Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; A widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families

BMC Structural Biology

Volumn 9, Issue , 2009, Pages

  Quistgaard, Esben M ^a,b   Thirup, Søren S ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; GLYCOSIDASE; PROTEIN VPS10; SORTILIN; UNCLASSIFIED DRUG; VESICULAR TRANSPORT PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ASPARTIC ACID BOX BETA PROPELLER MOTIF; ASPARTIC ACID BOX MOTIF; CLOSTRIDIUM PERFRINGENS; GENETIC CONSERVATION; GENETIC VARIABILITY; MATHEMATICAL COMPUTING; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN MOTIF; CHEMISTRY; MOLECULAR GENETICS; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; GLYCOSIDE HYDROLASES; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; VESICULAR TRANSPORT PROTEINS;

EID: 68149182718     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-9-46     Document Type: Article

References (60)

1. Conserved sequences in bacterial and viral sialidases. P Roggentin B Rothe JB Kaper J Galen L Lawrisuk ER Vimr R Schauer, Glycoconj J 1989 6 3 349 353 10.1007/BF01047853 2562507
2. Crystal structure of a bacterial sialidase (from Salmonella typhimurium LT2) shows the same fold as an influenza virus neuraminidase. SJ Crennell EF Garman WG Laver ER Vimr GL Taylor, Proc Natl Acad Sci USA 1993 90 21 9852 9856 8234325 10.1073/pnas.90.21.9852 (Pubitemid 23328208)
3. Sialidase-like Asp-boxes: sequence-similar structures within different protein folds. RR Copley RB Russell CP Ponting, Protein Sci 2001 10 2 285 292 11266614 10.1110/ps.31901 (Pubitemid 32225648)
4. Crystal structure of Vibrio cholerae neuraminidase reveals dual lectin-like domains in addition to the catalytic domain. S Crennell E Garman G Laver E Vimr G Taylor, Structure 1994 2 6 535 544 10.1016/S0969-2126(00)00053-8 7922030 (Pubitemid 2100410)
5. The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll. A Gaskell S Crennell G Taylor, Structure 1995 3 11 1197 1205 10.1016/S0969-2126(01)00255-6 8591030 (Pubitemid 3001427)
6. The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates. SL Newstead JA Potter JC Wilson G Xu CH Chien AG Watts SG Withers GL Taylor, J Biol Chem 2008 283 14 9080 9088 18218621 10.1074/jbc.M710247200
7. Structure of the catalytic domain of Streptococcus pneumoniae sialidase NanA. G Xu X Li PW Andrew GL Taylor, Acta Crystallogr Sect F Struct Biol Cryst Commun 2008 64 Pt 9 772 775 18765901 10.1107/S1744309108024044
8. Crystal structure of the NanB sialidase from Streptococcus pneumoniae. G Xu JA Potter RJ Russell MR Oggioni PW Andrew GL Taylor, J Mol Biol 2008 384 2 436 449 10.1016/j.jmb.2008.09.032 18835278
9. Structural Studies on the Pseudomonas aeruginosa Sialidase-Like Enzyme PA2794 Suggest Substrate and Mechanistic Variations. G Xu C Ryan MJ Kiefel JC Wilson GL Taylor, J Mol Biol 2009 386 3 828 40 10.1016/j.jmb.2008.12.084 19166860
10. Structural basis of sialyltransferase activity in trypanosomal sialidases. A Buschiazzo GA Tavares O Campetella S Spinelli ML Cremona G Paris MF Amaya AC Frasch PM Alzari, EMBO J 2000 19 1 16 24 10619840 10.1093/emboj/19.1.16
11. The crystal structure and mode of action of trans-sialidase, a key enzyme in Trypanosoma cruzi pathogenesis. A Buschiazzo MF Amaya ML Cremona AC Frasch PM Alzari, Mol Cell 2002 10 4 757 768 10.1016/S1097-2765(02)00680-9 12419220 (Pubitemid 35339437)
