X-ray structure of ILLS, an auxin-conjugate amidohydrolase from Arabidopsis thaliana

Proteins: Structure, Function and Bioinformatics

Volumn 74, Issue 1, 2009, Pages 61-71

  Bitto, Eduard ^a   Bingman, Craig A ^a   Bittova, Lenka ^a   Houston, Norma L ^b   Boston, Rebecca S ^b   Fox, Brian G ^a   Phillips Jr , George N ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

Auxin homeostasis; M20D peptidase family; Metalloenzyme; X ray structure

Indexed keywords

AMIDASE; AUXIN; BACTERIAL ENZYME; INDOLEACETIC ACID; METALLOPROTEIN; PEPTIDASE M20D; PHYTOHORMONE; UNCLASSIFIED DRUG; ARABIDOPSIS PROTEIN; BACTERIAL PROTEIN; EXOPEPTIDASE; ILL2 PROTEIN, ARABIDOPSIS; INDOLEACETIC ACID DERIVATIVE; METALLOPROTEINASE;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; BACILLUS SUBTILIS; ENZYME ACTIVE SITE; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; PSEUDOMONAS; SALMONELLA TYPHIMURIUM; STRUCTURE ANALYSIS; ANIMAL; BINDING SITE; CHEMICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; ENZYME SPECIFICITY; ENZYMOLOGY; PROTEIN QUATERNARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

ARABIDOPSIS THALIANA;

AMIDOHYDROLASES; ANIMALS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; EXOPEPTIDASES; INDOLEACETIC ACIDS; METALLOPROTEASES; MODELS, CHEMICAL; PROTEIN STRUCTURE, QUATERNARY; SUBSTRATE SPECIFICITY;

EID: 58949096831     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22124     Document Type: Article

References (47)

