Crystal structure of Proteus vulgaris chondroitin sulfate ABC lyase I at 1.9 Å resolution

Journal of Molecular Biology

Volumn 328, Issue 3, 2003, Pages 623-634

  Huang, Weijun ^a,b,e   Lunin, Vladimir V ^a,b   Li, Yunge ^a,b   Suzuki, Sakaru ^c   Sugiura, Nobuo ^c,d   Miyazono, Hirofumi ^d   Cygler, Miroslaw ^a,b  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^b Montreal Jt Ctr for Struct Biol   (Canada)

^c AICHI MEDICAL UNIVERSITY   (Japan)

^d SEIKAGAKU CORPORATION   (Japan)

^e UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Catalytic site; Chondroitin sulfate; GAG lyase ABC; Glycosaminoglycan lyase; elimination

Indexed keywords

BACTERIAL ENZYME; CHONDROITIN ABC LYASE; HYALURONIDASE; LECTIN; TRYPTOPHAN; XYLAN ENDO 1,3 BETA XYLOSIDASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTAL STRUCTURE; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEUS VULGARIS;

BACTERIA (MICROORGANISMS); PROTEUS VULGARIS;

EID: 0037414435     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00345-0     Document Type: Article

References (39)

1. Scott J.E. Extracellular matrix, supramolecular organisation and shape. J. Anat. 187:1995;259-269.
2. Iozzo R.V. Matrix proteoglycans: from molecular design to cellular function. Annu. Rev. Biochem. 67:1998;609-652.
3. Ernst S., Langer R., Cooney C.L., Sasisekharan R. Enzymatic degradation of glycosaminoglycans. Crit. Rev. Biochem. Mol. Biol. 30:1995;387-444.
4. Prydz K., Dalen K.T. Synthesis and sorting of proteoglycans. J. Cell Sci. Pt. 113. 2:2000;193-205.
5. Sawitzky D. Protein-glycosaminoglycan interactions: infectiological aspects. Med. Microbiol. Immunol. 184:1996;155-161.
6. Sutherland I.W. Polysaccharide lyases. FEMS Microbiol. Rev. 16:1995;323-347.
7. Imanari T., Toida T., Koshiishi I., Toyoda H. High-performance liquid chromatographic analysis of glycosaminoglycan-derived oligosaccharides. J. Chromatog. Sect. A. 720:1996;275-293.
8. Su H., Blain F., Musil R.A., Zimmermann J.J., Gu K., Bennett D.C. Isolation and expression in Escherichia coli of hepB and hepC, genes coding for the glycosaminoglycan-degrading enzymes heparinase II and heparinase III, respectively, from Flavobacterium heparinum. Appl. Environ. Microbiol. 62:1996;2723-2734.
9. Farrell A.M., Taylor D., Holland K.T. Cloning, nucleotide sequence determination and expression of the Staphylococcus aureus hyaluronate lyase gene. FEMS Microbiol. Letters. 130:1995;81-85.
10. Canard B., Garnier T., Saint-Joanis B., Cole S.T. Molecular genetic analysis of the nagH gene encoding a hyaluronidase of Clostridium perfringens. Mol. Gen. Genet. 243:1994;215-224.
11. Hynes W.L., Hancock L., Ferretti J.J. Analysis of a second bacteriophage hyaluronidase gene from Streptococcus pyogenes: evidence for a third hyaluronidase involved in extracellular enzymatic activity. Infect. Immun. 63:1995;3015-3020.
12. Berry A.M., Lock R.A., Thomas S.M., Rajan D.P., Hansman D., Paton J.C. Cloning and nucleotide sequence of the Streptococcus pneumoniae hyaluronidase gene and purification of the enzyme from recombinant Escherichia coli. Infect. Immun. 62:1994;1101-1108.
13. Hamai A., Hashimoto N., Mochizuki H., Kato F., Makiguchi Y., Horie K., Suzuki S. Two distinct chondroitin sulfate ABC lyases. An endoeliminase yielding tetrasaccharides and an exoeliminase preferentially acting on oligosaccharides. J. Biol. Chem. 272:1997;9123-9130.
