Structure and heme environment of beef liver catalase at 2.5 A resolution.

Reid, Thomas J.; Murthy, M.R.N.; Sicignano, Andrew; Tanaka, Nobuo; Musick, W.Donald L.; Rossmann, Michael G.

doi:10.1073/pnas.78.8.4767

Cited by 196 publications

(93 citation statements)

References 53 publications

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“…DR1998 oligomerizes as a homotetramer with 222 point-group symmetry, which is highly conserved among catalases [25,26]. The dimensions of the DR1998 tetramer along the three consensually defined orthogonal two-fold axes, P, Q, and R [13], are approximately 95, 70, and 95 A, respectively (Fig. 3).…”

Section: Overall Structure Of Dr1998mentioning

confidence: 99%

“…The three amino acids involved in the catalytic center are conserved among catalases: the proximal ligand is a tyrosine that coordinates the heme iron; a histidine and an asparagine located on the opposite, distal side of the heme plane also play a role in the catalytic mechanism. Although catalase was one of the first proteins to be crystallized (in 1937), the first catalase crystal structures only became available 40 years later: the bovine liver [Protein Data Bank (PDB) 1CAT] and the Penicillium vitale (PDB 4CAT) catalases [11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

“…The mechanisms underlying this radiation resistance have been studied by several groups, and different hypotheses have been proposed over the years, such as a condensed nucleoid structure, efficient DNA repair pathways, and a higher cellular Mn/Fe ratio [4,[7][8][9][10]. In order to detoxify the reactive oxygen species (ROS) formed under degrading conditions such as exposure to radiation, D. radiodurans possesses an enzymatic antioxidant system comprising superoxide dismutases, peroxidases and catalases that target the primary ROS, the superoxide radical and hydrogen peroxide [11][12][13][14][15][16]. Initial studies on the antioxidant activities of D. radiodurans extracts indicated that this organism contains more than one catalase.…”

Section: Introductionmentioning

confidence: 99%

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Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans

et al. 2014

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Deinococcus radiodurans is an aerobic organism with the ability to survive under conditions of high radiation doses or desiccation. As part of its protection system against oxidative stress, this bacterium encodes three monofunctional catalases. The DR1998 catalase belongs to clade 1, and is present at high levels under normal growth conditions. The crystals of DR1998 diffracted very weakly, and the merged diffraction data showed an R sym of 0.308. Its crystal structure was determined and refined to 2.6 Å. The four molecules present in the asymmetric unit form, by crystallographic symmetry, two homotetramers with 222 point‐group symmetry. The overall structure of DR1998 is similar to that of other monofunctional catalases, showing higher structural homology with the catalase structures of clade 1. Each monomer shows the typical catalase fold, and contains one heme b in the active site. The heme is coordinated by the proximal ligand Tyr369, and on the heme distal side the essential His81 and Asn159 are hydrogen‐bonded to a water molecule. A 25‐Å‐long channel is the main channel connecting the active site to the external surface. This channel starts with a hydrophobic region from the catalytic heme site, which is followed by a hydrophilic region that begins on Asp139 and expands up to the protein surface. Apart from this channel, an alternative channel, also near the heme active site, is presented and discussed. Database Coordinates and structure factors have been deposited in the Protein Data Bank in Europe under accession code http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4CAB

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Section: Overall Structure Of Dr1998mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans

et al. 2014

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“…22), stabilized by the ionized phenolic oxygen of Tyr-357, stabilized in turn by Arg-353, at an unusually short distance (2.0 Å) from the iron atom (23). However, the jF obs j − jF calc j Coulomb potential map calculated assuming Fe (III) and ionized phenolic oxygen, shows a large negative peak of −3.9 σ at the iron atom and a prominent positive peak of +4.0 σ near the phenolic oxygen of Tyr-357 (Fig.…”

Section: Significancementioning

confidence: 99%

Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges

Yonekura

Kato

Ogasawara

et al. 2015

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

181

165

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Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca 2+ -ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca 2+ -binding sites of Ca 2+ -ATPase and that of the iron atom in the heme in catalase.electron crystallography | protein crystal | Coulomb potential | Ca 2+ -ATPase | catalase P rotein atoms scatter electrons four to five orders of magnitude more strongly than they do X-rays, thus allowing individual protein molecules to be imaged by electron microscopy (1). Although not fully exploited so far, electron protein crystallography has great potential and indeed has yielded superb high-resolution (∼2.0-Å resolution) atomic structures from 2D crystals (2). However, electron crystallography of 3D crystals is problematic, as stacking of even a few layers makes diffraction patterns discrete in all directions, and methods developed for conventional electron crystallography of 2D crystals (3) are not useful (SI Appendix, Fig. S1A, Left). This problem can be overcome, however, as Gonen and coworkers demonstrated (4, 5), by rotating the crystal to spatially integrate the intensities of diffraction spots as in X-ray crystallography (SI Appendix, Fig. S1A, Right) or, in certain cases, even combining simple tilt series.Another important feature of electron scattering is that the diffraction pattern formed by elastically scattered electrons is directly related to the distribution of Coulomb potential. This is in marked contrast to X-rays, which, because they are scattered by electrons, yield an electron density map. Coulomb potential maps may be more difficult to interpret, compared with electron density maps by X-ray crystallography, as the appearance of the same residues may differ depending on their charged state, resolution, and surrounding environment ( Fig. 1 and SI Appendix, Fig. S2), but they provide unique information, not attainable by X-rays (6). Theoretical potential maps (F calc maps; Fig. 1 B-E) calculated from an atomic model of Ca 2+ -ATPase (7) using scattering factors for 300-keV electrons highlight these features. For instance, densities of acidic residues are absent or weak when lower-resolution data are included in the map calc...

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“…Crystal structures of several catalases have been described: beef liver (Reid et al, 1981;Fita et al, 1986), Penicillium vitale (Melik-Adamyan et al, 1986), Proteus mirablis (Gouet et al, 1995) and Escherichia coli (Bravo et al, 1995).…”

Section: Introductionmentioning

confidence: 99%

Crystallization and preliminary X-ray diffraction studies of human catalase

Nagem

Martins

Gonçalves

et al. 1999

Acta Crystallogr D Biol Cryst

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The enzyme catalase (H 2 O 2 ±H 2 O 2 oxidoreductase; E.C. 11.1.6) was puri®ed from haemolysate of human placenta and crystallized using the vapour-diffusion technique. Synchrotron-radiation diffraction data have been collected to 1.76 A Ê resolution. The enzyme crystallized in the space group P2 1 2 1 2 1 , with unit-cell dimensions a = 83.6, b = 139.4, c = 227.5 A Ê . A molecular-replacement solution of the structure has been obtained using beef liver catalase (PDB code 4blc) as a search model.

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Structure and heme environment of beef liver catalase at 2.5 A resolution.

Cited by 196 publications

References 53 publications

Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans

Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans

Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges

Crystallization and preliminary X-ray diffraction studies of human catalase

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