482A correlated with the loss of hydrogen bonding to the γ-phosphate of ATP. This study paves the way for FTIR-spectroscopic investigations of allocrite transport in full-length MsbA.

The roles of long-range proton-coupled electron transfer in the directionality and efficiency of [FeFe]-hydrogenases.

As paradigms for proton-coupled electron transfer in enzymes and benchmarks for a fully renewable H2 technology, [FeFe]-hydrogenases behave as highly reversible electrocatalysts when immobilized on an electrode, operating in both catalytic directions with minimal overpotential requirement. Using the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1) we have conducted site-directed mutagenesis and protein film electrochemistry to determine how efficient catalysis depends on the long-range coupling of electron and proton transfer steps. Importantly, the electron and proton transfer pathways in [FeFe]-hydrogenases are well separated from each other in space. Variants with conservative substitutions (glutamate to aspartate) in either of two positions in the proton-transfer pathway retain significant activity and reveal the consequences of slowing down proton transfer for both catalytic directions over a wide range of pH and potential values. Proton reduction in the variants is impaired mainly by limiting the turnover rate, which drops sharply as the pH is raised, showing that proton capture from bulk solvent becomes critical. In contrast, hydrogen oxidation is affected in two ways: by limiting the turnover rate and by a large overpotential requirement that increases as the pH is raised, consistent with the accumulation of a reduced and protonated intermediate. A unique observation having fundamental significance is made under conditions where the variants still retain sufficient catalytic activity in both directions: An inflection appears as the catalytic current switches direction at the 2H+/H2 thermodynamic potential, clearly signaling a departure from electrocatalytic reversibility as electron and proton transfers begin to be decoupled.

Cyanide Binding to [FeFe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway.

Hydrogenases are H2 converting enzymes that harbor catalytic cofactors in which iron (Fe) ions are coordinated by biologically unusual carbon monoxide (CO) and cyanide (CN- ) ligands. Extrinsic CO and CN- , however, inhibit hydrogenases. The mechanism by which CN- binds to [FeFe]-hydrogenases is not known. Here, we obtained crystal structures of the CN- -treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum. The high resolution of 1.39 Šallowed us to distinguish intrinsic CN- and CO ligands and to show that extrinsic CN- binds to the open coordination site of the cofactor where CO is known to bind. In contrast to other inhibitors, CN- treated crystals show conformational changes of conserved residues within the proton transfer pathway which could allow a direct proton transfer between E279 and S319. This configuration has been proposed to be vital for efficient proton transfer, but has never been observed structurally.

Characterization of three novel DyP-type peroxidases from Streptomyces chartreusis NRRL 3882.

AIMS: Actinobacteria are known to produce extracellular enzymes including DyPs. We set out to identify and characterize novel peroxidases from Streptomyces chartreusis NRRL 3882, because S. chartreusis belongs to the small group of actinobacteria with three different DyPs. METHODS AND RESULTS: The genome of the actinomycete S. chartreusis NRRL 3882 was mined for novel DyP-type peroxidases. Three genes encoding for DyP-type peroxidases were cloned and overexpressed in Escherichia coli. Subsequent characterization of the recombinant proteins included examination of operating conditions such as pH, temperature and H2 O2 concentrations, as well as substrate spectrum. Despite their high sequence similarity, the enzymes named SCDYP1-SCDYP3 presented distinct preferences regarding their operating conditions. They showed great divergence in H2 O2 tolerance and stability, with SCDYP2 being most active at concentrations above 50 mmol l-1 . Moreover, SCDYP1 and SCDYP3 preferred acidic pH (typical for DyP-type peroxidases), whereas SCDYP2 was most active at pH 8. CONCLUSIONS: Regarding the function of DyPs in nature, these results suggest that availability of different DyP variants with complementary activity profiles in one organism might convey evolutionary benefits. SIGNIFICANCE AND IMPACT OF THE STUDY: DyP-type peroxidases are able to degrade xenobiotic compounds and thus can be applied in biocatalysis and bioremediation. However, the native function of DyPs and the benefits for their producers largely remain to be elucidated.

The Energy Transfer Yield between Carotenoids and Chlorophylls in Peridinin Chlorophyll a Protein Is Robust against Mutations.

