• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of embojLink to Publisher's site
EMBO J. Feb 15, 1999; 18(4): 793–803.
PMCID: PMC1171172

Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S.


The lysosomal cysteine proteases cathepsins S and L play crucial roles in the degradation of the invariant chain during maturation of MHC class II molecules and antigen processing. The p41 form of the invariant chain includes a fragment which specifically inhibits cathepsin L but not S. The crystal structure of the p41 fragment, a homologue of the thyroglobulin type-1 domains, has been determined at 2.0 A resolution in complex with cathepsin L. The structure of the p41 fragment demonstrates a novel fold, consisting of two subdomains, each stabilized by disulfide bridges. The first subdomain is an alpha-helix-beta-strand arrangement, whereas the second subdomain has a predominantly beta-strand arrangement. The wedge shape and three-loop arrangement of the p41 fragment bound to the active site cleft of cathepsin L are reminiscent of the inhibitory edge of cystatins, thus demonstrating the first example of convergent evolution observed in cysteine protease inhibitors. However, the different fold of the p41 fragment results in additional contacts with the top of the R-domain of the enzymes, which defines the specificity-determining S2 and S1' substrate-binding sites. This enables inhibitors based on the thyroglobulin type-1 domain fold, in contrast to the rather non-selective cystatins, to exhibit specificity for their target enzymes.

