Yoshimitsu Kakuta

Crystal structure of estrogen sulphotransferase.

The structure of estrogen sulphotransferase has been solved in the presence of inactive cofactor PAP and substrate 17β-estradiol. This structure reveals structural similarities between cytosolic sulphotransf erases and nucleotide kinases.

Crystal structure of archaeal toxin-antitoxin RelE-RelB complex with implications for toxin activity and antitoxin effects

The Escherichia coli chromosome encodes toxin-antitoxin pairs. The toxin RelE cleaves mRNA positioned at the A-site in ribosomes, whereas the antitoxin RelB relieves the effect of RelE. The hyperthermophilic archaeon Pyrococcus horikoshii OT3 has the archaeal homologs aRelE and aRelB. Here we report the crystal structure of aRelE in complex with aRelB determined at a resolution of 2.3 Å. aRelE folds into an α/β structure, whereas aRelB lacks a distinct hydrophobic core and extensively wraps around the molecular surface of aRelE. Neither component shows structural homology to known ribonucleases or their inhibitors. Site-directed mutagenesis suggests that Arg85, in the C-terminal region, is strongly involved in the functional activity of aRelE, whereas Arg40, Leu48, Arg58 and Arg65 play a modest role in the toxins activity.

Crystal Structure of the Sulfotransferase Domain of Human Heparan Sulfate N-Deacetylase/ N-Sulfotransferase 1

Heparan sulfateN-deacetylase/N-sulfotransferase (HSNST) catalyzes the first and obligatory step in the biosynthesis of heparan sulfates and heparin. The crystal structure of the sulfotransferase domain (NST1) of human HSNST-1 has been determined at 2.3-Å resolution in a binary complex with 3′-phosphoadenosine 5′-phosphate (PAP). NST1 is approximately spherical with an open cleft, and consists of a single α/β fold with a central five-stranded parallel β-sheet and a three-stranded anti-parallel β-sheet bearing an interstrand disulfide bond. The structural regions α1, α6, β1, β7, 5′-phosphosulfate binding loop (between β1 and α1), and a random coil (between β8 and α13) constitute the PAP binding site of NST1. The α6 and random coil (between β2 and α2), which form an open cleft near the 5′-phosphate of the PAP molecule, may provide interactions for substrate binding. The conserved residue Lys-614 is in position to form a hydrogen bond with the bridge oxygen of the 5′-phosphate.

The Sulfuryl Transfer Mechanism CRYSTAL STRUCTURE OF A VANADATE COMPLEX OF ESTROGEN SULFOTRANSFERASE AND MUTATIONAL ANALYSIS

Estrogen sulfotransferase (EST) catalyzes transfer of the 5′-sulfuryl group of adenosine 3′-phosphate 5′-phosphosulfate (PAPS) to the 3α-phenol group of estrogenic steroids such as estradiol (E2). The recent crystal structure of EST-adenosine 3′,5′-diphosphate (PAP)- E2complex has revealed that residues Lys48, Thr45, Thr51, Thr52, Lys106, His108, and Try240 are in position to play a catalytic role in the sulfuryl transfer reaction of EST (Kakuta Y., Pedersen, L. G., Carter, C. W., Negishi, M., and Pedersen, L. C. (1997) Nat. Struct. Biol. 4, 904–908). Mutation of Lys48, Lys106, or His108 nearly abolishes EST activity, indicating that they play a critical role in catalysis. A present 2.2-Å resolution structure of EST-PAP-vanadate complex indicates that the vanadate molecule adopts a trigonal bipyramidal geometry with its equatorial oxygens coordinated to these three residues. The apical positions of the vanadate molecule are occupied by a terminal oxygen of the 5′-phosphate of PAP (2.1 Å) and a possible water molecule (2.3 Å). This water molecule superimposes well to the 3α-phenol group of E2 in the crystal structure of the EST·PAP·E2 complex. These structures are characteristic of the transition state for an in-line sulfuryl transfer reaction from PAPS to E2. Moreover, residues Lys48, Lys106, and His108 are found to be coordinated with the vanadate molecule at the transition state of EST.

Crystal structure of rat heme oxygenase-1 in complex with heme

Heme oxygenase catalyzes the oxidative cleavage of protoheme to biliverdin, the first step of heme metabolism utilizing O2 and NADPH. We determined the crystal structures of rat heme oxygenase‐1 (HO‐1)–heme and selenomethionyl HO‐1–heme complexes. Heme is sandwiched between two helices with the δ‐meso edge of the heme being exposed to the surface. Gly143N forms a hydrogen bond to the distal ligand of heme, OH−. The distance between Gly143N and the ligand is shorter than that in the human HO‐1–heme complex. This difference may be related to a pH‐dependent change of the distal ligand of heme. Flexibility of the distal helix may control the stability of the coordination of the distal ligand to heme iron. The possible role of Gly143 in the heme oxygenase reaction is discussed.

The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity

RecJ, a 5′ to 3′ exonuclease specific for single-stranded DNA, functions in DNA repair and recombination systems. We determined the crystal structure of RecJ bound to Mn2+ ion essential for its activity. RecJ has a novel fold in which two domains are interconnected by a long helix, forming a central groove. Mn2+ is located on the wall of the groove and is coordinated by conserved residues characteristic of a family of phosphoesterases that includes RecJ proteins. The groove is composed of residues conserved among RecJ proteins and is positively charged. These findings and the narrow width of the groove indicate that the groove binds single- instead of double-stranded DNA.