The energy transfer (ET) from carotenoids (Cars) to chlorophylls (Chls) in photosynthetic complexes occurs with almost unitary efficiency thanks to the synergistic action of multiple finely tuned channels whose photophysics and dynamics are not fully elucidated yet. We investigated the energy flow from the Car peridinin (Per) to Chl a in the peridinin chlorophyll a protein (PCP) from marine algae Amphidinium carterae by using two-dimensional electronic spectroscopy (2DES) with a 10 fs temporal resolution. Recently debated hypotheses regarding the S2-to-S1 relaxation of the Car via a conical intersection and the involvement of possible intermediate states in the ET were examined. The comparison with an N89L mutant carrying the Per donor in a lower-polarity environment helped us unveil relevant details on the mechanisms through which excitation was transferred: the ET yield was conserved even when a mutation perturbed the optimization of the system thanks to the coexistence of multiple channels exploited during the process.

Crystal structure of the first eukaryotic bilin reductase GtPEBB reveals a flipped binding mode of dihydrobiliverdin.

Phycobilins are light-harvesting pigments of cyanobacteria, red algae, and cryptophytes. The biosynthesis of phycoerythrobilin (PEB) is catalyzed by the subsequent action of two ferredoxin-dependent bilin reductases (FDBRs). Although 15,16-dihydrobiliverdin (DHBV):ferredoxin oxidoreductase (PebA) catalyzes the two-electron reduction of biliverdin IXα to 15,16-DHBV, PEB:ferredoxin oxidoreductase (PebB) reduces this intermediate further to PEB. Interestingly, marine viruses encode the FDBR PebS combining both activities within one enzyme. Although PebA and PebS share a canonical fold with similar substrate-binding pockets, the structural determinants for the stereo- and regiospecific modification of their tetrapyrrole substrates are incompletely understood, also because of the lack of a PebB structure. Here, we solved the X-ray crystal structures of both substrate-free and -bound PEBB from the cryptophyte Guillardia theta at 1.90 and 1.65 Å, respectively. The structures of PEBB exhibit the typical α/ß/α-sandwich fold. Interestingly, the open-chain tetrapyrrole substrate DHBV is bound in an unexpected flipped orientation within the canonical FDBR active site. Biochemical analyses of the WT enzyme and active site variants identified two central aspartate residues Asp-99 and Asp-219 as essential for catalytic activity. In addition, the conserved Arg-215 plays a critical role in substrate specificity, binding orientation, and active site integrity. Because these critical residues are conserved within certain FDBRs displaying A-ring reduction activity, we propose that they present a conserved mechanism for this reaction. The flipped substrate-binding mode indicates that two-electron reducing FDBRs utilize the same primary site within the binding pocket and that substrate orientation is the determinant for A- or D-ring regiospecificity.

Distinctive structural properties of THB11, a pentacoordinate Chlamydomonas reinhardtii truncated hemoglobin with N- and C-terminal extensions.

Hemoglobins (Hbs) utilize heme b as a cofactor and are found in all kingdoms of life. The current knowledge reveals an enormous variability of Hb primary sequences, resulting in topological, biochemical and physiological individuality. As Hbs appear to modulate their reactivities through specific combinations of structural features, predicting the characteristics of a given Hb is still hardly possible. The unicellular green alga Chlamydomonas reinhardtii contains 12 genes encoding diverse Hbs of the truncated lineage, several of which possess extended N- or C-termini of unknown function. Studies on some of the Chlamydomonas Hbs revealed yet unpredictable structural and biochemical variations, which, along with a different expression of their genes, suggest diverse physiological roles. Chlamydomonas thus represents a promising system to analyze the diversification of Hb structure, biochemistry and physiology. Here, we report the crystal structure, resolved to 1.75 Å, of the heme-binding domain of cyanomet THB11 (Cre16.g662750), one of the pentacoordinate algal Hbs, which offer a free Fe-coordination site in the reduced state. The overall fold of THB11 is conserved, but individual features such as a kink in helix E, a tilted heme plane and a clustering of methionine residues at a putative tunnel exit appear to be unique. Both N- and C-termini promote the formation of oligomer mixtures, and the absence of the C terminus results in reduced nitrite reduction rates. This work widens the structural and biochemical knowledge on the 2/2Hb family and suggests that the N- and C-terminal extensions of the Chlamydomonas 2/2Hbs modulate their reactivity by intermolecular interactions.

