Structural Basis for Different Substrate Specificities of Two ADP-Ribose Pyrophosphatases from Thermus thermophilus HB8

ABSTRACT ADP-ribose (ADPR) is one of the main substrates of Nudix proteins. Among the eight Nudix proteins of Thermus thermophilus HB8, we previously determined the crystal structure of Ndx4, an ADPR pyrophosphatase (ADPRase). In this study we show that Ndx2 of T. thermophilus also preferentially hydrolyzes ADPR and flavin adenine dinucleotide and have determined its crystal structure. We have determined the structures of Ndx2 alone and in complex with Mg2+, with Mg2+ and AMP, and with Mg2+ and a nonhydrolyzable ADPR analogue. Although Ndx2 recognizes the AMP moiety in a manner similar to those for other ADPRases, it recognizes the terminal ribose in a distinct manner. The residues responsible for the recognition of the substrate in Ndx2 are not conserved among ADPRases. This may reflect the diversity in substrate specificity among ADPRases. Based on these results, we propose the classification of ADPRases into two types: ADPRase-I enzymes, which exhibit high specificity for ADPR; and ADPRase-II enzymes, which exhibit low specificity for ADPR. In the active site of the ternary complexes, three Mg2+ ions are coordinated to the side chains of conserved glutamate residues and water molecules. Substitution of Glu90 and Glu94 with glutamine suggests that these residues are essential for catalysis. These results suggest that ADPRase-I and ADPRase-II enzymes have nearly identical catalytic mechanisms but different mechanisms of substrate recognition.

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High resolution crystal structure of PedB: a structural basis for the classification of pediocin-like immunity proteins

BMC Structural Biology ◽

10.1186/1472-6807-7-35 ◽

2007 ◽

Vol 7 (1) ◽

pp. 35 ◽

Cited By ~ 7

Author(s):

In-Kwon Kim ◽

Min-Kyu Kim ◽

Ji-Hye Kim ◽

Hyung-Soon Yim ◽

Sun-Shin Cha ◽

...

Keyword(s):

Crystal Structure ◽

High Resolution ◽

Structural Basis

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The crystal-structure determination and redefinition of eztlite, Pb22+ Fe33+(Te4+O3)3(SO4)O2Cl

Mineralogical Magazine ◽

10.1180/mgm.2018.108 ◽

2018 ◽

Vol 82 (6) ◽

pp. 1355-1367 ◽

Cited By ~ 3

Author(s):

Owen P. Missen ◽

Stuart J. Mills ◽

John Spratt ◽

Mark D. Welch ◽

William D. Birch ◽

...

Keyword(s):

Crystal Structure ◽

Mixed Valence ◽

Lone Pair ◽

Water Molecules ◽

Monoclinic Space Group ◽

Charge Balance ◽

X Ray Diffraction ◽

International Mineralogical Association ◽

Bond Valence Analysis

ABSTRACTThe crystal structure of eztlite has been determined using single-crystal synchrotron X-ray diffraction and supported using electron microprobe analysis and powder diffraction. Eztlite, a secondary tellurium mineral from the Moctezuma mine, Mexico, is monoclinic, space group Cm, with a = 11.466(2) Å, b = 19.775(4) Å, c = 10.497(2) Å, β = 102.62(3)° and V = 2322.6(9) Å3. The chemical formula of eztlite has been revised to ${\rm Pb}_{\rm 2}^{2 +} {\rm Fe}_3^{3 +} $(Te4+O3)3(SO4)O2Cl from that stated previously as ${\rm Fe}_6^{3 +} {\rm Pb}_{\rm 2}^{2 +} $(Te4+O3)3(Te6+O6)(OH)10·nH2O. This change has been accepted by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association, Proposal 18-A. Eztlite was reported originally to be a mixed-valence Te oxysalt; however the crystal structure, bond-valence analysis and charge balance considerations clearly show that all Te is tetravalent. Eztlite contains a unique combination of elements and is only the second Te oxysalt to contain both sulfate and chloride. The crystal structure of eztlite contains mitridatite-like layers, with a repeating triangular nonameric [${\rm Fe}_9^{3 +} $O36]45– arrangement formed by nine edge-sharing Fe3+O6 octahedra, decorated by four trigonal pyramidal Te4+O3 groups, compared to PO4 or AsO4 tetrahedra in mitridatite-type minerals. In eztlite, all four tellurite groups associated with one nonamer are orientated with the lone pair of the Te atoms pointing in the same direction, whereas in mitridatite the central tetrahedron is orientated in the opposite direction to the others. In mitridatite-type structures, interlayer connections are formed exclusively via Ca2+ and water molecules, whereas the eztlite interlayer contains Pb2+, sulfate tetrahedra and Cl–. Interlayer connectivity in eztlite is achieved primarily by connections via the long bonds of Pbφ8 and Pbφ9 groups to sulfate tetrahedra and to Cl–. Secondary connectivity is via Te–O and Te–Cl bonds.