12. The crystal structure of an intramolecular trans-sialidase with a NeuAc alpha2 - 3Gal specificity. Y Luo SC Li MY Chou YT Li M Luo, Structure 1998 6 4 521 530 10.1016/S0969-2126(98)00053-7 9562562
13. Crystal structure of the human cytosolic sialidase Neu2. Evidence for the dynamic nature of substrate recognition. LM Chavas C Tringali P Fusi B Venerando G Tettamanti R Kato E Monti S Wakatsuki, J Biol Chem 2005 280 1 469 475 15501818
14. Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F. K Stummeyer A Dickmanns M Muhlenhoff R Gerardy-Schahn R Ficner, Nat Struct Mol Biol 2005 12 1 90 96 10.1038/nsmb874 15608653 (Pubitemid 40082922)
15. Evolution of the beta-propeller fold. I Chaudhuri J Soding AN Lupas, Proteins 2008 71 2 795 803 10.1002/prot.21764 17979191
16. Tandem repeat of a seven-bladed beta-propeller domain in oligoxyloglucan reducing-end-specific cellobiohydrolase. K Yaoi H Kondo N Noro M Suzuki S Tsuda Y Mitsuishi, Structure 2004 12 7 1209 1217 10.1016/j.str.2004.04.020 15242597 (Pubitemid 38900763)
17. Crystal structures of Clostridium thermocellum xyloglucanase, XGH74A, reveal the structural basis for xyloglucan recognition and degradation. C Martinez-Fleites CI Guerreiro MJ Baumann EJ Taylor JA Prates LM Ferreira CM Fontes H Brumer GJ Davies, J Biol Chem 2006 281 34 24922 24933 10.1074/jbc.M603583200 16772298 (Pubitemid 44274263)
18. Ligand recognition and domain structure of Vps10p, a vacuolar protein sorting receptor in Saccharomyces cerevisiae. MU Jorgensen SD Emr JR Winther, Eur J Biochem 1999 260 2 461 469 10.1046/j.1432-1327.1999.00176.x 10095782 (Pubitemid 29122543)
19. Ligands bind to Sortilin in the tunnel of a ten-bladed beta-propeller domain. EM Quistgaard P Madsen MK Groftehauge P Nissen CM Petersen SS Thirup, Nat Struct Mol Biol 2009 16 1 96 98 10.1038/nsmb.1543 19122660
20. Structure of a signaling-competent reelin fragment revealed by X-ray crystallography and electron tomography. T Nogi N Yasui M Hattori K Iwasaki J Takagi, EMBO J 2006 25 15 3675 3683 16858396 10.1038/sj.emboj.7601240 (Pubitemid 44264877)
21. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. RB Russell, J Mol Biol 1998 279 5 1211 1227 10.1006/jmbi.1998.1844 9642096 (Pubitemid 28302396)
22. Site-directed mutations of the catalytic and conserved amino acids of the neuraminidase gene, nanH, of Clostridium perfringens ATCC 10543. CH Chien YJ Shann SY Sheu, Enzyme Microb Technol 1996 19 4 267 276 10.1016/0141-0229(95) 00245-6 8987487 (Pubitemid 26293739)
23. Protein folds propelled by diversity. M Paoli, Prog Biophys Mol Biol 2001 76 1-2 103 130 10.1016/S0079-6107(01)00007-4 11389935 (Pubitemid 32523899)
24. Bacterial sialidases-roles in pathogenicity and nutrition. T Corfield, Glycobiology 1992 2 6 509 521 10.1093/glycob/2.6.509 1472757
25. Invasive phenotype of Trypanosoma cruzi restricted to a population expressing trans-sialidase. ME Pereira K Zhang Y Gong EM Herrera M Ming, Infect Immun 1996 64 9 3884 3892 8751943
26. Surface sialic acids taken from the host allow trypanosome survival in tsetse fly vectors. K Nagamune A Acosta-Serrano H Uemura R Brun C Kunz-Renggli Y Maeda MA Ferguson T Kinoshita, J Exp Med 2004 199 10 1445 1450 15136592 10.1084/jem.20030635 (Pubitemid 38685735)
27. Human sialidase as a cancer marker. T Miyagi T Wada K Yamaguchi K Shiozaki I Sato Y Kakugawa H Yamanami T Fujiya, Proteomics 2008 8 16 3303 3311 10.1002/pmic.200800248 18651674
28. Roles of plasma membrane-associated sialidase NEU3 in human cancers. T Miyagi T Wada K Yamaguchi, Biochim Biophys Acta 2008 1780 3 532 537 18023981