Loss of Specific Active-Site Iron Atoms in Oxygen-Exposed [FeFe]-Hydrogenase Determined by Detailed X-ray Structure Analyses.

The [FeFe]-hydrogenases catalyze the uptake and evolution of hydrogen with unmatched speed at low overpotential. However, oxygen induces the degradation of the unique [6Fe-6S] cofactor within the active site, termed the H-cluster. We used X-ray structural analyses to determine possible modes of irreversible oxygen-driven inactivation. To this end, we exposed crystals of the [FeFe]-hydrogenase CpI from Clostridium pasteurianum to oxygen and quantitatively investigated the effects on the H-cluster structure over several time points using multiple data sets, while correlating it to decreases in enzyme activity. Our results reveal the loss of specific Fe atoms from both the diiron (2FeH) and the [4Fe-4S] subcluster (4FeH) of the H-cluster. Within the 2FeH, the Fe atom more distal to the 4FeH is strikingly more affected than the more proximal Fe atom. The 4FeH interconverts to a [2Fe-2S] cluster in parts of the population of active CpIADT, but not in crystals of the inactive apoCpI initially lacking the 2FeH. We thus propose two parallel processes: dissociation of the distal Fe atom and 4FeH interconversion. Both pathways appear to play major roles in the oxidative damage of [FeFe]-hydrogenases under electron-donor deprived conditions probed by our experimental setup.

His-Ligation to the [4Fe-4S] Subcluster Tunes the Catalytic Bias of [FeFe] Hydrogenase.

[FeFe] hydrogenases interconvert H2 into protons and electrons reversibly and efficiently. The active site H-cluster is composed of two sites: a unique [2Fe] subcluster ([2Fe]H) covalently linked via cysteine to a canonical [4Fe-4S] cluster ([4Fe-4S]H). Both sites are redox active and electron transfer is proton-coupled, such that the potential of the H-cluster lies very close to the H2 thermodynamic potential, which confers the enzyme with the ability to operate quickly in both directions without energy losses. Here, one of the cysteines coordinating [4Fe-4S]H (Cys362) in the [FeFe] hydrogenase from the green algae Chlamydomonas reinhardtii ( CrHydA1) was exchanged with histidine and the resulting C362H variant was shown to contain a [4Fe-4S] cluster with a more positive redox potential than the wild-type. The change in the [4Fe-4S] cluster potential resulted in a shift of the catalytic bias, diminishing the H2 production activity but giving significantly higher H2 oxidation activity, albeit with a 200 mV overpotential requirement. These results highlight the importance of the [4Fe-4S] cluster as an electron injection site, modulating the redox potential and the catalytic properties of the H-cluster.

Changing the site energy of per-614 in the Peridinin-chlorophyll a-protein does not alter its capability of chlorophyll triplet quenching.

The peridinin-chlorophyll-a protein (PCP) is a water-soluble light harvesting protein of the dinoflagellate Amphidinium carterae, employing peridinin (Per) as the main carotenoid to fulfil light harvesting and photo-protective functions. Per molecules bound to the protein experience specific molecular surroundings which lead to different electronic and spectral properties. In the refolded N89 L variant PCP (N89 L-RFPCP) a significant part of the intensity on the long wavelength side of the absorption spectrum is shifted to shorter wavelengths due to a significant change in the Per-614 site energy. Since Per-614 has been shown to be the main chlorophyll (Chl) triplet quencher in the protein, and the relative geometry of pigments is not affected by the mutation as verified by X-ray crystallography, this variant is ideally suited to study the dependence of the triplet-triplet energy transfer (TTET) mechanism on the pigment site energy. By using a combination of Optically Detected Magnetic Resonance (ODMR), pulse Electron Paramagnetic Resonance (EPR) and Electron Nuclear DOuble Resonance (ENDOR) we found that PCP maintains the efficient Per-614-to-Chl-a TTET despite the change of Per-614 local energy. This shows the robustness of the photoprotective site, which is very important for the protection of the system.