1. Woodward AW, Barrel B. Auxin: regulation, action, and interaction. Ann Bot 2005; 95:707-735.
2. Bartel B. Auxin biosynthesis. Annu Rev Plant Physiol Plant Mol Biol 1997; 48:51-66.
3. Ljung K, Hull AK, Kowalczyk M, Marchant A, Celenza J, Cohen JD, Sandberg G. Biosynthesis, conjugation, catabolism and homeostasis of indole-3-acetic acid in Arabidopsis thaliana. Plant Mol Biol 2002; 49:249-272.
4. Kowalczyk M, Sandberg G. Quantitative analysis of indole-3-acetic acid metabolites in Arabidopsis. Plant Physiol 2001; 127:1845-1853.
5. Tan X, Calderon-Villalobos LI, Sharon M, Zheng C, Robinson CV, Estelle M, Zheng N. Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 2007; 446:640-645.
6. Tuominen H, Ostin A, Sandberg G, Sundberg B. A novel metabolic pathway for indole-3-acetic acid in apical shoots of Populus tremula (L.) X Populus tremuloides (Michx.). Plant Physiol 1994; 106:1511-1520.
7. Rampey RA, LeClere S, Kowalczyk M, Ljung K, Sandberg G, Bartel B. A family of auxin-conjugate hydrolases that contributes to free indole-3-acetic acid levels during Arabidopsis germination. Plant Physiol 2004; 135:978-988.
8. Bartel B, Fink GR. ILR1, an amidohydrolase that releases active indole-3-acetic acid from conjugates. Science 1995; 268:1745-1748.
9. Davies RT, Goetz DH, Lasswell J, Anderson MN, Bartel B. IAR3 encodes an auxin conjugate hydrolase from Arabidopsis. The Plant Cell 1999; 11:365-376.
10. LeClere S, Tellez R, Rampey RA, Matsuda SP, Bartel B. Characterization of a family of IAA-amino acid conjugate hydrolases from Arabidopsis. J Biol Chem 2002; 277:20446-20452.
11. Campanella JJ, Larko D, Smalley J. A molecular phylogenomic analysis of the ILRI-like family of IAA amidohydrolase genes. Comp Funct Genom 2003; 4:584-600.
12. Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997; 10:1-6.
13. Pelham HRB. The retention signal for soluble-proteins of the endoplasmic-reticulum. Trends Biochem Sci 1990; 15:483-486.
14. Derkx PM, Madrid SM. The foldase CYPB is a component of the secretory pathway of Aspergillus niger and contains the endoplasmic reticulum retention signal HEEL. Mol Genet Genom 2001; 266:537-545.
15. Raykhel I, Alanen H, Salo K, Jurvansuu J, Nguyen VD, Latva-Ranta M, Ruddock L. A molecular specificity code for the three mammalian KDEL receptors. J Cell Biol 2007; 179:1193-1204.
16. Bartel B, LeClere S, Magidin M, Zolman BK. Inputs to the active indole-3-acetic acid pool: de novo synthesis, conjugate hydrolysis, and indole-3-butyric acid beta-oxidation. J Plant Growth Regul 2001; 20:198-216.
17. Titarenko E, Rojo E, Leon J, Sanchez-Serrano JJ. Jasmonic acid-dependent and -independent signaling pathways control wound- induced gene activation in Arabidopsis thaliana. Plant Physiol 1997; 115:817-826.
18. Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeck-mann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 2006; 34(Database issue):D187-D191.
19. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000; 28:235-242.
20. Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 2000; 300:1005-1016.
21. Bannai H, Tamada Y, Maruyama O, Nakai K, Miyano S. Extensive feature detection of N-terminal protein sorting signals. Bioinformatics (Oxford Engl) 2002; 18:298-305.
22. Thao S, Zhao Q, Kimball T, Steffen E, Blommel PG, Riters M, Newman CS, Fox BG, Wrobel RL. Results from high-throughput DNA cloning of Arabidopsis thaliana target genes using site-specific recombination. J Struct Funct Genom 2004; 5:267-276.
23. Sreenath HK, Bingman CA, Buchan BW, Seder KD, Burns BT, Geema HV, Jeon WB, Vojtik FC, Aceti DJ, Frederick RO, Phillips GN Jr., Fox BG. Protocols for production of selenomethionine-labeled proteins in 2-L polyethylene terephthalate bottles using auto-induction medium. Protein Expr Purif 2005; 40:256-267.
24. Jeon WB, Aceti DJ, Bingman CA, Vojtik FC, Olson AC, Ellefson JM, McCombs JE, Sreenath HK, Blommel PG, Seder KD, Burns BT, Geetha HV, Harms AC, Sabat G, Sussman MR, Fox BG, Phillips GN, Jr. High-throughput purification and quality assurance of Arabidopsis thaliana proteins for eukaryotic structural genomics. J Struct Funct Genom 2005; 6:143-147.
25. Zolnai Z, Lee PT, Li J, Chapman MR, Newman CS, Phillips GN, Jr, Rayment I, Ulrich EL, Volkman BF, Markley JL. Project management system for structural and functional proteomics: sesame. J Struct Funct Genom 2003; 4:11-23.
26. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol 1997; 276:307-326.
27. Terwilliger TC. Maximum-likelihood density modification. Acta Crystallogr D Biol Crystallogr 2000; 56(Pt 8):965-972.
28. Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr Sect D: Biol Crystallogr 1999; 55:849-861.
29. Perrakis A, Morris R, Lamzin VS. Automated protein model building combined with iterative structure refinement. Nat Struct Biol 1999; 6:458-463.
30. McRee DE. XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density. J Struct Biol 1999; 125:156-165.
31. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystal- logr D Biol Crystallogr 1997; 53(Pt 3):240-255.
32. Lovell SC, Davis IW, Arendall WB, III, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Calpha geometry: φ, ψ and Cβ deviation. Proteins 2003; 50:437-450.
33. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004; 60:2126-2132.
34. DeLano WL. The PYMOL molecular graphic system. San Carlos, CA: De Lano Scientific LLC; 2002.
35. Rice LM, Earnest TN, Brunger AT. Single-wavelength anomalous diffraction phasing revisited. Acta Crystallogr D Biol Crystallogr 2000; 56(Pt 11):1413-1420.
36. Wang BC. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol 1985; 115:90-112.
37. Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA. The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res 2003; 31:452-455.
38. Hakansson K, Miller CG. Structure of peptidase T from Salmonella typhimurium. Eur J Biochem/FEBS 2002; 269:443-450.
39. Rowsell S, Pauptit RA, Tucker AD, Melton RG, Blow DM, Brick P. Crystal structure of carboxypeptidase G2, a bacterial enzyme with applications in cancer therapy. Structure 1997; 5:337-347.
40. Madej T, Gibrat JF, Bryant SH. Threading a database of protein cores. Proteins 1995; 23:356-369.
41. Minasov G, Shuvalova L, Brunzelle JS, Collart FR, Anderson WF. Structure of Bacillus subtilis YXEP protein, a dinuclear metal binding peptidase from M20 family. Protein Data Bank (www.rcsborg/pdb/home) 2005:PDB ID:1ysj, DOI: 10.2210/pdb2211ysj/pdb.
42. Chou JC, Welch WH, Cohen JD. His-404 and His-405 are essential for enzyme catalytic activities of a bacterial indole-3-acetyl-L-aspartic acid hydrolase. Plant Cell Physiol 2004; 45:1335-1341.
43. Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A. FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res 2005; 33 (Web Server issue):W284-W288.
44. Mesters JR, Barinka C, Li W, Tsukamoto T, Majer P, Slusher BS, Konvalinka J, Hilgenfeld R. Structure of glutamate carboxypeptidase II, a drug target in neuronal damage and prostate cancer. EMBO J 2006; 25:1375-1384.
45. Christianson DW, Lipscomb WN. Carboxypeptidase-A. Acc Chem Res 1989; 22:62-69.
46. Lipscomb WN. Carboxypeptidase A mechanisms. Proc Natl Acad Sci USA 1980; 77:3875-3878.
47. Campanella JJ, Olajide AF, Magnus V, Ludwig-Muller J. A novel auxin conjugate hydrolase from wheat with substrate specificity for longer side-chain auxin amide conjugates. Plant Physiol 2004; 135: 2230-2240.