14. Féthière J., Eggimann B., Cygler M. Crystal structure of chondroitin AC lyase, a representative of a family of glycosaminoglycan degrading enzymes. J. Mol. Biol. 288:1999;635-647.
15. Li S., Kelly S.J., Lamani E., Ferraroni M., Jedrzejas M.J. Structural basis of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. EMBO J. 19:2000;1228-1240.
16. Li S., Jedrzejas M.J. Hyaluronan binding and degradation by Streptococcus agalactiae hyaluronate lyase. J. Biol. Chem. 276:2001;41407-41416.
17. Huang W., Matte A., Li Y., Kim Y.S., Linhardt R.J., Su H., Cygler M. Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 Å resolution. J. Mol. Biol. 294:1999;1257-1269.
18. Zuo J., Neubauer D., Graham J., Krekoski C.A., Ferguson T.A., Muir D. Regeneration of axons after nerve transection repair is enhanced by degradation of chondroitin sulfate proteoglycan. Exptl. Neurol. 176:2002;221-228.
19. Bradbury E.J., Moon L.D., Popat R.J., King V.R., Bennett G.S., Patel P.N., et al. Chondroitinase ABC promotes functional recovery after spinal cord injury. Nature. 416:2002;636-640.
20. Olson L. Medicine: clearing a path for nerve growth. Nature. 416:2002;589-590.
21. Sato N., Shimada M., Nakajima H., Oda H., Kimura S. Cloning and expression in Escherichia coli of the gene encoding the Proteus vulgaris chondroitin ABC lyase. Appl. Microbiol. Biotechnol. 41:1994;39-46.
22. Yoon H.J., Mikami B., Hashimoto W., Murata K. Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 Å resolution. J. Mol. Biol. 290:1999;505-514.
23. Higgins D.G., Thompson J.D., Gibson T.J. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266:1996;383-402.
24. Lo C.L., Ailey B., Hubbard T.J., Brenner S.E., Murzin A.G., Chothia C. SCOP: a structural classification of proteins database. Nucl. Acids Res. 28:2000;257-259.
25. Holm L., Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucl. Acids Res. 25:1997;231-234.
26. Huang W., Boju L., Tkalec L., Su H., Yang H.O., Gunay N.S., et al. Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis. Biochemistry. 40:2001;2359-2372.
27. Gacesa P. Alginate-modifying enzymes. A proposed unified mechanism of action for the lyases and epimerases. FEBS Letters. 212:1987;199-202.
28. Huang W., Matte A., Suzuki S., Sugiura N., Miyazono H., Cygler M. Crystallization and preliminary X-ray analysis of chondroitin sulfate ABC lyases I and II from Proteus vulgaris. Acta Crystallog. sect. D. 56:2000;904-906.
29. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
30. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763.
31. Otwinowski Z. Maximum likelihood refinement of heavy atom parameters in isomorphous replacement and anormalous scattering. Wolf W., Evans P.R., Leslie A.G.W. Proceedings of the CCP4 study weekend. 1991;80-88 Daresbury Laboratory, Warrington, UK.
32. Cowtan K.D., Zhang K.Y. Density modification for macromolecular phase improvement. Prog. Biophys. Mol. Biol. 72:1999;245-270.
33. Kleywegt G.J., Jones T.A. Software for handling macromolecular envelopes. Acta Crystallog. sect. D. 55:1999;941-944.
34. Jones T.A., Zhou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
35. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D. 54:1998;905-921.
36. Read R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallog. sect. A. 42:1986;140-149.
37. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D. 53:1997;240-255.
38. Engh R.A., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallog. sect. A. 47:2002;392-400.
39. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.