Distinct Features of Cyanophage-encoded T-type Phycobiliprotein Lyase ΦCpeT: THE ROLE OF AUXILIARY METABOLIC GENES.

Auxiliary metabolic genes (AMG) are commonly found in the genomes of phages that infect cyanobacteria and increase the fitness of the cyanophage. AMGs are often homologs of host genes, and also typically related to photosynthesis. For example, the ΦcpeT gene in the cyanophage P-HM1 encodes a putative phycobiliprotein lyase related to cyanobacterial T-type lyases, which facilitate attachment of linear tetrapyrrole chromophores to Cys-155 of phycobiliprotein ß-subunits, suggesting that ΦCpeT may also help assemble light-harvesting phycobiliproteins during infection. To investigate this possibility, we structurally and biochemically characterized recombinant ΦCpeT. The solved crystal structure of ΦCpeT at 1.8-Å resolution revealed that the protein adopts a similar fold as the cyanobacterial T-type lyase CpcT from Nostoc sp. PCC7120 but overall is more compact and smaller. ΦCpeT specifically binds phycoerythrobilin (PEB) in vitro leading to a tight complex that can also be formed in Escherichia coli when it is co-expressed with genes encoding PEB biosynthesis (i.e. ho1 and pebS). The formed ΦCpeT·PEB complex was very stable as the chromophore was not lost during chromatography and displayed a strong red fluorescence with a fluorescence quantum yield of ΦF = 0.3. This complex was not directly able to transfer PEB to the host phycobiliprotein ß-subunit. However, it could assist the host lyase CpeS in its function by providing a pool of readily available PEB, a feature that might be important for fast phycobiliprotein assembly during phage infection.

Triplet-triplet energy transfer from chlorophylls to carotenoids in two antenna complexes from dinoflagellate Amphidinium carterae.

Room temperature transient absorption spectroscopy with nanosecond resolution was used to study quenching of the chlorophyll triplet states by carotenoids in two light-harvesting complexes of the dinoflagellate Amphidinium carterae: the water soluble peridinin-chlorophyll protein complex and intrinsic, membrane chlorophyll a-chlorophyll c2-peridinin protein complex. The combined study of the two complexes facilitated interpretation of a rather complicated relaxation observed in the intrinsic complex. While a single carotenoid triplet state was resolved in the peridinin-chlorophyll protein complex, evidence of at least two different carotenoid triplets was obtained for the intrinsic light-harvesting complex. Most probably, each of these carotenoids protects different chlorophylls. In both complexes the quenching of the chlorophyll triplet states by carotenoids occurs with a very high efficiency (~100%), and with transfer times estimated to be in the order of 0.1ns or even faster. The triplet-triplet energy transfer is thus much faster than formation of the chlorophyll triplet states by intersystem crossing. Since the triplet states of chlorophylls are formed during the whole lifetime of their singlet states, the apparent lifetimes of both states are the same, and observed to be equal to the carotenoid triplet state rise time (~5ns).

Distance measurements in peridinin-chlorophyll a-protein by light-induced PELDOR spectroscopy. Analysis of triplet state localization.

Triplet-triplet energy transfer from chlorophylls to carotenoids is the mechanism underlying the photoprotective role played by carotenoids in many light harvesting complexes, during photosynthesis. The peridinin-chlorophyll-a protein (PCP) is a water-soluble light harvesting protein of the dinoflagellate Amphidinium carterae, employing peridinin as the main carotenoid to fulfil this function. The dipolar coupling of the triplet state of peridinin, populated under light excitation in isolated PCP, to the MTSSL nitroxide, introduced in the protein by site-directed mutagenesis followed by spin labeling, has been measured by Pulse ELectron-electron DOuble Resonance (PELDOR) spectroscopy. The triplet-nitroxide distance derived by this kind of experiments, performed for the first time in a protein system, allowed the assignment of the triplet state to a specific peridinin molecule belonging to the pigment cluster. The analysis strongly suggests that this peridinin is the one in close contact with the water ligand to the chlorophyll a, thus supporting previous evidences based on ENDOR and time resolved-EPR.