29. Disorders of Glycoprotein Degradation: -Mannosidosis, -Mannosidosis, Fucosidosis, and Sialidosis. GH Thomas, The metabolic and molecular bases of inherited disease New York: McGraw-Hill, Beaudet AL, Sly SD, Valle D, 2001 3507 3534
30. VPS10P-domain receptors - regulators of neuronal viability and function. TE Willnow CM Petersen A Nykjaer, Nat Rev Neurosci 2008 9 12 899 909 10.1038/nrn2516 19002190
31. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. BL Sibanda TL Blundell JM Thornton, J Mol Biol 1989 206 4 759 777 10.1016/0022-2836(89)90583-4 2500530 (Pubitemid 19137429)
32. A revised set of potentials for beta-turn formation in proteins. EG Hutchinson JM Thornton, Protein Sci 1994 3 12 2207 2216 7756980 10.1002/pro.5560031206
33. Crystal structure of a type III pantothenate kinase: insight into the mechanism of an essential coenzyme A biosynthetic enzyme universally distributed in bacteria. K Yang Y Eyobo LA Brand D Martynowski D Tomchick E Strauss H Zhang, J Bacteriol 2006 188 15 5532 5540 16855243 10.1128/JB.00469-06 (Pubitemid 44157310)
34. Complex of ribonuclease from Streptomyces aureofaciens with 2'-GMP at 1.7 A resolution. J Sevcik CP Hill Z Dauter KS Wilson, Acta Crystallogr D Biol Crystallogr 1993 49 Pt 2 257 271 10.1107/S0907444992007261 15299531
35. RNA cleavage without hydrolysis. Splitting the catalytic activities of binase with Asn101 and Thr101 mutations. AL Okorokov KI Panov WA Offen VG Mukhortov AA Antson MY Karpeisky AJ Wilkinson GG Dodson, Protein Eng 1997 10 3 273 278 10.1093/protein/10.3.273 9153077
36. Tyrosine hydrogen bonds make a large contribution to protein stability. CN Pace G Horn EJ Hebert J Bechert K Shaw L Urbanikova JM Scholtz J Sevcik, J Mol Biol 2001 312 2 393 404 10.1006/jmbi.2001.4956 11554795 (Pubitemid 32928134)
37. Novel missense mutations in the human lysosomal sialidase gene in sialidosis patients and prediction of structural alterations of mutant enzymes. K Itoh Y Naganawa F Matsuzawa S Aikawa H Doi N Sasagasako T Yamada J Kira T Kobayashi AV Pshezhetsky H Sakuraba, J Hum Genet 2002 47 1 29 37 10.1007/s10038-002-8652-7 11829139 (Pubitemid 34131971)
38. Carbohydrate-binding modules: fine-tuning polysaccharide recognition. AB Boraston DN Bolam HJ Gilbert GJ Davies, Biochem J 2004 382 Pt 3 769 781 15214846
39. Stereochemical metrics of lectin-carbohydrate interactions: comparison with protein-protein interfaces. E Garcia-Hernandez RA Zubillaga A Rodriguez-Romero A Hernandez-Arana, Glycobiology 2000 10 10 993 1000 10.1093/glycob/10.10.993 11030745
40. Structural basis of lectin-carbohydrate recognition. WI Weis K Drickamer, Annu Rev Biochem 1996 65 441 473 10.1146/annurev.bi.65.070196.002301 8811186
41. Sialic acid recognition by Vibrio cholerae neuraminidase. I Moustafa H Connaris M Taylor V Zaitsev JC Wilson MJ Kiefel M von Itzstein G Taylor, J Biol Chem 2004 279 39 40819 40826 10.1074/jbc.M404965200 15226294 (Pubitemid 39287679)
42. Galactose recognition by the carbohydrate-binding module of a bacterial sialidase. SL Newstead JN Watson AJ Bennet G Taylor, Acta Crystallogr D Biol Crystallogr 2005 61 Pt 11 1483 1491 10.1107/S0907444905026132 16239725 (Pubitemid 43934584)
43. Beta propellers: structural rigidity and functional diversity. V Fulop DT Jones, Curr Opin Struct Biol 1999 9 6 715 721 10.1016/S0959-440X(99)00035-4 10607670
44. Supersites within superfolds. Binding site similarity in the absence of homology. RB Russell PD Sasieni MJ Sternberg, J Mol Biol 1998 282 4 903 918 10.1006/jmbi.1998.2043 9743635 (Pubitemid 28442355)
