Crystal Structures of [NiFe] Hydrogenase Maturation Proteins HypC, HypD, and HypE: Insights into Cyanation Reaction by Thiol Redox Signaling

Watanabe, Satoshi; Matsumi, Rie; Arai, Takayuki; Atomi, Haruyuki; Imanaka, Tadayuki; Miki, Kunio

doi:10.1016/j.molcel.2007.05.039

Cited by 97 publications

(171 citation statements)

References 62 publications

Supporting

Mentioning

157

Contrasting

Unclassified

Order By: Relevance

“…For example, the synthesis of the two CN À ligands from carbamoyl phosphate has been elucidated both functionally and structurally [16,17]. It is not possible to express active [NiFe]-enzymes heterologously even in Escherichia coli that has three hydrogenases of its own [18].…”

Section: Introductionmentioning

confidence: 99%

The role of the maturase HydG in [FeFe]‐hydrogenase active site synthesis and assembly

et al. 2009

View full text Add to dashboard Cite

a b s t r a c t[FeFe]-hydrogenases catalyze the protons/hydrogen interconversion through a unique di-iron active site consisting of three CO and two CN ligands, and a non-protein SCH 2 XCH 2 S (X = N or O) dithiolate bridge. Site assembly requires two ''Radical-S-adenosylmethionine (SAM or AdoMet)" iron-sulfur enzymes, HydE and HydG, and one GTPase, HydF. The sequence homology between HydG and ThiH, a Radical-SAM enzyme which cleaves tyrosine into p-cresol and dehydroglycine, and the finding of a similar cleavage reaction catalyzed by HydG suggests a mechanism for hydrogenase maturation. Here we propose that HydG is specifically involved in the synthesis of the dithiolate ligand, with two tyrosine-derived dehydroglycines as precursors along with an [FeS] cluster of HydG functioning both as electron shuttle and source of the sulfur atoms.

show abstract

Section: Introductionmentioning

confidence: 99%

The role of the maturase HydG in [FeFe]‐hydrogenase active site synthesis and assembly

et al. 2009

View full text Add to dashboard Cite

show abstract

“…NiFe(CN) 2 CO biosynthesis requires specific maturation machinery, in which six Hyp proteins (HypA-HypF) play key roles (6,7). Four Hyp proteins (HypC-HypF) are involved in the biosynthesis and incorporation of the Fe(CN) 2 CO group (8)(9)(10)(11)(12)(13)(14)(15). After Fe insertion, HypA and HypB insert the Ni ion into the hydrogenase large subunit (16).…”

