Mini-intein Structures from Extremophiles Suggest a Strategy for Finding Novel Robust Inteins

Inteins are prevalent among extremophiles. Mini-inteins with robust splicing properties are of particular interest for biotechnological applications due to their small size. However, biochemical and structural characterization has still been limited to a small number of inteins, and only a few inteins serve as widely used tools in protein engineering approaches. We determined the crystal structure of a naturally-occurring Pol-II mini-intein from Pyrococcus horikoshii and compared it with two other natural mini-inteins from Pyrococcus horikoshii. Despite the similar sizes, the comparison revealed distinct differences in insertions and deletions, implying specific evolutionary pathways from distinct ancestral origins. Our studies suggest that sporadically distributed mini-inteins might be more promising for further protein engineering applications than the highly conserved mini-inteins. Structural investigations of more inteins could guide the shortest path to finding novel robust mini-inteins suitable for protein engineering purposes.

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Mini-Intein Structures from Extremophiles Suggest a Strategy for Finding Novel Robust Inteins

Microorganisms ◽

10.3390/microorganisms9061226 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1226

Author(s):

Mimmu K. Hiltunen ◽

Hannes M. Beyer ◽

Hideo Iwaï

Keyword(s):

Crystal Structure ◽

Protein Engineering ◽

Shortest Path ◽

Structural Characterization ◽

Biotechnological Applications ◽

Structural Investigations ◽

Pyrococcus Horikoshii ◽

Pol Ii ◽

Naturally Occurring ◽

Evolutionary Pathways

Inteins are prevalent among extremophiles. Mini-inteins with robust splicing properties are of particular interest for biotechnological applications due to their small size. However, biochemical and structural characterization has still been limited to a small number of inteins, and only a few serve as widely used tools in protein engineering. We determined the crystal structure of a naturally occurring Pol-II mini-intein from Pyrococcus horikoshii and compared all three mini-inteins found in the genome of P. horikoshii. Despite their similar sizes, the comparison revealed distinct differences in the insertions and deletions, implying specific evolutionary pathways from distinct ancestral origins. Our studies suggest that sporadically distributed mini-inteins might be more promising for further protein engineering applications than highly conserved mini-inteins. Structural investigations of additional inteins could guide the shortest path to finding novel robust mini-inteins suitable for various protein engineering purposes.

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Faculty Opinions recommendation of Crystal structure of the ADP-dependent glucokinase from Pyrococcus horikoshii at 2.0-A resolution: a large conformational change in ADP-dependent glucokinase.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1009782.135407 ◽

2002 ◽

Author(s):

Patricia C Weber

Keyword(s):

Crystal Structure ◽

Conformational Change ◽

Pyrococcus Horikoshii ◽

Large Conformational Change

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Structural Investigations of C-Nitrosobenzenes. Part 3.1 Solid-state and Solution 13C NMR Studies, and Crystal Structure of E-(4-CIC6H4NO)2

Journal of Chemical Research ◽

10.1177/174751989902300316 ◽

1999 ◽

Vol 23 (3) ◽

pp. 202-203

Author(s):

Daniel A. Fletcher ◽

Brian G. Gowenlock ◽

Keith G. Orrell ◽

David C. Apperley ◽

Michael B. Hursthouse ◽

...

Keyword(s):

Crystal Structure ◽

Solid State ◽

13C Nmr ◽

Nmr Studies ◽

Structural Investigations ◽

Nmr Data ◽

C Nmr

Solid-state and solution 13C NMR data for the monomers and dimers of 3- and 4-substituted nitrosobenzenes, and the crystal structure of E-(4-CIC6H4NO)2 are reported.

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The crystal structure of the first ether solvate of hexaphenyldistannane [(Ph3Sn)2 • 2 THF]

Main Group Metal Chemistry ◽

10.1515/mgmc-2020-0001 ◽

2020 ◽

Vol 43 (1) ◽

pp. 1-6 ◽

Cited By ~ 2

Author(s):

Jonathan O. Bauer

Keyword(s):

Crystal Structure ◽

Inclusion Compounds ◽

Molecular Crystal ◽

Structural Features ◽

Structural Investigations ◽

Crystal Solvates

AbstractStructural investigations of molecular crystal solvates can provide important information for the targeted crystallization of particular inclusion compounds. Here, the crystal structure of the first ether solvate of hexaphenyldistannane [(Ph3Sn)2 • 2 THF] is reported. Structural features in terms of host-guest interactions and in the context of the previously reported polymorphs and solvates of (Ph3Sn)2 are discussed.