Full Text

The Full Text of this article is available as a PDF (719K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Alliel PM, Perin JP, Jollès P, Bonnet FJ. Testican, a multidomain testicular proteoglycan resembling modulators of cell social behaviour. Eur J Biochem. 1993 May 15;214(1):347–350. [PubMed]
  • Ashkenas J, Muschler J, Bissell MJ. The extracellular matrix in epithelial biology: shared molecules and common themes in distant phyla. Dev Biol. 1996 Dec 15;180(2):433–444. [PMC free article] [PubMed]
  • Aumailley M, Battaglia C, Mayer U, Reinhardt D, Nischt R, Timpl R, Fox JW. Nidogen mediates the formation of ternary complexes of basement membrane components. Kidney Int. 1993 Jan;43(1):7–12. [PubMed]
  • Bevec T, Stoka V, Pungercic G, Dolenc I, Turk V. Major histocompatibility complex class II-associated p41 invariant chain fragment is a strong inhibitor of lysosomal cathepsin L. J Exp Med. 1996 Apr 1;183(4):1331–1338. [PMC free article] [PubMed]
  • Bode W, Huber R. Natural protein proteinase inhibitors and their interaction with proteinases. Eur J Biochem. 1992 Mar 1;204(2):433–451. [PubMed]
  • Brinkman A, Groffen C, Kortleve DJ, Geurts van Kessel A, Drop SL. Isolation and characterization of a cDNA encoding the low molecular weight insulin-like growth factor binding protein (IBP-1). EMBO J. 1988 Aug;7(8):2417–2423. [PMC free article] [PubMed]
  • Chapman HA. Endosomal proteolysis and MHC class II function. Curr Opin Immunol. 1998 Feb;10(1):93–102. [PubMed]
  • Coulombe R, Grochulski P, Sivaraman J, Ménard R, Mort JS, Cygler M. Structure of human procathepsin L reveals the molecular basis of inhibition by the prosegment. EMBO J. 1996 Oct 15;15(20):5492–5503. [PMC free article] [PubMed]
  • Cresswell P. Invariant chain structure and MHC class II function. Cell. 1996 Feb 23;84(4):505–507. [PubMed]
  • Cubbage ML, Suwanichkul A, Powell DR. Insulin-like growth factor binding protein-3. Organization of the human chromosomal gene and demonstration of promoter activity. J Biol Chem. 1990 Jul 25;265(21):12642–12649. [PubMed]
  • Cygler M, Sivaraman J, Grochulski P, Coulombe R, Storer AC, Mort JS. Structure of rat procathepsin B: model for inhibition of cysteine protease activity by the proregion. Structure. 1996 Apr 15;4(4):405–416. [PubMed]
  • Deussing J, Roth W, Saftig P, Peters C, Ploegh HL, Villadangos JA. Cathepsins B and D are dispensable for major histocompatibility complex class II-mediated antigen presentation. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4516–4521. [PMC free article] [PubMed]
  • Downing AK, Driscoll PC, Harvey TS, Dudgeon TJ, Smith BO, Baron M, Campbell ID. Solution structure of the fibrin binding finger domain of tissue-type plasminogen activator determined by 1H nuclear magnetic resonance. J Mol Biol. 1992 Jun 5;225(3):821–833. [PubMed]
  • Drake FH, Dodds RA, James IE, Connor JR, Debouck C, Richardson S, Lee-Rykaczewski E, Coleman L, Rieman D, Barthlow R, et al. Cathepsin K, but not cathepsins B, L, or S, is abundantly expressed in human osteoclasts. J Biol Chem. 1996 May 24;271(21):12511–12516. [PubMed]
  • Fowlkes JL, Thrailkill KM, George-Nascimento C, Rosenberg CK, Serra DM. Heparin-binding, highly basic regions within the thyroglobulin type-1 repeat of insulin-like growth factor (IGF)-binding proteins (IGFBPs) -3, -5, and -6 inhibit IGFBP-4 degradation. Endocrinology. 1997 Jun;138(6):2280–2285. [PubMed]
  • Fineschi B, Miller J. Endosomal proteases and antigen processing. Trends Biochem Sci. 1997 Oct;22(10):377–382. [PubMed]
  • Fineschi B, Arneson LS, Naujokas MF, Miller J. Proteolysis of major histocompatibility complex class II-associated invariant chain is regulated by the alternatively spliced gene product, p41. Proc Natl Acad Sci U S A. 1995 Oct 24;92(22):10257–10261. [PMC free article] [PubMed]
  • Fujishima A, Imai Y, Nomura T, Fujisawa Y, Yamamoto Y, Sugawara T. The crystal structure of human cathepsin L complexed with E-64. FEBS Lett. 1997 Apr 21;407(1):47–50. [PubMed]
  • Germain RN, Margulies DH. The biochemistry and cell biology of antigen processing and presentation. Annu Rev Immunol. 1993;11:403–450. [PubMed]
  • Goldberg AL, Rock KL. Proteolysis, proteasomes and antigen presentation. Nature. 1992 Jun 4;357(6377):375–379. [PubMed]
  • Groves MR, Taylor MA, Scott M, Cummings NJ, Pickersgill RW, Jenkins JA. The prosequence of procaricain forms an alpha-helical domain that prevents access to the substrate-binding cleft. Structure. 1996 Oct 15;4(10):1193–1203. [PubMed]
  • Guncar G, Podobnik M, Pungercar J, Strukelj B, Turk V, Turk D. Crystal structure of porcine cathepsin H determined at 2.1 A resolution: location of the mini-chain C-terminal carboxyl group defines cathepsin H aminopeptidase function. Structure. 1998 Jan 15;6(1):51–61. [PubMed]
  • Holm L, Sander C. Alignment of three-dimensional protein structures: network server for database searching. Methods Enzymol. 1996;266:653–662. [PubMed]
  • Illy C, Quraishi O, Wang J, Purisima E, Vernet T, Mort JS. Role of the occluding loop in cathepsin B activity. J Biol Chem. 1997 Jan 10;272(2):1197–1202. [PubMed]
  • Lenarcic B, Bevec T. Thyropins--new structurally related proteinase inhibitors. Biol Chem. 1998 Feb;379(2):105–111. [PubMed]
  • Lenarcic B, Ritonja A, Strukelj B, Turk B, Turk V. Equistatin, a new inhibitor of cysteine proteinases from Actinia equina, is structurally related to thyroglobulin type-1 domain. J Biol Chem. 1997 May 23;272(21):13899–13903. [PubMed]
  • Llewellyn LE, Bell PM, Moczydlowski EG. Phylogenetic survey of soluble saxitoxin-binding activity in pursuit of the function and molecular evolution of saxiphilin, a relative of transferrin. Proc Biol Sci. 1997 Jun 22;264(1383):891–902. [PMC free article] [PubMed]
  • Linnenbach AJ, Wojcierowski J, Wu SA, Pyrc JJ, Ross AH, Dietzschold B, Speicher D, Koprowski H. Sequence investigation of the major gastrointestinal tumor-associated antigen gene family, GA733. Proc Natl Acad Sci U S A. 1989 Jan;86(1):27–31. [PMC free article] [PubMed]
