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Title: Crystallization and preliminary X-ray crystallographic studies of the [NiFe] hydrogenase maturation proteins HypC and HypD

Abstract

The [NiFe] hydrogenase maturation proteins HypC and HypD were purified and crystallized. Crystals of HypC and HypD suitable for data collection diffracted to 1.80 and 2.07 Å resolution, respectively. HypC and HypD proteins are required for the insertion of the Fe atom with diatomic ligands into the large subunit of [NiFe] hydrogenases, an important step in the maturation process of this type of hydrogenase. The crystallization and preliminary crystallographic analysis of HypC and HypD from Thermococcus kodakaraensis KOD1 are reported. Crystals of HypC grew in two different forms. Monoclinic crystals of HypC in space group C2 with unit-cell parameters a = 78.2, b = 59.1, c = 54.0 Å, β = 109.0° were obtained using PEG 4000 and ammonium sulfate or sodium bromide as precipitants. They diffracted X-rays to 1.8 Å resolution and were suitable for structure determination. Crystals of HypD were also obtained in two different forms. The monoclinic crystals obtained using PEG 4000 and magnesium chloride diffracted X-rays to beyond 2.1 Å resolution, despite growing as clusters. They belong to space group P2{sub 1}, with unit-cell parameters a = 42.3, b = 118.4, c = 81.2 Å, β = 100.9°, and are suitable for data collection.

Authors:
 [1]; ; ;  [2];  [1];  [3]
  1. Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan)
  2. Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510 (Japan)
  3. (Japan)
Publication Date:
OSTI Identifier:
22360352
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section F; Journal Volume: 63; Journal Issue: Pt 6; Other Information: PMCID: PMC2335088; PMID: 17554182; PUBLISHER-ID: pu5187; OAI: oai:pubmedcentral.nih.gov:2335088; Copyright (c) International Union of Crystallography 2007; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United Kingdom
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; AMMONIUM SULFATES; ATOMS; CRYSTALLIZATION; CRYSTALS; LIGANDS; RESOLUTION; SPACE GROUPS

