4.0 Article

Crystallization and preliminary X-ray crystallographic analysis of the membrane-binding haemprotein nitrophorin 7 from Rhodnius prolixus

Publisher

INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S1744309111044708

Keywords

nitrophorins; Rhodnius prolixus; ss-barrel proteins; haem; membrane

Funding

  1. Max Planck Society

Ask authors/readers for more resources

Nitrophorins (nitric oxide transport proteins) are haemproteins originating from the blood-feeding insect Rhodnius prolixus. They consist of an eight-stranded beta-barrel, which classifies them into the lipocalin family. Nitrophorin 7 (NP7) and the E27V mutant protein NP7(E27V) were crystallized at 277 K using the vapour-diffusion method with PEG as the precipitating agent. Data sets for wild-type NP7 and NP7(E27V) were collected to 1.80 angstrom resolution from single crystals at 100 K using synchrotron radiation. The crystals belonged to space group P21, with unit-cell parameters a = 38, b = 67, c = 39 angstrom, beta = 117 degrees. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (VM) of 2.11 angstrom 3 Da-1; the solvent content was estimated to be 41.8%.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.0
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Multidisciplinary Sciences

Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase

Hideaki Ogata, Koji Nishikawa, Wolfgang Lubitz

NATURE (2015)

Article Chemistry, Physical

Structural differences between the active sites of the Ni-A and Ni-B states of the [NiFe] hydrogenase: an approach by quantum chemistry and single crystal ENDOR spectroscopy

Jessica L. Barilone, Hideaki Ogata, Wolfgang Lubitz, Maurice van Gastel

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2015)

Article Biochemistry & Molecular Biology

Importance of Hydrogen Bonding in Fine Tuning the [2Fe-2S] Cluster Redox Potential of HydC from Thermotoga maritima

James A. Birrell, Christoph Laurich, Edward J. Reijerse, Hideaki Ogata, Wolfgang Lubitz

BIOCHEMISTRY (2016)

Review Biochemistry & Molecular Biology

Structure and function of [NiFe] hydrogenases

Hideaki Ogata, Wolfgang Lubitz, Yoshiki Higuchi

JOURNAL OF BIOCHEMISTRY (2016)

Article Chemistry, Physical

Solvent water interactions within the active site of the membrane type I matrix metalloproteinase

Elena Decaneto, Tatiana Vasilevskaya, Yuri Kutin, Hideaki Ogata, Moran Grossman, Irit Sagi, Martina Havenith, Wolfgang Lubitz, Walter Thiel, Nicholas Cox

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)

Article Chemistry, Multidisciplinary

Unique Spectroscopic Properties of the H-Cluster in a Putative Sensory [FeFe] Hydrogenase

Nipa Chongdar, James A. Birrell, Krzysztof Pawlak, Constanze Sommer, Edward J. Reijerse, Olaf Ruediger, Wolfgang Lubitz, Hideaki Ogata

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

Article Multidisciplinary Sciences

Electrostatic Tuning of the Ligand Binding Mechanism by Glu27 in Nitrophorin 7

Stefania Abbruzzetti, Alessandro Allegri, Axel Bidon-Chanal, Hideaki Ogata, Giancarlo Soavi, Giulio Cerullo, Stefano Bruno, Chiara Montali, F. Javier Luque, Cristiano Viappiani

SCIENTIFIC REPORTS (2018)

Article Multidisciplinary Sciences

Role of APS reductase in biogeochemical sulfur isotope fractionation

Min Sub Sim, Hideaki Ogata, Wolfgang Lubitz, Jess F. Adkins, Alex L. Sessions, Victoria J. Orphan, Shawn E. McGlynn

NATURE COMMUNICATIONS (2019)

Review Chemistry, Multidisciplinary

Structural Basis of the Function of [NiFe]-hydrogenases

Koji Nishikawa, Hideaki Ogata, Yoshiki Higuchi

CHEMISTRY LETTERS (2020)

Article Biochemistry & Molecular Biology

Spectroscopic and biochemical insight into an electron-bifurcating [FeFe] hydrogenase

Nipa Chongdar, Krzysztof Pawlak, Olaf Ruediger, Edward J. Reijerse, Patricia Rodriguez-Macia, Wolfgang Lubitz, James A. Birrell, Hideaki Ogata

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY (2020)

Article Biochemical Research Methods

Structural and spectroscopic characterization of CO inhibition of [NiFe]-hydrogenase from Citrobacter sp. S-77

Takahiro Imanishi, Koji Nishikawa, Midori Taketa, Katsuhiro Higuchi, Hulin Tai, Shun Hirota, Hironobu Hojo, Toru Kawakami, Kiriko Hataguchi, Kayoko Matsumoto, Hideaki Ogata, Yoshiki Higuchi

Summary: This study investigated the binding state of CO with the hydrogenase in Citrobacter sp. S-77 using activity assays, spectroscopic techniques, and X-ray crystallography. The results showed a positive correlation between CO tolerance and oxygen tolerance in [NiFe]-hydrogenases.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2022)

Review Chemistry, Multidisciplinary

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Sven T. Stripp, Benjamin R. Duffus, Vincent Fourmond, Christophe Leger, Silke Leimkueshler, Shun Hirota, Yilin Hu, Andrew Jasniewski, Hideaki Ogata, Markus W. Ribbe

Summary: Gases like H-2, N-2, CO2, and CO are important feedstock for green energy conversion and as sources of nitrogen and carbon. However, their industrial transformation and production require significant energy input, whereas nature efficiently converts them at ambient conditions using gas-processing metalloenzymes (GPMs). In this review, the importance of the cofactor/protein interface in GPMs is emphasized, and the effects of second and outer coordination sphere on catalytic activity are discussed.

CHEMICAL REVIEWS (2022)

Article Chemistry, Multidisciplinary

Redox tuning of the H-cluster by second coordination sphere amino acids in the sensory [FeFe] hydrogenase from Thermotoga maritima

Nipa Chongdar, Patricia Rodriguez-Macia, Edward J. Reijerse, Wolfgang Lubitz, Hideaki Ogata, James A. Birrell

Summary: This study investigates the influence of the protein environment on the catalytic, spectroscopic, and redox properties of [FeFe] hydrogenases. Mutations at the non-conserved serine 267 site resulted in a significant decrease in activity and a lower redox potential for the [4Fe-4S] subcluster. These findings highlight the important role of the secondary coordination sphere in tuning the catalytic properties of [FeFe] hydrogenases.

CHEMICAL SCIENCE (2023)

Article Chemistry, Multidisciplinary

New insights into the oxidation process from neutron and X-ray crystal structures of an O2sensitive [NiFe]-hydrogenase

Takeshi Hiromoto, Koji Nishikawa, Seiya Inoue, Hideaki Ogata, Yuta Hori, Katsuhiro Kusaka, Yu Hirano, Kazuo Kurihara, Yasuteru Shigeta, Taro Tamada, Yoshiki Higuchi

Summary: This study reports that [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F can recover its catalytic activity by reacting with H2 under anaerobic conditions after being inactivated in the presence of O2. Neutron structure analysis revealed that a part of the Ni ion dissociates from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. The analysis also found that the Cys17(S) thiolate forms an unusual hydrogen bond with the main-chain amide N atom of Gly19(S), providing insights into the redox reaction of the Fe-S cluster.

CHEMICAL SCIENCE (2023)

No Data Available