45. Crystal structure of the HGF beta-chain in complex with the Sema domain of the Met receptor. J Stamos RA Lazarus X Yao D Kirchhofer C Wiesmann, EMBO J 2004 23 12 2325 2335 15167892 10.1038/sj.emboj.7600243 (Pubitemid 38954840)
46. Crystal structure of hemopexin reveals a novel high-affinity heme site formed between two beta-propeller domains. M Paoli BF Anderson HM Baker WT Morgan A Smith EN Baker, Nat Struct Biol 1999 6 10 926 931 10.1038/13294 10504726 (Pubitemid 29463305)
47. Tachylectin-2: crystal structure of a specific GlcNAc/GalNAc-binding lectin involved in the innate immunity host defense of the Japanese horseshoe crab Tachypleus tridentatus. HG Beisel S Kawabata S Iwanaga R Huber W Bode, EMBO J 1999 18 9 2313 2322 10228146 10.1093/emboj/18.9.2313 (Pubitemid 29213265)
48. Structural principles for the propeller assembly of beta-sheets: the preference for seven-fold symmetry. AG Murzin, Proteins 1992 14 2 191 201 10.1002/prot.340140206 1409568
49. RCC1-like repeat proteins: a pangenomic, structurally diverse new superfamily of beta-propeller domains. TJ Stevens M Paoli, Proteins 2008 70 2 378 387 10.1002/prot.21521 17680689
50. Engineering of beta-propeller protein scaffolds by multiple gene duplication and fusion of an idealized WD repeat. M Nikkhah Z Jawad-Alami M Demydchuk D Ribbons M Paoli, Biomol Eng 2006 23 4 185 194 10.1016/j.bioeng.2006. 02.002 16651025 (Pubitemid 44142330)
51. Carbohydrate-active enzymes: an integrated database approach. PM Coutinho B Henrissat, Recent advances in Carbohydrate Bioenginerring Cambridge: Royal Society of Chemistry, Gilbert HJ, Davies GJ, Henrissat B, Svensson B, 1999 3 12
52. Pfam: clans, web tools and services. RD Finn J Mistry B Schuster-Bockler S Griffiths-Jones V Hollich T Lassmann S Moxon M Marshall A Khanna R Durbin SR Eddy EL Sonnhammer A Bateman, Nucleic Acids Res 2006 34 Database D247 51 16381856 10.1093/nar/gkj149
53. InterPro: the integrative protein signature database. S Hunter R Apweiler TK Attwood A Bairoch A Bateman D Binns P Bork U Das L Daugherty L Duquenne RD Finn J Gough D Haft N Hulo D Kahn E Kelly A Laugraud I Letunic D Lonsdale R Lopez M Madera J Maslen C McAnulla J McDowall J Mistry A Mitchell N Mulder D Natale C Orengo AF Quinn JD Selengut CJ Sigrist M Thimma PD Thomas F Valentin D Wilson CH Wu C Yeats, Nucleic Acids Res 2009 37 Database D211 5 18940856 10.1093/nar/gkn785
54. Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. RM Bennett-Lovsey AD Herbert MJ Sternberg LA Kelley, Proteins 2008 70 3 611 625 10.1002/prot.21688 17876813 (Pubitemid 351161924)
55. Recognition of spatial motifs in protein structures. GJ Kleywegt, J Mol Biol 1999 285 4 1887 1897 10.1006/jmbi.1998.2393 9917419 (Pubitemid 29060478)
56. The Protein Data Bank. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne, Nucleic Acids Res 2000 28 1 235 242 10592235 10.1093/nar/28.1.235
57. WL DeLano, The PyMol User's Manual CA, USA, San Carlos: DeLano Scientific 2002
58. PDBsum new things. RA Laskowski, Nucleic Acids Res 2009 37 Database D355 9 18996896 10.1093/nar/gkn860
59. MUSTANG: a multiple structural alignment algorithm. AS Konagurthu JC Whisstock PJ Stuckey AM Lesk, Proteins 2006 64 3 559 574 10.1002/prot.20921 16736488 (Pubitemid 44100724)
60. The Jalview Java alignment editor. M Clamp J Cuff SM Searle GJ Barton, Bioinformatics 2004 20 3 426 427 10.1093/bioinformatics/btg430 14960472 (Pubitemid 38262778)