Crystal structure of gyra intein from mycobacterium xenopi reveals structural basis of protein splicing

Crystal structure of gyra intein from mycobacterium xenopi reveals structural basis of protein splicing

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ABSTRACT Several genes from prokaryotes and lower eukaryotes have been found to contain an in-frame open reading frame, which encodes for an _in_ternal pro_tein_ (intein). Post-translationally, the internal polypeptide auto-splices and ligates the external sequences to yield a functional external pro_tein_ (extein) and an intein. Most, but not all inteins, contain, apart from a splicing domain, a separate endonucleolytic domain that enables them to maintain their presence by a homing mechanism. We report here the crystal structure of an intein found in the gyrase A subunit from _Mycobacterium xenopi_ at 2.2 Å resolution. The structure contains an unusual β-fold with the catalytic splice junctions at the ends of two adjacent antiparallel β-strands. The arrangement of the active site residues Ser 1, Thr 72, His 75, His 197, and Asn 198 is consistent with a four-step mechanism for the cleavage–ligation reaction. Using site-directed mutagenesis, the N-terminal cysteine, proposed as the nucleophile in the first step of the splicing reaction, was changed to a Ser 1 and Ala 0, thus capturing the intein in a pre-spliced state. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS OPTIONS Access through your institution Subscribe to this journal Receive 12 print issues and online access $209.00 per year only $17.42 per issue Learn more Buy this article * Purchase on SpringerLink * Instant access to full article PDF Buy now Prices may be subject to local taxes which are calculated during checkout ADDITIONAL ACCESS OPTIONS: * Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS AN ALTERNATIVE DOMAIN-SWAPPED STRUCTURE OF THE _PYROCOCCUS HORIKOSHII_ POLII MINI-INTEIN Article Open access 03 June 2021 CONDITIONAL PROTEIN SPLICING OF THE _MYCOBACTERIUM TUBERCULOSIS_ RECA INTEIN IN ITS NATIVE HOST Article Open access 05 September 2024 INOSITOL HEXAKISPHOSPHATE IS REQUIRED FOR INTEGRATOR FUNCTION Article Open access 30 September 2022 REFERENCES * Perler, F.B. _et al_. Protein splicing elements: Inteins and exteins—a definition of terms and recommended nomenclature. _Nucleic Acids Res._ 22, 1125–1127 (1994). Article  CAS  Google Scholar  * Cooper, A.A. & Stevens, T.H. Protein splicing: self-splicing of genetically mobile elements at the protein level. _Trends Biochem. Sci._ 20, 351–356 (1995). Article  CAS  Google Scholar  * Guan, C. _et al_. Activation of glycosylasparaginase. Formation of active N-terminal threonine by intramolecular autoproteolysis. _J. Biol. Chem._ 271, 1732–1737 (1996). Article  CAS  Google Scholar  * Porter, J.A. _et al_. Hedgehog patterning activity: role of a lipophilic modification mediated by the carboxy-terminal autoprocessing domain. _Cell_ 86, 21–34 (1996). Article  CAS  Google Scholar  * van Poelje, P.D. & Snell, E.E. Pyruvoyl-dependent enzymes. _Annu. Rev. Biochem._ 59, 29–59 (1990). Article  CAS  Google Scholar  * Kane, P.M. _et al_. Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H+-adenosine triphosphatase. _Science_ 250, 651–657 (1990). Article  CAS  Google Scholar  * Perler, F.B., Olsen, G.J. & Adams, E. Compilation and analysis of intein sequences. _Nucleic Acids Res._ 25, 1087–1094 (1997). Article  CAS  Google Scholar  * Gimble, F.S. & Thorner, J. Homing of a DNA endonuclease gene by meiotic gene conversion in _Saccharomyces cerevisiae_. _Nature_ 357, 301–306 (1992). Article  CAS  Google Scholar  * Bremer, M.C.D., Gimble, F.S., Thorner, J. & Smith, C.L. VDE endonuclease cleaves _Saccharomyces cerevisiae_ genomic DNA at a single site: physical mapping of the VMA1 gene. _Nucleic Acids Res._ 20, 5484 (1992). Article  CAS  Google Scholar  * Pietrokovski, S. Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins. _Protein Sci._ 3, 2340–2350 (1994). Article  CAS  Google Scholar  * Perler, F.B. _et al_. Intervening sequences in an archaea DNA polymerase gene. _Proc. Natl. Acad. Sci. USA_ 89, 5577–5581 (1992). Article  CAS  Google Scholar  * Duan, X., Gimble, F.S. & Quiocho, F.A. Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. _Cell_ 89, 555–564 (1996). Article  Google Scholar  * Xu, M.-Q. & Perler, F.B. The mechanism of protein splicing and its modulation by mutation. _EMBO J._ 15, 5146–5153 (1996). Article  CAS  Google Scholar  * Davis, E.O. _et al_. Protein splicing in the maturation of _M. tuberculosis_ recA protein: a mechanism for tolerating a novel class of intervening sequence. _Cell_ 71, 201–210 (1992). Article  CAS  Google Scholar  * Hirata, R. & Anraku, Y. Mutations at the putative junction sites of the yeast VMA1 protein, the catalytic subunit of the vacuolar membrane H+-ATPase, inhibit its processing by protein splicing. _Biochem. Biophys. Res. Comm._ 188, 40–47 (1992). Article  CAS  Google Scholar  * Cooper, A.A., Chen, Y., Lindorfer, M.A. & Stevens, T.H. Protein splicing of the yeast TFP1 intervening protein sequence: a model of self-excision. _EMBO J._ 12, 2575–2583 (1993). Article  CAS  Google Scholar  * Xu, M.