ERRγ tethers strongly bisphenol A and 4-α-cumylphenol in an induced-fit manner

A receptor-binding assay and X-ray crystal structure analysis demonstrated that the endocrine disruptor bisphenol A (BPA) strongly binds to human estrogen-related receptor gamma (ERRgamma). BPA is well anchored to the ligand-binding pocket, forming hydrogen bonds with its two phenol-hydroxyl groups. In this study, we found that 4-alpha-cumylphenol lacking one of its phenol-hydroxyl groups also binds to ERRgamma very strongly. The 2.0 A crystal structure of the 4-alpha-cumylphenol/ERRgamma complex clearly revealed that ERRgammas Leu345-beta-isopropyl plays a role in the tight binding of 4-alpha-cumylphenol and BPA, rotating in a back-and-forth induced-fit manner.

Klotho-related Protein Is a Novel Cytosolic Neutral β-Glycosylceramidase

Using C6-NBD-glucosylceramide (GlcCer) as a substrate, we detected the activity of a conduritol B epoxide-insensitive neutral glycosylceramidase in cytosolic fractions of zebrafish embryos, mouse and rat brains, and human fibroblasts. The candidates for the enzyme were assigned to the Klotho (KL), whose family members share a β-glucosidase-like domain but whose natural substrates are unknown. Among this family, only the KL-related protein (KLrP) is capable of degrading C6-NBD-GlcCer when expressed in CHOP cells, in which Myc-tagged KLrP was exclusively distributed in the cytosol. In addition, knockdown of the endogenous KLrP by small interfering RNA increased the cellular level of GlcCer. The purified recombinant KLrP hydrolyzed 4-methylumbelliferyl-glucose, C6-NBD-GlcCer, and authentic GlcCer at pH 6.0. The enzyme also hydrolyzed the corresponding galactosyl derivatives, but each kcat/Km was much lower than that for glucosyl derivatives. The x-ray structure of KLrP at 1.6Å resolution revealed that KLrP is a (β/α)8 TIM barrel, in which Glu165 and Glu373 at the carboxyl termini of β-strands 4 and 7 could function as an acid/base catalyst and nucleophile, respectively. The substrate-binding cleft of the enzyme was occupied with palmitic acid and oleic acid when the recombinant protein was crystallized in a complex with glucose. GlcCer was found to fit well the cleft of the crystal structure of KLrP. Collectively, KLrP was identified as a cytosolic neutral glycosylceramidase that could be involved in a novel nonlysosomal catabolic pathway of GlcCer.

Crystal Structure of Tapes japonica Lysozyme with Substrate Analogue: STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND MANIFESTATION OF ITS CHITINASE ACTIVITY ACCOMPANIED BY QUATERNARY STRUCTURAL CHANGE

Tapes japonica lysozyme (TJL) is classified as a member of the recently established i-type lysozyme family. In this study, we solved the crystal structure of TJL complexed with a trimer of N-acetylglucosamine to 1.6Å resolution. Based on structure and mutation analyses, we demonstrated that Glu-18 and Asp-30 are the catalytic residues of TJL. Furthermore, the present findings suggest that the catalytic mechanism of TJL is a retaining mechanism that proceeds through a covalent sugar-enzyme intermediate. On the other hand, the quaternary structure in the crystal revealed a dimer formed by the electrostatic interactions of catalytic residues (Glu-18 and Asp-30) in one molecule with the positive residues at the C terminus in helix 6 of the other molecule. Gel chromatography analysis revealed that the TJL dimer remained intact under low salt conditions but that it dissociated to TJL monomers under high salt conditions. With increasing salt concentrations, the chitinase activity of TJL dramatically increased. Therefore, this study provides novel evidence that the lysozyme activity of TJL is modulated by its quaternary structure.

Substrate Gating Confers Steroid Specificity to Estrogen Sulfotransferase

Estrogen sulfotransferase (EST) exhibits a high substrate specificity and catalytic efficiency toward estrogens such as estradiol (E2) but insignificant ability to sulfate hydroxysteroids such as dehydroepiandrosterone (DHEA). To provide the structural basis for this estrogen specificity, we mutated amino acid residues that constitute the substrate-binding site of EST. Among these mutants, only Tyr-81 decreased E2 and increased DHEA sulfotransferase activities. Substitution for Tyr-81 by smaller hydrophobic residues increasedK m (E2) for E2 activity, whereas thek cat(E2) remained relatively constant. The Y81L mutant exhibited the same DHEA activity as wild-type hydroxysteroid sulfotransferase, for whichK m (DHEA) remained relatively constant, and k cat(DHEA) was markedly increased. The side chain of Tyr-81 is directed at the A-ring of the E2 molecule in the substrate-binding pocket of EST, constituting a steric gate with Phe-142 sandwiching E2 from the opposite side. The present mutagenesis study indicates that the 3β-hydroxyl group of the DHEA molecule is excluded from the catalytic site of EST through steric hindrance of Tyr-81 with the C-19 methyl group of DHEA. Thus, this stricture-like gating caused by steric hindrance appears to be a structural principle for conferring estrogen specificity to EST.