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KCTD proteins as Cullin3 E3 Ligase adapters

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314096946 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C305-C305

Author(s):

Alan Ji ◽

Gilbert Privé

Keyword(s):

Crystal Structure ◽

Structural Characterization ◽

Dissociation Constants ◽

E3 Ligase ◽

Terminal Region ◽

Btb Domain ◽

Substrate Protein ◽

Ubiquitin E3 Ligase ◽

Ubiquitin Moiety

Cullin3 (Cul3) is an ubiquitin E3 ligase responsible for catalyzing the transfer of an ubiquitin moiety from an E2 enzyme to a target substrate protein. The C-terminal region of Cul3 binds RBX1/E2-ubiquitin, while, the N-terminal region interacts with various BTB domain proteins which serve as substrate adaptors. Previously, our group determined the crystal structures of the homodimeric BTB proteins SPOP and KLHL3 in complex with the N-terminal domain of Cul3, revealing the determinants responsible for the BTB/Cul3 interaction [1, 2]. A second class of BTB-domain containing proteins, the KCTD proteins, are also Cul3 substrate adaptors but these do not share many of the previously determined features for Cul3 binding. Furthermore, KCTD proteins form homotetramers and homopentamers via BTB oligomerization rather than the previously described homodimers. Despite these differences, many KCTD proteins interact with Cul3 with dissociation constants of approximately 50 nM. While the target substrates for many of the KCTD/Cul3 E3 ligase complexes are unknown, recent studies have implicated the GABAβ2 receptor as an interactor of KCTD 8, 12, 12b and 16. Here, we report the pentameric crystal structure of the KCTD9 BTB domain and our progress on the structural characterization of Cul3/KCTD/substrate complexes.

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Crystal structure of a component of glycine cleavage system: T-protein from Pyrococcus horikoshii OT3 at 1.5 Å resolution

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20345 ◽

2004 ◽

Vol 58 (3) ◽

pp. 769-773 ◽

Cited By ~ 7

Author(s):

Neratur K. Lokanath ◽

Chizu Kuroishi ◽

Nobuo Okazaki ◽

Naoki Kunishima

Keyword(s):

Crystal Structure ◽

Glycine Cleavage System ◽

Pyrococcus Horikoshii ◽

Glycine Cleavage

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Structural Systematics of Rare Earth Complexes. VII. Crystal Structure of Bis(2,2'/6',2␛-Terpyridinium) Octaaquaterbium(III) Heptachloride Hydrate

Australian Journal of Chemistry ◽

10.1071/ch9940391 ◽

1994 ◽

Vol 47 (2) ◽

pp. 391 ◽

Cited By ~ 15

Author(s):

CJ Kepert ◽

BW Skeleton ◽

AH White

Keyword(s):

Crystal Structure ◽

Rare Earth ◽

Single Crystal ◽

Structural Characterization ◽

Title Compound ◽

Room Temperature ◽

Chloride Ions ◽

Full Matrix ◽

X Ray

The room-temperature single-crystal X-ray structural characterization of the title compound (tpyH2)2[Tb(OH2)8]Cl7.~2⅓H2O is recorded. Crystals are triclinic, Pī , a 17.063(5), b 16.243(3), c 7.878(3) Ǻ, α 84.78(2), β 84.39(3), γ 87.81(2)°, Z = 2 formula units; 3167 'observed' diffractometer reflections were refined by full-matrix least-squares procedures to a residual of 0.057. Notable features of interest of the compound are the 'chelation' of chloride ions by the terpyridinium cations , and the existence of a free [Tb(OH2)8]2+ cation in the presence of an abundance of chloride ions.

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A-Pr2S3, D-Ho2S3 und E-Yb2S3:Synthese und Einkristallstrukturuntersuchungen / A-Pr2S3, D-Ho2S3 and E-Yb2S3:Synthesis and Single Crystal Structure Investigations

Zeitschrift für Naturforschung B ◽

10.1515/znb-1996-0519 ◽

1996 ◽

Vol 51 (5) ◽

pp. 733-738 ◽

Cited By ~ 16

Author(s):

Thomas Schleid ◽

Falk Lissner

Keyword(s):

Crystal Structure ◽

Crystal Growth ◽

Single Crystals ◽

Alkali Halides ◽

Structural Investigations ◽

Coordination Numbers ◽

Trivalent Lanthanides ◽

Trivalent Cations ◽

Structure Investigations ◽

Type Orthorhombic

The oxidation of reduced chlorides (MCl2) or chloride-hydrides (MClHx) of the lanthanides with sulfur (700-850 °C, 7 d, sealed tantalum capsules or evacuated silica vessels) usually results in the formation of the sesquisulfides M2S3 as the main products. In the presence of appropriate fluxes (e.g., alkali halides), the products often are obtained as single crystals, and the flux decides which modification is favoured. Ternary halides of the trivalent lanthanides with the corresponding alkali metal can mostly be found as the second components. Crystal growth and structural investigations of thus produced single crystals of Pr2S3 (from PrClH0.67 + S + NaCl, 5:5:1, A type: orthorhombic, Pnma (No. 62), Z = 4, a = 748.22(5), b = 405.51(3), c = 1560.74(9) pm, R = 0.024, Rw = 0.020), Ho2S3, (from U - Ho2S3, + KI, 1:1, D type: monoclinic, P21/m (No. 12), Z = 6, a = 1746.15(9), b = 400.23(3), c = 1012.43(6) pm, β = 98.529(4)°, R = 0.041, Rw = 0.035), and Yb2S3 (from T-Yb2S3 + KI, 1:1, E type: trigonal, R3̄c (No. 167), Z = 6, a = 674.97(2), c = 1820.11(9) pm, R = 0.019, Rw = 0.018) are reported here. In accordance with the lanthanide contraction, the trivalent cations (M3+) exhibit sulfur coordination numbers of 7 and 8 in A -Pr2S3, 6 and 7 in D -Ho2S3, and 6 in E -Yb2S3 (corundum-type structure).

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