-Q. _et al_. Protein splicing: an analysis of the branched intermediate and its resolution by succinimide formation. _EMBO J._ 13, 5517–5522 (1994). Article  CAS  Google Scholar  * Dawson, P.E., Muir, T.W., Clark-Lewis, I. & Kent, S.B. Synthesis of proteins by native chemical ligation. _Science_ 266, 776–779 (1994). Article  CAS  Google Scholar  * Storer, A.C. & Ménard, R. Catalytic mechanism in papain family of cysteine peptidases. _Meth. Enz._ 244, 486–500 (1994). Article  CAS  Google Scholar  * Drenth, J., Jansonius, J.N., Koekoek, R., Swen, H.M. & Wolthers, B.G. Structure of papain. _Nature_ 218, 929–932 (1968). Article  CAS  Google Scholar  * Ramachandran, G.N. & Mitra, A.K. An explanation for the rare occurrence of _cis_ peptide units in proteins and polypeptides. _J. Mol. Biol._ 107, 85–92 (1976). Article  CAS  Google Scholar  * Fsihi, H., Vincent, V. & Cole, S.T. Homing events in the gyrA gene of some mycobacteria. _Proc. Natl. Acad. Sci. USA_ 93, 3410–3415 (1996). Article  CAS  Google Scholar  * Oinonen, C., Tikkanen, R., Rouvinen, J. & Peltonen, L. Three-dimensional structure of human lyosomal aspartylglucosaminidase. _Nature Struct. Biol._ 2, 1102–1107 (1995). Article  CAS  Google Scholar  * Smith, J.L. _et al_. Structure of the allosteric regulatory enzyme of purine biosynthesis. _Science_ 264, 1427–1433 (1994). Article  CAS  Google Scholar  * Duggleby, H.J. _et al_. Penicillin acylase has a single-amino-acid catalytic center. _Nature_ 373, 264–268 (1995). Article  CAS  Google Scholar  * Löwe, J. _et al_. Crystal structure of the 20S proteasome from the archaeon _T. acidophilum_ at 3.4 Å resolution. _Science_ 268, 533–539 (1995). Article  Google Scholar  * Brannigan, J.A. _et al_. A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. _Nature_ 378, 416–419 (1995). Article  CAS  Google Scholar  * Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data in oscillation mode. _Meth. Enz._ 276, 307–326 (1997). Article  CAS  Google Scholar  * Collaborative Computational Project No. 4. The CCP4 suite: programs for protein crystallography. _Acta Crystallogr. D_ 50, 760–763 (1994). * Furey, W. & Swaminathan, S. PHASES. _Am. Crystallogr. Assoc. Annu. Mtg. Program. Abstr._ 18, 73 (1990). Google Scholar  * Jones, T.A., Zou, J.-Y., Kjelgaard, M. & Cowan, S.W. Improved methods for building protein models in electron-density maps and the location of errors in these models. _Acta Crystallogr. A_ 47, 110–119 (1991). Article  Google Scholar  * Brünger, A. _X-PLOR Version 3.1: A System for X-ray crystallography and NMR_. (Yale University Press, New Haven, Connecticut; 1992). Google Scholar  * Evans, S.V. SETOR: hardware lighted three-dimensional solid model representations of macromolecules. _J. Mol. Graphics_ 11, 134–138 (1993). Article  CAS  Google Scholar  * Hall, T.M.T. _et al_. Crystal structure of a hedgehog autoprocessing domain: homology between hedgehog and self-splicing proteins. _Cell_ 91, 85–97 (1997). Article  CAS  Google Scholar  Download references AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA Thomas Klabunde, Sujata Sharma & James C. Sacchettini * Institute for Medical Microbiology, University of Bern, 3010, Bern, Switzerland Amalio Telenti * Departments of Microbiology and Immunology and Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New York, 10461, USA William R. Jacobs Jr. Authors * Thomas Klabunde View author publications You can also search for this author inPubMed Google Scholar * Sujata Sharma View author publications You can also search for this author inPubMed Google Scholar * Amalio Telenti View author publications You can also search for this author inPubMed Google Scholar * William R. Jacobs Jr. View author publications You can also search for this author inPubMed Google Scholar * James C. Sacchettini View author publications You can also search for this author inPubMed Google Scholar CORRESPONDING AUTHOR Correspondence to James C. Sacchettini. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Klabunde, T., Sharma, S., Telenti, A. _et al._ Crystal structure of GyrA intein from _Mycobacterium xenopi_ reveals structural basis of protein splicing. _Nat Struct Mol Biol_ 5, 31–36 (1998). https://doi.org/10.1038/nsb0198-31 Download citation * Received: 28 September 1997 * Accepted: 07 November 1997 * Issue Date: 01 January 1998 * DOI: https://doi.org/10.1038/nsb0198-31 SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not currently available for this article. Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative

ABSTRACT Several genes from prokaryotes and lower eukaryotes have been found to contain an in-frame open reading frame, which encodes for an _in_ternal pro_tein_ (intein).


Post-translationally, the internal polypeptide auto-splices and ligates the external sequences to yield a functional external pro_tein_ (extein) and an intein. Most, but not all inteins,


contain, apart from a splicing domain, a separate endonucleolytic domain that enables them to maintain their presence by a homing mechanism. We report here the crystal structure of an intein


found in the gyrase A subunit from _Mycobacterium xenopi_ at 2.2 Å resolution. The structure contains an unusual β-fold with the catalytic splice junctions at the ends of two adjacent


antiparallel β-strands. The arrangement of the active site residues Ser 1, Thr 72, His 75, His 197, and Asn 198 is consistent with a four-step mechanism for the cleavage–ligation reaction.


Using site-directed mutagenesis, the N-terminal cysteine, proposed as the nucleophile in the first step of the splicing reaction, was changed to a Ser 1 and Ala 0, thus capturing the intein


in a pre-spliced state. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS OPTIONS Access through your institution


Subscribe to this journal Receive 12 print issues and online access $209.00 per year only $17.42 per issue Learn more Buy this article * Purchase on SpringerLink * Instant access to full


article PDF Buy now Prices may be subject to local taxes which are calculated during checkout ADDITIONAL ACCESS OPTIONS: * Log in * Learn about institutional subscriptions * Read our FAQs *


Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS AN ALTERNATIVE DOMAIN-SWAPPED STRUCTURE OF THE _PYROCOCCUS HORIKOSHII_ POLII MINI-INTEIN Article Open access 03 June 2021


CONDITIONAL PROTEIN SPLICING OF THE _MYCOBACTERIUM TUBERCULOSIS_ RECA INTEIN IN ITS NATIVE HOST Article Open access 05 September 2024 INOSITOL HEXAKISPHOSPHATE IS REQUIRED FOR INTEGRATOR


FUNCTION Article Open access 30 September 2022 REFERENCES * Perler, F.B. _et al_. Protein splicing elements: Inteins and exteins—a definition of terms and recommended nomenclature. _Nucleic


Acids Res._ 22, 1125–1127 (1994). Article  CAS  Google Scholar  * Cooper, A.A. & Stevens, T.H. Protein splicing: self-splicing of genetically mobile elements at the protein level.