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Crystal structure of Staphylococcus aureus exfoliative toxin D-like protein: Structural basis for the high specificity of exfoliative toxins

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2015.08.083 ◽

2015 ◽

Vol 467 (1) ◽

pp. 171-177 ◽

Cited By ~ 3

Author(s):

Ricardo B. Mariutti ◽

Tatiana A.C.B. Souza ◽

Anwar Ullah ◽

Icaro P. Caruso ◽

Fábio R. de Moraes ◽

...

Keyword(s):

Crystal Structure ◽

Staphylococcus Aureus ◽

High Specificity ◽

Structural Basis ◽

Exfoliative Toxin

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X-ray Structure of the ZnII β-Lactamase from Bacteroides fragilis in an Orthorhombic Crystal Form

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s090744499700927x ◽

1998 ◽

Vol 54 (1) ◽

pp. 47-57 ◽

Cited By ~ 45

Author(s):

Andrea Carfi ◽

Emile Duée ◽

Raquel Paul-Soto ◽

Moreno Galleni ◽

Jean-Marie Frère ◽

...

Keyword(s):

Crystal Structure ◽

Catalytic Mechanism ◽

Bacteroides Fragilis ◽

Crystal Form ◽

Water Molecules ◽

Orthorhombic Crystal ◽

X Ray ◽

Class B ◽

Catalytic Mechanisms ◽

Zn Ions

β-Lactamases are extracellular or periplasmic bacterial enzymes which confer resistance to β-lactam antibiotics. On the basis of their catalytic mechanisms, they can be divided into two major groups: active-site serine enzymes (classes A, C and D) and the ZnII enzymes (class B). The first crystal structure of a class B enzyme, the metallo-β-lactamase from Bacillus cereus, has been solved at 2.5 Å resolution [Carfi, Pares, Duée, Galleni, Duez, Frère & Dideberg (1995). EMBO J. 14, 4914–4921]. Recently, the crystal structure of the metallo-β-lactamase from Bacteroides fragilis has been determined in a tetragonal space group [Concha, Rasmussen, Bush & Herzberg (1996). Structure, 4, 823–836]. The structure of the metallo-β-lactamase from B. fragilis in an orthorhombic crystal form at 2.0 Å resolution is reported here. The final crystallographic R is 0.196 for all the 32 501 observed reflections in the range 10–2.0 Å. The refined model includes 458 residues, 437 water molecules, four zinc and two sodium ions. These structures are discussed with reference to Zn binding and activity. A catalytic mechanism is proposed which is coherent with metallo-β-lactamases being active with either one Zn ion (as in Aeromonas hydrophila) or two Zn ions (as in B. fragilis) bound to the protein.

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The Elusive Crystal Structure of Uric Acid Dihydrate: Implication for Epitaxial Growth During Biomineralization

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768196013067 ◽

1997 ◽

Vol 53 (3) ◽

pp. 498-503 ◽

Cited By ~ 9

Author(s):

G. Artioli ◽

N. Masciocchi ◽

E. Galli

Keyword(s):

Crystal Structure ◽

Uric Acid ◽

Epitaxial Growth ◽

Short Range ◽

Structural Basis ◽

Water Molecules ◽

X Ray Diffraction ◽

X Ray ◽

Short Range Ordering ◽

Uric Acid Dihydrate

The crystal structure of the elusive uric acid dihydrate phase, a known component of human pathological biomineralizations, has been investigated by a combination of synchrotron and conventional X-ray diffraction experiments. C5H4N4O3.2H2O, orthorhombic, Pnab, a = 7.409 (1), b = 17.549 (3), c = 6.332 (1) Å, Z = 4, wR = 0.030 and 0.041 for two independently measured datasets. The molecular packing, encompassing hydrogen-bonded layers of water molecules and statistically disordered organic moieties, fully clarifies on a structural basis the observed epitaxic growth of uric acid dihydrate with associated phases in human stones, such as anhydrous uric acid and whewellite. Synchrotron data confirmed the existence of weak reflections violating the extinction conditions and are interpreted by the presence of short-range ordering of the uric acid molecules at distances of the order of a few adjacent cells.

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