Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis

Acta Crystallographica. Section F, Structural Biology Communications
T E PetrovaV O Popov

Abstract

The crystal structure of the aminopeptidase APDkam589 from the thermophilic crenarchaeon Desulfurococcus kamchatkensis was determined at a resolution of 3.0 Å. In the crystal, the monomer of APDkam589 and its symmetry-related monomers are densely packed to form a 12-subunit complex. Single-particle electron-microscopy analysis confirms that APDkam589 is present as a compact dodecamer in solution. The APDkam589 molecule is built similarly to the molecules of the PhTET peptidases, which have the highest sequence identity to APDkam589 among known structures and were isolated from the more thermostable archaeon Pyrococcus horikoshii. A comparison of the interactions of the subunits in APDkam589 with those in PhTET1, PhTET2 and PhTET3 reveals that APDkam589 has a much lower total number of salt bridges, which correlates with the lower thermostability of APDkam589. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. A superposition of the structure of APDkam589 with those having a high sequence similarity to APDkam589 reveals that, although the positions of Trp45, Trp252 and Trp358 are not conserved in the sequences, the spatial locations of the Trp residues in these models are s...Continue Reading

References

Jan 1, 1996·Journal of Structural Biology·M van HeelM Schatz
Oct 23, 1997·Nature Structural Biology·J SakonP A Karplus
Jul 22, 1998·Extremophiles : Life Under Extreme Conditions·J M GonzálezC Kato
Dec 22, 1999·Journal of Structural Biology·S J LudtkeW Chiu
Mar 14, 2000·Proteins·U SamantaP Chakrabarti
May 1, 2002·The EMBO Journal·B FranzettiG Zaccai
May 10, 2003·Trends in Immunology·Ursula GrohmannPaolo Puccetti
Dec 19, 2003·Nucleic Acids Research·Neil D RawlingsAlan J Barrett
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Sep 18, 2004·The Journal of Biological Chemistry·Santina Russo, Ulrich Baumann
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·Paul Emsley, Kevin Cowtan
Feb 17, 2005·Journal of Molecular Biology·Ljudmila Borissenko, Michael Groll
Sep 16, 2006·The Journal of Biological Chemistry·Guy SchoehnBruno Franzetti
Dec 21, 2007·Acta Crystallographica. Section D, Biological Crystallography·Fei LongGarib N Murshudov
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Jul 8, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Sachiko TakahashiYoshihiro Urade
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Martyn D WinnKeith S Wilson
Oct 13, 2011·Molecular Systems Biology·Fabian SieversDesmond G Higgins
Mar 16, 2012·Doklady. Biochemistry and Biophysics·E S SlutskayaV M Lipkin
Apr 17, 2012·Acta Crystallographica. Section D, Biological Crystallography·Pavel V AfoninePaul D Adams
May 23, 2013·The Journal of Biological Chemistry·Alexandre AppolaireBruno Franzetti
Oct 24, 2013·Archaea : an International Microbiological Journal·Christopher J ReedCaryn Evilia
Oct 30, 2013·Nucleic Acids Research·Victor M MarkowitzNikos C Kyrpides
Jan 1, 1997·Methods in Enzymology·Zbyszek Otwinowski, Wladek Minor

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Citations

Nov 8, 2015·Biochimie·Alexandre AppolaireBruno Franzetti
Jul 30, 2015·European Biophysics Journal : EBJ·Elvira SlutskayaVladimir Popov
Jun 6, 2018·Journal of Bacteriology·Hind BasbousBruno Franzetti
Dec 1, 2018·Emerging Topics in Life Sciences·Julie A Maupin-Furlow
Oct 16, 2019·The Journal of Biological Chemistry·Raphaël DutoitLouis Droogmans

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