mentioning

confidence: 99%

Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer

Watanabe

Kawashima

Nishitani

et al. 2015

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

Self Cite

View full text Add to dashboard Cite

The Ni atom at the catalytic center of [NiFe] hydrogenases is incorporated by a Ni-metallochaperone, HypA, and a GTPase/ATPase, HypB. We report the crystal structures of the transient complex formed between HypA and ATPase-type HypB (HypB AT ) with Ni ions. Transient association between HypA and HypB AT is controlled by the ATP hydrolysis cycle of HypB AT, which is accelerated by HypA. Only the ATP-bound form of HypB AT can interact with HypA and induces drastic conformational changes of HypA. Consequently, upon complex formation, a conserved His residue of HypA comes close to the N-terminal conserved motif of HypA and forms a Ni-binding site, to which a Ni ion is bound with a nearly square-planar geometry. The Ni binding site in the HypAB AT complex has a nanomolar affinity (K d = 7 nM), which is in contrast to the micromolar affinity (K d = 4 μM) observed with the isolated HypA. The ATP hydrolysis and Ni binding cause conformational changes of HypB AT , affecting its association with HypA. These findings indicate that HypA and HypB AT constitute an ATP-dependent Ni acquisition cycle for [NiFe]-hydrogenase maturation, wherein HypB AT functions as a metallochaperone enhancer and considerably increases the Ni-binding affinity of HypA.X-ray crystallography | metalloprotein | transient complex | metallochaperone A pproximately one-half of all cellular proteins require specific metal ions for proper function, which are delivered by specific metallochaperones (1, 2). However, the mechanisms of correct acquisition and delivery to target proteins of many metallochaperones remain poorly understood.[NiFe] hydrogenases harbor a complex metal cofactor, NiFe(CN) 2 CO, in their active sites (3). This cofactor catalyzes reversible H 2 production. The Ni atom in the NiFe(CN) 2 CO cofactor is bound to four thiolate groups, two of which also bridge the Fe(CN) 2 CO group (4, 5). NiFe(CN) 2 CO biosynthesis requires specific maturation machinery, in which six Hyp proteins (HypA-HypF) play key roles (6, 7). Four Hyp proteins (HypC-HypF) are involved in the biosynthesis and incorporation of the Fe(CN) 2 CO group (8-15). After Fe insertion, HypA and HypB insert the Ni ion into the hydrogenase large subunit (16).HypA is a Ni-metallochaperone that binds to a Ni ion with micromolar affinity (17-19), and its structure consists of a Ni-binding domain (NiBD) and a Zn-binding domain (ZnBD) (20, 21). The NiBD contains a highly conserved MHE motif that is essential for Ni binding at the N terminus (20,22). HypB consists of a common GTPase domain and a less conserved metal-binding region (23)(24)(25). Recently, ATPase-type HypB (HypB AT , previously abbreviated as mmHypB) proteins were identified from Thermococcales (26). GTPase and ATPase types of HypB belong to the SIMIBI class NTPase family and share a similar architecture, despite their low sequence similarity (27). HypA and HypB form a transient complex in the Ni insertion process (17,22,28,29). In the Escherichia coli system, Ni transfer occurs from HypB to HypA (30). However, the functi...

show abstract

“…Molecular Modeling-The structural model of HypC protein was constructed by homology modeling with SwissModel (35, 36) using as a template the chain B of HypC crystal structure from Thermococcus kodakaraensis, PDB code 2Z1C (37). Although the sequence identity between both HypC proteins is low (34.25%), the resulting model structure for the R. leguminosarum protein shows a high QMEAN (38) quality estimate Z-score ϭ 0.697 and is virtually identical to the crystal structure of the template (r.m.s.d.…”

Section: Methodsmentioning

confidence: 99%

“…The resulting model structures generated with the R. leguminosarum sequences are shown in Fig. 2 superimposed to reference structures: chain B of HypC protein from Thermococcus kodakarensis (37) and the large subunit of the [NiFe] hydrogenase from A. vinosum (56).…”

Section: Hupk Is Essential For Hydrogenase Activity In R Leguminosarmentioning

confidence: 99%

Maturation of Rhizobium leguminosarum Hydrogenase in the Presence of Oxygen Requires the Interaction of the Chaperone HypC and the Scaffolding Protein HupK

Albareda

Pacios

Manyani

et al. 2014

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: [NiFe] hydrogenase biosynthesis requires the interaction among multiple accessory proteins for metal cofactor assembly. Results: Combined bioinformatic protein modeling and mutant analysis on HupK and HypC proteins identify key residues required for hydrogenase maturation. Conclusion: HypC-HupK interaction is a relevant step for hydrogenase biosynthesis in the presence of oxygen. Significance: The results expand our knowledge on the mechanism of hydrogenase biosynthesis in aerobic bacteria.

show abstract

Crystal Structures of [NiFe] Hydrogenase Maturation Proteins HypC, HypD, and HypE: Insights into Cyanation Reaction by Thiol Redox Signaling

Cited by 97 publications

References 62 publications

The role of the maturase HydG in [FeFe]‐hydrogenase active site synthesis and assembly

The role of the maturase HydG in [FeFe]‐hydrogenase active site synthesis and assembly

Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer

Maturation of Rhizobium leguminosarum Hydrogenase in the Presence of Oxygen Requires the Interaction of the Chaperone HypC and the Scaffolding Protein HupK

Contact Info

Product

Resources

About