_Trends Biochem. Sci._ 20, 351–356 (1995). Article  CAS  Google Scholar  * Guan, C. _et al_. Activation of glycosylasparaginase. Formation of active N-terminal threonine by intramolecular


autoproteolysis. _J. Biol. Chem._ 271, 1732–1737 (1996). Article  CAS  Google Scholar  * Porter, J.A. _et al_. Hedgehog patterning activity: role of a lipophilic modification mediated by the


carboxy-terminal autoprocessing domain. _Cell_ 86, 21–34 (1996). Article  CAS  Google Scholar  * van Poelje, P.D. & Snell, E.E. Pyruvoyl-dependent enzymes. _Annu. Rev. Biochem._ 59,


29–59 (1990). Article  CAS  Google Scholar  * Kane, P.M. _et al_. Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H+-adenosine triphosphatase.


_Science_ 250, 651–657 (1990). Article  CAS  Google Scholar  * Perler, F.B., Olsen, G.J. & Adams, E. Compilation and analysis of intein sequences. _Nucleic Acids Res._ 25, 1087–1094


(1997). Article  CAS  Google Scholar  * Gimble, F.S. & Thorner, J. Homing of a DNA endonuclease gene by meiotic gene conversion in _Saccharomyces cerevisiae_. _Nature_ 357, 301–306


(1992). Article  CAS  Google Scholar  * Bremer, M.C.D., Gimble, F.S., Thorner, J. & Smith, C.L. VDE endonuclease cleaves _Saccharomyces cerevisiae_ genomic DNA at a single site: physical


mapping of the VMA1 gene. _Nucleic Acids Res._ 20, 5484 (1992). Article  CAS  Google Scholar  * Pietrokovski, S. Conserved sequence features of inteins (protein introns) and their use in


identifying new inteins and related proteins. _Protein Sci._ 3, 2340–2350 (1994). Article  CAS  Google Scholar  * Perler, F.B. _et al_. Intervening sequences in an archaea DNA polymerase


gene. _Proc. Natl. Acad. Sci. USA_ 89, 5577–5581 (1992). Article  CAS  Google Scholar  * Duan, X., Gimble, F.S. & Quiocho, F.A. Crystal structure of PI-SceI, a homing endonuclease with


protein splicing activity. _Cell_ 89, 555–564 (1996). Article  Google Scholar  * Xu, M.-Q. & Perler, F.B. The mechanism of protein splicing and its modulation by mutation. _EMBO J._ 15,


5146–5153 (1996). Article  CAS  Google Scholar  * Davis, E.O. _et al_. Protein splicing in the maturation of _M. tuberculosis_ recA protein: a mechanism for tolerating a novel class of


intervening sequence. _Cell_ 71, 201–210 (1992). Article  CAS  Google Scholar  * Hirata, R. & Anraku, Y. Mutations at the putative junction sites of the yeast VMA1 protein, the catalytic


subunit of the vacuolar membrane H+-ATPase, inhibit its processing by protein splicing. _Biochem. Biophys. Res. Comm._ 188, 40–47 (1992). Article  CAS  Google Scholar  * Cooper, A.A., Chen,


Y., Lindorfer, M.A. & Stevens, T.H. Protein splicing of the yeast TFP1 intervening protein sequence: a model of self-excision. _EMBO J._ 12, 2575–2583 (1993). Article  CAS  Google


Scholar  * Xu, M.-Q. _et al_. Protein splicing: an analysis of the branched intermediate and its resolution by succinimide formation. _EMBO J._ 13, 5517–5522 (1994). Article  CAS  Google


Scholar  * Dawson, P.E., Muir, T.W., Clark-Lewis, I. & Kent, S.B. Synthesis of proteins by native chemical ligation. _Science_ 266, 776–779 (1994). Article  CAS  Google Scholar  *


Storer, A.C. & Ménard, R. Catalytic mechanism in papain family of cysteine peptidases. _Meth. Enz._ 244, 486–500 (1994). Article  CAS  Google Scholar  * Drenth, J., Jansonius, J.N.,


Koekoek, R., Swen, H.M. & Wolthers, B.G. Structure of papain. _Nature_ 218, 929–932 (1968). Article  CAS  Google Scholar  * Ramachandran, G.N. & Mitra, A.K. An explanation for the


rare occurrence of _cis_ peptide units in proteins and polypeptides. _J. Mol. Biol._ 107, 85–92 (1976). Article  CAS  Google Scholar  * Fsihi, H., Vincent, V. & Cole, S.T. Homing events


in the gyrA gene of some mycobacteria. _Proc. Natl. Acad. Sci. USA_ 93, 3410–3415 (1996). Article  CAS  Google Scholar  * Oinonen, C., Tikkanen, R., Rouvinen, J. & Peltonen, L.