  • McGrath ME, Palmer JT, Brömme D, Somoza JR. Crystal structure of human cathepsin S. Protein Sci. 1998 Jun;7(6):1294–1302. [PMC free article] [PubMed]
  • Mellman I, Pierre P, Amigorena S. Lonely MHC molecules seeking immunogenic peptides for meaningful relationships. Curr Opin Cell Biol. 1995 Aug;7(4):564–572. [PubMed]
  • Molina F, Bouanani M, Pau B, Granier C. Characterization of the type-1 repeat from thyroglobulin, a cysteine-rich module found in proteins from different families. Eur J Biochem. 1996 Aug 15;240(1):125–133. [PubMed]
  • Molina F, Pau B, Granier C. The type-1 repeats of thyroglobulin regulate thyroglobulin degradation and T3, T4 release in thyrocytes. FEBS Lett. 1996 Aug 12;391(3):229–231. [PubMed]
  • Morabito MA, Moczydlowski E. Molecular cloning of bullfrog saxiphilin: a unique relative of the transferrin family that binds saxitoxin. Proc Natl Acad Sci U S A. 1994 Mar 29;91(7):2478–2482. [PMC free article] [PubMed]
  • Musil D, Zucic D, Turk D, Engh RA, Mayr I, Huber R, Popovic T, Turk V, Towatari T, Katunuma N, et al. The refined 2.15 A X-ray crystal structure of human liver cathepsin B: the structural basis for its specificity. EMBO J. 1991 Sep;10(9):2321–2330. [PMC free article] [PubMed]
  • Nagayoshi T, Sanborn D, Hickok NJ, Olsen DR, Fazio MJ, Chu ML, Knowlton R, Mann K, Deutzmann R, Timpl R, et al. Human nidogen: complete amino acid sequence and structural domains deduced from cDNAs, and evidence for polymorphism of the gene. DNA. 1989 Oct;8(8):581–594. [PubMed]
  • Nakagawa T, Roth W, Wong P, Nelson A, Farr A, Deussing J, Villadangos JA, Ploegh H, Peters C, Rudensky AY. Cathepsin L: critical role in Ii degradation and CD4 T cell selection in the thymus. Science. 1998 Apr 17;280(5362):450–453. [PubMed]
  • Newcomb JR, Cresswell P. Characterization of endogenous peptides bound to purified HLA-DR molecules and their absence from invariant chain-associated alpha beta dimers. J Immunol. 1993 Jan 15;150(2):499–507. [PubMed]
  • Nicholls A, Sharp KA, Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991;11(4):281–296. [PubMed]
  • Ogrinc T, Dolenc I, Ritonja A, Turk V. Purification of the complex of cathepsin L and the MHC class II-associated invariant chain fragment from human kidney. FEBS Lett. 1993 Dec 28;336(3):555–559. [PubMed]
  • O'Sullivan DM, Noonan D, Quaranta V. Four Ia invariant chain forms derive from a single gene by alternate splicing and alternate initiation of transcription/translation. J Exp Med. 1987 Aug 1;166(2):444–460. [PMC free article] [PubMed]
  • Peterson M, Miller J. Antigen presentation enhanced by the alternatively spliced invariant chain gene product p41. Nature. 1992 Jun 18;357(6379):596–598. [PubMed]
  • Pierre P, Mellman I. Developmental regulation of invariant chain proteolysis controls MHC class II trafficking in mouse dendritic cells. Cell. 1998 Jun 26;93(7):1135–1145. [PubMed]
  • Podobnik M, Kuhelj R, Turk V, Turk D. Crystal structure of the wild-type human procathepsin B at 2.5 A resolution reveals the native active site of a papain-like cysteine protease zymogen. J Mol Biol. 1997 Sep 5;271(5):774–788. [PubMed]
  • Riese RJ, Wolf PR, Brömme D, Natkin LR, Villadangos JA, Ploegh HL, Chapman HA. Essential role for cathepsin S in MHC class II-associated invariant chain processing and peptide loading. Immunity. 1996 Apr;4(4):357–366. [PubMed]
  • Riese RJ, Mitchell RN, Villadangos JA, Shi GP, Palmer JT, Karp ER, De Sanctis GT, Ploegh HL, Chapman HA. Cathepsin S activity regulates antigen presentation and immunity. J Clin Invest. 1998 Jun 1;101(11):2351–2363. [PMC free article] [PubMed]
  • Roche PA, Cresswell P. Proteolysis of the class II-associated invariant chain generates a peptide binding site in intracellular HLA-DR molecules. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3150–3154. [PMC free article] [PubMed]
  • Rodriguez GM, Diment S. Destructive proteolysis by cysteine proteases in antigen presentation of ovalbumin. Eur J Immunol. 1995 Jul;25(7):1823–1827. [PubMed]
  • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993 Dec 5;234(3):779–815. [PubMed]
  • Strnad J, Hamilton AE, Beavers LS, Gamboa GC, Apelgren LD, Taber LD, Sportsman JR, Bumol TF, Sharp JD, Gadski RA. Molecular cloning and characterization of a human adenocarcinoma/epithelial cell surface antigen complementary DNA. Cancer Res. 1989 Jan 15;49(2):314–317. [PubMed]
  • Strubin M, Berte C, Mach B. Alternative splicing and alternative initiation of translation explain the four forms of the Ia antigen-associated invariant chain. EMBO J. 1986 Dec 20;5(13):3483–3488. [PMC free article] [PubMed]
  • Stubbs MT, Laber B, Bode W, Huber R, Jerala R, Lenarcic B, Turk V. The refined 2.4 A X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction. EMBO J. 1990 Jun;9(6):1939–1947. [PMC free article] [PubMed]
  • Turk B, Turk V, Turk D. Structural and functional aspects of papain-like cysteine proteinases and their protein inhibitors. Biol Chem. 1997 Mar-Apr;378(3-4):141–150. [PubMed]
  • Turk D, Podobnik M, Kuhelj R, Dolinar M, Turk V. Crystal structures of human procathepsin B at 3.2 and 3.3 Angstroms resolution reveal an interaction motif between a papain-like cysteine protease and its propeptide. FEBS Lett. 1996 Apr 22;384(3):211–214. [PubMed]
  • Turk D, Guncar G, Podobnik M, Turk B. Revised definition of substrate binding sites of papain-like cysteine proteases. Biol Chem. 1998 Feb;379(2):137–147. [PubMed]
  • Yamashita M, Konagaya S. A novel cysteine protease inhibitor of the egg of chum salmon, containing a cysteine-rich thyroglobulin-like motif. J Biol Chem. 1996 Jan 19;271(3):1282–1284. [PubMed]

Articles from The EMBO Journal are provided here courtesy of The European Molecular Biology Organization


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...