Thirty years of heme catalases structural biology

Dı́az, Adelaida; Loewen, P.C.; Fita, Ignacio; Carpena, X.

doi:10.1016/j.abb.2011.12.011

Cited by 104 publications

(102 citation statements)

References 74 publications

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“…This feature is common to the catalases in clade 1, whereas, in those in clade 3, the heme plane is rotated by 180°, resulting in a His-III orientation [25]. His81 NE2 is 5.1 A distant from the iron atom, and 2.7…”

Section: Heme Active Site and Heme Pocketmentioning

confidence: 99%

“…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.…”

Section: Overall Structure Of Dr1998mentioning

confidence: 99%

“…Clade 3 consists of small-subunit (43-75 kDa) catalases containing heme b. These are widespread in different archaeons, bacteria, and eukaryotes, and some have NADPH as a cofactor [25,27,28].…”

Section: Introductionmentioning

confidence: 99%

“…These proteins can be divided into heme-containing enzymes, including monofunctional catalases or bifunctional catalase-peroxidases, and manganese catalases. For reviews, see, for example, [23][24][25][26][27]. Monofunctional catalases are further subdivided into clade 1 and clade 2.…”

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: Heme Active Site and Heme Pocketmentioning

confidence: 99%

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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“…Although the amino acid sequence of the putative KatE from Methanosarcina acetivorans is 88 % identical to characterized Methanosarcina barkeri KatE (Shima et al, 1999), sequencing of ma2081 confirms that the gene contains a frameshift causing a nonsense mutation that results in the synthesis of a truncated protein (173 of 496 predicted amino acids). Since half of the active-site residues identified in KatE (Díaz et al, 2012) are missing in the truncated protein ( Fig. S1), Methanosarcina acetivorans likely does not possess a functional KatE, unlike Methanosarcina barkeri.…”

Section: Genome Of Methanosarcina Acetivorans Encodes Catalase But Cmentioning

confidence: 99%

Expression of a bacterial catalase in a strictly anaerobic methanogen significantly increases tolerance to hydrogen peroxide but not oxygen

et al. 2014

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Haem-dependent catalase is an antioxidant enzyme that degrades H2O2, producing H2O and O2, and is common in aerobes. Catalase is present in some strictly anaerobic methane-producing archaea (methanogens), but the importance of catalase to the antioxidant system of methanogens is poorly understood. We report here that a survey of the sequenced genomes of methanogens revealed that the majority of species lack genes encoding catalase. Moreover, Methanosarcina acetivorans is a methanogen capable of synthesizing haem and encodes haem-dependent catalase in its genome; yet, Methanosarcina acetivorans cells lack detectable catalase activity. However, inducible expression of the haem-dependent catalase from Escherichia coli (EcKatG) in the chromosome of Methanosarcina acetivorans resulted in a 100-fold increase in the endogenous catalase activity compared with uninduced cells. The increased catalase activity conferred a 10-fold increase in the resistance of EcKatG-induced cells to H2O2 compared with uninduced cells. The EcKatG-induced cells were also able to grow when exposed to levels of H2O2 that inhibited or killed uninduced cells. However, despite the significant increase in catalase activity, growth studies revealed that EcKatG-induced cells did not exhibit increased tolerance to O2 compared with uninduced cells. These results support the lack of catalase in the majority of methanogens, since methanogens are more likely to encounter O2 rather than high concentrations of H2O2 in the natural environment. Catalase appears to be a minor component of the antioxidant system in methanogens, even those that are aerotolerant, including Methanosarcina acetivorans. Importantly, the experimental approach used here demonstrated the feasibility of engineering beneficial traits, such as H2O2 tolerance, in methanogens.

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Heme binding and peroxidase activity of a secreted minicatalase

et al. 2016

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Microbial pathogens often require efficient and robust H O scavenger activities to survive in the presence of reactive oxygen species generated by inflammatory responses. In addition to catalases and peroxidases, enzymes known to scavenge H O , a novel class of secreted minicatalases is found in diderm bacteria. Here, we characterize the Helicobacter pylori (Hp) minicatalase: a monomeric hemoprotein with catalase core homology. Overexpression of Hp minicatalase rescued a catalase/peroxidase-deficient Escherichia coli phenotype under aerobic conditions and limited H O stress. The purified enzyme lacks catalase activity, but has strong (k > 100 s ) H O -dependent peroxidase activity toward a variety of organic substrates. Our investigations into heme binding revealed that the heme cofactor is assembled in the periplasm to form the functional holoprotein. Furthermore, we observed the presence of a disulfide bond near the heme cavity of Hp minicatalase, which is conserved in secreted minicatalases and, therefore, may play a role in heme binding.

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Thirty years of heme catalases structural biology

Cited by 104 publications

References 74 publications

Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans

Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans

Expression of a bacterial catalase in a strictly anaerobic methanogen significantly increases tolerance to hydrogen peroxide but not oxygen

Heme binding and peroxidase activity of a secreted minicatalase

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