Three-dimensional structure of human lyosomal aspartylglucosaminidase. _Nature Struct. Biol._ 2, 1102–1107 (1995). Article  CAS  Google Scholar  * Smith, J.L. _et al_. Structure of the


allosteric regulatory enzyme of purine biosynthesis. _Science_ 264, 1427–1433 (1994). Article  CAS  Google Scholar  * Duggleby, H.J. _et al_. Penicillin acylase has a single-amino-acid


catalytic center. _Nature_ 373, 264–268 (1995). Article  CAS  Google Scholar  * Löwe, J. _et al_. Crystal structure of the 20S proteasome from the archaeon _T. acidophilum_ at 3.4 Å


resolution. _Science_ 268, 533–539 (1995). Article  Google Scholar  * Brannigan, J.A. _et al_. A protein catalytic framework with an N-terminal nucleophile is capable of self-activation.


_Nature_ 378, 416–419 (1995). Article  CAS  Google Scholar  * Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data in oscillation mode. _Meth. Enz._ 276, 307–326 (1997).


Article  CAS  Google Scholar  * Collaborative Computational Project No. 4. The CCP4 suite: programs for protein crystallography. _Acta Crystallogr. D_ 50, 760–763 (1994). * Furey, W. &


Swaminathan, S. PHASES. _Am. Crystallogr. Assoc. Annu. Mtg. Program. Abstr._ 18, 73 (1990). Google Scholar  * Jones, T.A., Zou, J.-Y., Kjelgaard, M. & Cowan, S.W. Improved methods for


building protein models in electron-density maps and the location of errors in these models. _Acta Crystallogr. A_ 47, 110–119 (1991). Article  Google Scholar  * Brünger, A. _X-PLOR Version


3.1: A System for X-ray crystallography and NMR_. (Yale University Press, New Haven, Connecticut; 1992). Google Scholar  * Evans, S.V. SETOR: hardware lighted three-dimensional solid model


representations of macromolecules. _J. Mol. Graphics_ 11, 134–138 (1993). Article  CAS  Google Scholar  * Hall, T.M.T. _et al_. Crystal structure of a hedgehog autoprocessing domain:


homology between hedgehog and self-splicing proteins. _Cell_ 91, 85–97 (1997). Article  CAS  Google Scholar  Download references AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of


Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA Thomas Klabunde, Sujata Sharma & James C. Sacchettini * Institute for Medical Microbiology,


University of Bern, 3010, Bern, Switzerland Amalio Telenti * Departments of Microbiology and Immunology and Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New


York, 10461, USA William R. Jacobs Jr. Authors * Thomas Klabunde View author publications You can also search for this author inPubMed Google Scholar * Sujata Sharma View author publications


You can also search for this author inPubMed Google Scholar * Amalio Telenti View author publications You can also search for this author inPubMed Google Scholar * William R. Jacobs Jr.


View author publications You can also search for this author inPubMed Google Scholar * James C. Sacchettini View author publications You can also search for this author inPubMed Google


Scholar CORRESPONDING AUTHOR Correspondence to James C. Sacchettini. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Klabunde, T., Sharma, S., Telenti,


A. _et al._ Crystal structure of GyrA intein from _Mycobacterium xenopi_ reveals structural basis of protein splicing. _Nat Struct Mol Biol_ 5, 31–36 (1998).


https://doi.org/10.1038/nsb0198-31 Download citation * Received: 28 September 1997 * Accepted: 07 November 1997 * Issue Date: 01 January 1998 * DOI: https://doi.org/10.1038/nsb0198-31 SHARE


THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not currently available for this article. Copy to


clipboard Provided by the Springer Nature SharedIt content-sharing initiative