Dirigent Protein Mode of Action Revealed by the Crystal Structure of AtDIR6.

Dirigent proteins impart stereoselectivity to phenoxy radical coupling reactions in plants and, thus, play an essential role in the biosynthesis of biologically active natural products. This includes the regioselective and enantioselective coupling and subsequent cyclization of two coniferyl alcohol radicals to pinoresinol as the committed step of lignan biosynthesis. The reaction is controlled by dirigent proteins, which, depending on the species and protein, direct the reaction to either (+)- or (-)-pinoresinol. We present the crystal structure of the (-)-pinoresinol forming DIRIGENT PROTEIN6 (AtDIR6) from Arabidopsis (Arabidopsis thaliana) with data to 1.4 Å resolution. The structure shows AtDIR6 as an eight-stranded antiparallel ß-barrel that forms a trimer with spatially well-separated cavities for substrate binding. The binding cavities are two lobed, exhibiting two opposing pockets, each lined with a set of hydrophilic and potentially catalytic residues, including essential aspartic acids. These residues are conserved between (+) and (-)-pinoresinol-forming DIRs and required for activity. The structure supports a model in which two substrate radicals bind to each of the DIR monomers. With the aromatic rings fixed in the two pockets, the propionyl side chains face each other for radical-radical coupling, and stereoselectivity is determined by the exact positioning of the side chains. Extensive mutational analysis supports a previously unrecognized function for DIRs in catalyzing the cyclization of the bis-quinone methide reaction intermediate to yield (+)- or (-)-pinoresinol.

Chloroplast SRP54 Was Recruited for Posttranslational Protein Transport via Complex Formation with Chloroplast SRP43 during Land Plant Evolution.

In bacteria, membrane proteins are targeted cotranslationally via a signal recognition particle (SRP). During the evolution of higher plant chloroplasts from cyanobacteria, the SRP pathway underwent striking adaptations that enable the posttranslational transport of the abundant light-harvesting chlorophyll-a/b-binding proteins (LHCPs). The conserved 54-kDa SRP subunit in higher plant chloroplasts (cpSRP54) is not bound to an SRP RNA, an essential SRP component in bacteria, but forms a stable heterodimer with the chloroplast-specific cpSRP43. This heterodimeric cpSRP recognizes LHCP and delivers it to the thylakoid membrane whereby cpSRP43 plays a central role. This study shows that the cpSRP system in the green alga Chlamydomonas reinhardtii differs significantly from that of higher plants as cpSRP43 is not complexed to cpSRP54 in Chlamydomonas and cpSRP54 is not involved in LHCP recognition. This divergence is attributed to altered residues within the cpSRP54 tail and the second chromodomain of cpSRP43 that are crucial for the formation of the binding interface in Arabidopsis. These changes are highly conserved among chlorophytes, whereas all land plants contain cpSRP proteins with typical interaction motifs. These data demonstrate that the coevolution of LHCPs and cpSRP43 occurred independently of complex formation with cpSRP54 and that the interaction between cpSRP54 and cpSRP43 evolved later during the transition from chlorophytes to land plants. Furthermore, our data show that in higher plants a heterodimeric form of cpSRP is required for the formation of a low molecular weight transit complex with LHCP.

[FeFe]-Hydrogenase with Chalcogenide Substitutions at the H-Cluster Maintains Full H2 Evolution Activity.

The [FeFe]-hydrogenase HYDA1 from Chlamydomonas reinhardtii is particularly amenable to biochemical and biophysical characterization because the H-cluster in the active site is the only inorganic cofactor present. Herein, we present the complete chemical incorporation of the H-cluster into the HYDA1-apoprotein scaffold and, furthermore, the successful replacement of sulfur in the native [4FeH ] cluster with selenium. The crystal structure of the reconstituted pre-mature HYDA1[4Fe4Se]H protein was determined, and a catalytically intact artificial H-cluster variant was generated upon in vitro maturation. Full hydrogen evolution activity as well as native-like composition and behavior of the redesigned enzyme were verified through kinetic assays, FTIR spectroscopy, and X-ray structure analysis. These findings reveal that even a bioinorganic active site with exceptional complexity can exhibit a surprising level of compositional plasticity.