Citation Formats

Watanabe, Satoshi, Matsumi, Rie, Atomi, Haruyuki, Imanaka, Tadayuki, Miki, Kunio, E-mail: miki@kuchem.kyoto-u.ac.jp, and RIKEN SPring-8 Center at Harima Institute, Koto 1-1-1, Sayo, Hyogo 679-5148. Crystallization and preliminary X-ray crystallographic studies of the [NiFe] hydrogenase maturation proteins HypC and HypD. United Kingdom: N. p., 2007. Web. doi:10.1107/S1744309107023391.
Watanabe, Satoshi, Matsumi, Rie, Atomi, Haruyuki, Imanaka, Tadayuki, Miki, Kunio, E-mail: miki@kuchem.kyoto-u.ac.jp, & RIKEN SPring-8 Center at Harima Institute, Koto 1-1-1, Sayo, Hyogo 679-5148. Crystallization and preliminary X-ray crystallographic studies of the [NiFe] hydrogenase maturation proteins HypC and HypD. United Kingdom. doi:10.1107/S1744309107023391.
Watanabe, Satoshi, Matsumi, Rie, Atomi, Haruyuki, Imanaka, Tadayuki, Miki, Kunio, E-mail: miki@kuchem.kyoto-u.ac.jp, and RIKEN SPring-8 Center at Harima Institute, Koto 1-1-1, Sayo, Hyogo 679-5148. Fri . "Crystallization and preliminary X-ray crystallographic studies of the [NiFe] hydrogenase maturation proteins HypC and HypD". United Kingdom. doi:10.1107/S1744309107023391.
@article{osti_22360352,
title = {Crystallization and preliminary X-ray crystallographic studies of the [NiFe] hydrogenase maturation proteins HypC and HypD},
author = {Watanabe, Satoshi and Matsumi, Rie and Atomi, Haruyuki and Imanaka, Tadayuki and Miki, Kunio, E-mail: miki@kuchem.kyoto-u.ac.jp and RIKEN SPring-8 Center at Harima Institute, Koto 1-1-1, Sayo, Hyogo 679-5148},
abstractNote = {The [NiFe] hydrogenase maturation proteins HypC and HypD were purified and crystallized. Crystals of HypC and HypD suitable for data collection diffracted to 1.80 and 2.07 Å resolution, respectively. HypC and HypD proteins are required for the insertion of the Fe atom with diatomic ligands into the large subunit of [NiFe] hydrogenases, an important step in the maturation process of this type of hydrogenase. The crystallization and preliminary crystallographic analysis of HypC and HypD from Thermococcus kodakaraensis KOD1 are reported. Crystals of HypC grew in two different forms. Monoclinic crystals of HypC in space group C2 with unit-cell parameters a = 78.2, b = 59.1, c = 54.0 Å, β = 109.0° were obtained using PEG 4000 and ammonium sulfate or sodium bromide as precipitants. They diffracted X-rays to 1.8 Å resolution and were suitable for structure determination. Crystals of HypD were also obtained in two different forms. The monoclinic crystals obtained using PEG 4000 and magnesium chloride diffracted X-rays to beyond 2.1 Å resolution, despite growing as clusters. They belong to space group P2{sub 1}, with unit-cell parameters a = 42.3, b = 118.4, c = 81.2 Å, β = 100.9°, and are suitable for data collection.},
doi = {10.1107/S1744309107023391},
journal = {Acta Crystallographica. Section F},
number = Pt 6,
volume = 63,
place = {United Kingdom},
year = {Fri Jun 01 00:00:00 EDT 2007},
month = {Fri Jun 01 00:00:00 EDT 2007}
}
  • The [NiFe]-hydrogenase maturation protein HypE was purified and crystallized. Crystals of HypE suitable for data collection diffracted to 1.55 Å resolution. The hydrogenase maturation protein HypE is involved in the biosynthesis of the CN ligands of the active-site iron of [NiFe] hydrogenases using carbamoylphosphate as a substrate. Here, the crystallization and preliminary crystallographic analysis of HypE from Thermococcus kodakaraensis KOD1 are reported. Crystals of HypE (338 amino acids, 35.9 kDa) have been obtained by the sitting-drop vapour-diffusion method using 2-methyl-2,4-pentanediol (MPD) as a precipitant. The crystals belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 88.3, bmore » = 45.8, c = 75.1 Å. There is one HypE molecule in the asymmetric unit. A complete native X-ray diffraction data set was collected to a maximum resolution of 1.55 Å at 100 K.« less
  • This article describes the first successful crystallization of a membrane-bound [NiFe] hydrogenase isolated from a photosynthetic organism (A. vinosum). The crystals obtained produced diffraction patterns up to 2.5 Å resolution. The membrane-bound [NiFe] hydrogenase is a unique metalloprotein that is able to catalyze the reversible oxidation of hydrogen to protons and electrons during a complex reaction cycle. The [NiFe] hydrogenase was isolated from the photosynthetic purple sulfur bacterium Allochromatium vinosum and its crystallization and preliminary X-ray analysis are reported. It was crystallized by the hanging-drop vapour-diffusion method using sodium citrate and imidazole as crystallization agents. The crystals belong to spacemore » group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 205.00, b = 217.42, c = 120.44 Å. X-ray diffraction data have been collected to 2.5 Å resolution.« less
  • An N-terminal acetyltransferase ARD1 subunit-related protein (Ta0058) and an N-terminal acetyltransferase-related protein (Ta1140) from T. acidophilum were crystallized. X-ray diffraction data were collected to 2.17 and 2.40 Å, respectively. N-terminal acetylation is one of the most common protein modifications in eukaryotes, occurring in approximately 80–90% of cytosolic mammalian proteins and about 50% of yeast proteins. ARD1 (arrest-defective protein 1), together with NAT1 (N-acetyltransferase protein 1) and possibly NAT5, is responsible for the NatA activity in Saccharomyces cerevisiae. In mammals, ARD1 is involved in cell proliferation, neuronal development and cancer. Interestingly, it has been reported that mouse ARD1 (mARD1{sup 225}) mediatesmore » ∊-acetylation of hypoxia-inducible factor 1α (HIF-1α) and thereby enhances HIF-1α ubiquitination and degradation. Here, the preliminary X-ray crystallographic analyses of two N-terminal acetyltransferase-related proteins encoded by the Ta0058 and Ta1140 genes of Thermoplasma acidophilum are reported. The Ta0058 protein is related to an N-terminal acetyltransferase complex ARD1 subunit, while Ta1140 is a putative N-terminal acetyltransferase-related protein. Ta0058 shows 26% amino-acid sequence identity to both mARD1{sup 225} and human ARD1{sup 235}.The sequence identity between Ta0058 and Ta1140 is 28%. Ta0058 and Ta1140 were overexpressed in Escherichia coli fused with an N-terminal purification tag. Ta0058 was crystallized at 297 K using a reservoir solution consisting of 0.1 M sodium acetate pH 4.6, 8%(w/v) polyethylene glycol 4000 and 35%(v/v) glycerol. X-ray diffraction data were collected to 2.17 Å. The Ta0058 crystals belong to space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 49.334, c = 70.384 Å, α = β = γ = 90°. The asymmetric unit contains a monomer, giving a calculated crystal volume per protein weight (V{sub M}) of 2.13 Å{sup 3} Da{sup −1} and a solvent content of 42.1%. Ta1140 was also crystallized at 297 K using a reservoir solution consisting of 0.1 M trisodium citrate pH 5.6, 20%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4000 and 0.2 M sodium chloride. X-ray diffraction data were collected to 2.40 Å. The Ta1140 crystals belong to space group R3, with hexagonal unit-cell parameters a = b = 75.174, c = 179.607 Å, α = β = 90, γ = 120°. Two monomers are likely to be present in the asymmetric unit, with a V{sub M} of 2.51 Å{sup 3} Da{sup −1} and a solvent content of 51.0%.« less
  • Vascular apoptosis-inducing protein 1 (VAP1) and VAP2 from C. atrox venom were crystallized in variety of different crystal forms. Diffraction data sets were obtained to 2.5 and 2.15 Å resolution for VAP1 and VAP2, respectively. VAPs are haemorrhagic snake-venom toxins belonging to the reprolysin family of zinc metalloproteinases. In vitro, VAPs induce apoptosis specifically in cultured vascular endothelial cells. VAPs have a modular structure that bears structural homology to mammalian ADAMs (a disintegrin and metalloproteinases). VAP1 is a homodimer with a MW of 110 kDa in which the monomers are connected by a single disulfide bridge. VAP2 is homologous tomore » VAP1 and exists as a monomer with a MW of 55 kDa. In the current study, several crystal forms of VAP1 and VAP2 were obtained using the vapour-diffusion method and diffraction data sets were collected using SPring-8 beamlines. The best crystals of VAP1 and VAP2 generated data sets to 2.5 and 2.15 Å resolution, respectively.« less