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

ABSTRACT: 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 (HypBAT) with Ni ions. Transient association between HypA and HypBAT is controlled by the ATP hydrolysis cycle of HypBAT, which is accelerated by HypA. Only the ATP-bound form of HypBAT 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 HypABAT complex has a nanomolar affinity (Kd = 7 nM), which is in contrast to the micromolar affinity (Kd = 4 µM) observed with the isolated HypA. The ATP hydrolysis and Ni binding cause conformational changes of HypBAT, affecting its association with HypA. These findings indicate that HypA and HypBAT constitute an ATP-dependent Ni acquisition cycle for [NiFe]-hydrogenase maturation, wherein HypBAT functions as a metallochaperone enhancer and considerably increases the Ni-binding affinity of HypA.

SUBMITTER: Watanabe S

PROVIDER: S-EPMC4485131 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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

Watanabe Satoshi S Kawashima Takumi T Nishitani Yuichi Y Kanai Tamotsu T Wada Takehiko T Inaba Kenji K Atomi Haruyuki H Imanaka Tadayuki T Miki Kunio K

Proceedings of the National Academy of Sciences of the United States of America 20150608 25

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 (HypBAT) with Ni ions. Transient association between HypA and HypBAT is controlled by the ATP hydrolysis cycle of HypBAT, which is accelerated by HypA. Only the ATP-bound form of HypBAT can interact with HypA and induces drastic conformational changes of HypA. Conseq ...[more]

PMID: 26056269

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Project description:BACKGROUND:Photosynthetic microorganisms that directly channel solar energy to the production of molecular hydrogen are a potential future biofuel system. Building such a system requires installation of a hydrogenase in the photosynthetic organism that is both tolerant to oxygen and capable of hydrogen production. Toward this end, we have identified the [NiFe] hydrogenase from the marine bacterium Alteromonas macleodii "Deep ecotype" that is able to be heterologously expressed in cyanobacteria and has tolerance to partial oxygen. The A. macleodii enzyme shares sequence similarity with the uptake hydrogenases that favor hydrogen uptake activity over hydrogen evolution. To improve hydrogen evolution from the A. macleodii hydrogenase, we examined the three Fe-S clusters found in the small subunit of many [NiFe] uptake hydrogenases that presumably act as a molecular wire to guide electrons to or from the active site of the enzyme. Studies by others altering the medial cluster of a Desulfovibrio fructosovorans hydrogenase from 3Fe-4S to 4Fe-4S resulted in two-fold improved hydrogen evolution activity. RESULTS:We adopted a strategy of screening for improved hydrogenase constructs using an Escherichia coli expression system before testing in slower growing cyanobacteria. From the A. macleodii enzyme, we created a mutation in the gene encoding the hydrogenase small subunit that in other systems is known to convert the 3Fe-4S medial cluster to 4Fe-4S. The medial cluster substitution did not improve the hydrogen evolution activity of our hydrogenase. However, modifying both the medial cluster and the ligation of the distal Fe-S cluster improved in vitro hydrogen evolution activity relative to the wild type hydrogenase by three- to four-fold. Other properties of the enzyme including thermostability and tolerance to partial oxygen did not appear to be affected by the substitutions. CONCLUSIONS:Our results show that substitution of amino acids altering the ligation of Fe-S clusters in the A. macleodii [NiFe] uptake hydrogenase resulted in increased hydrogen evolution activity. This activity can be recapitulated in multiple host systems and with purified protein. These results validate the approach of using an E. coli-cyanobacteria shuttle system for enzyme expression and improvement.

Project description:The complex cation in the title compound, (carbonyl-1?C)(1?5-penta-methyl-cyclo-penta-dien-yl)(?-2,3,9,10-tetra-methyl-1,4,8,11-tetra-thia-undeca-2,9-diene-1,11-diido-1?2S,S''':2?4S,S',S'',S''')ironnickel(Fe-Ni) hexa-fluoro-phosphate, [FeNi(C10H15)(C11H18S4)(CO)]PF6 or [Ni(L')FeCp*(CO)]PF6, is composed of the nickel complex fragment [Ni(L')] coordinated as a metalloligand (using S1 and S4) to the [FeCp*(CO)]+ fragment, where (L')2- is [S-C(Me)=C(Me)-S-(CH2)3-S-C(Me)=C(Me)-S]2- and where Cp*- is cyclo-C5(Me)5- (penta-methyl-cyclo-penta-dien-yl). The ratio of hexa-fluoro-phosphate anion per complex cation is 1:1. The structure at 150?K has ortho-rhom-bic (Pbcn) symmetry. The atoms of the complex cation are located on general positions (multiplicity = 8), whereas there are two independent hexa-fluoro-phosphate anions, each located on a twofold axis (Wyckoff position 4c; multiplicity = 4). The structure of the new dimetallic cation [Ni(L')FeCp*(CO)]+ can be described as containing a three-legged piano-stool environment for iron [Cp*Fe(CO)'S2'] and an approximately square-planar 'S4' environment for Ni. The NiS2Fe diamond-shaped substructure is notably folded at the S-S hinge: the angle between the NiS2 plane and the FeS2 plane normals is 64.85?(6)°. Largely because of this fold, the nickel-iron distance is relatively short, at 2.9195?(8)?Å. The structural data for the complex cation, which contains a new unsaturated 'S4' ligand (two C=C double bonds), provide an inter-esting comparison with the known NiFe hydrogenase models containing a saturated 'S4'-ligand analogue having the same number of carbon atoms in the ligand backbone, namely with the structures of [Ni(L)FeCp(CO)]+ (as the PF6- salt, CH2Cl2 solvate) and [Ni(L)FeCp*(CO)]+ (as the PF6- salt), where (L)2- is [S-CH2-CH2-S-(CH2)3-S-CH2-CH2-S]2- and Cp- is cyclo-penta-dienyl. The saturated analogues [Ni(L)FeCp(CO)]+ and [Ni(L)FeCp*(CO)]+ have similar Ni-Fe distances: 3.1727?(6), 3.1529?(7)?Å (two independent mol-ecules in the unit cell) and 3.111?(5)?Å, respectively, for the two complexes, whereas [Ni(L')FeCp*(CO)]+ described here stands out with a much shorter Ni-Fe distance [2.9196?(8)?Å]. Also, [Ni(L)FeCp(CO)]+ and [Ni(L)FeCp*(CO)]+ show inter-planar fold angles that are similar between the two: 39.56?(5), 41.99?(5) (independent mol-ecules in the unit cell) and 47.22?(9) °, respectively, whereas [Ni(L')FeCp*(CO)]+ possesses a much more pronounced fold [64.85?(6)°]. Given that larger fold angles and shorter Ni-Fe distances are considered to be structurally closer to the enzyme, unsaturation in an 'S4'-ligand of the type (S-C2-S-C3-S-C2-S)2- seems to increase structural resemblance to the enzyme for structural models of the type [Ni('S4')FeCp R (CO)]+ (Cp R = Cp or Cp*).

Dataset Information

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

Publications

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

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