Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily

Protein Science

Volumn 14, Issue 11, 2005, Pages 2887-2894

  Caruthers, Jonathan ^a   Zucker, Frank ^a   Worthey, Elizabeth ^c   Myler, Peter J ^c   Buckner, Fred ^b   Van Voorhuis, Wes ^b   Mehlin, Chris ^a   Boni, Erica ^a   Feist, Tiffany ^a   Luft, Joseph ^d   Gulde, Stacey ^d   Lauricella, Angela ^d   Kaluzhniy, Oleksandr ^a   Anderson, Lori ^a   Le Trong, Isolde ^a   Holmes, Margaret A ^a   Earnest, Thomas ^e   Soltis, Michael ^f   Hodgson, Keith O ^f   Hol, Wim G J ^a,b   Merritt, Ethan A ^a,b   more..

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c SEATTLE BIOMEDICAL RESEARCH INSTITUTE   (United States)

^d HAUPTMAN WOODWARD MEDICAL RESEARCH INSTITUTE   (United States)

^e LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^f SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

Cysteine hydrolase; Evolutionary relationships; Functional annotation; Leishmania; Protein families; Structural genomics; Trypanosoma

Indexed keywords

ASPARTYL HYDROLASE; CYSTEINE HYDROLASE; HYDROLASE; ISOCHORISMATASE; MATRIX ATTACHMENT REGION BINDING PROTEIN; N CARBAMOYLSARCOSINE AMIDOHYDROLASE; PHENAZINE; PROTOZOAL PROTEIN; RIBONUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME SPECIFICITY; ENZYME SUBUNIT; GENETIC CONSERVATION; LEISHMANIA DONOVANI; LEISHMANIA MAJOR; LIGAND BINDING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; STRUCTURAL HOMOLOGY; TRYPANOSOMA CRUZI;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HYDROLASES; LEISHMANIA DONOVANI; LEISHMANIA MAJOR; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTOZOAN PROTEINS; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN; TRYPANOSOMA CRUZI;

LEISHMANIA DONOVANI; LEISHMANIA MAJOR; LEISHMANIA TARENTOLAE; PROTOZOA; TRYPANOSOMA; TRYPANOSOMA CRUZI;

EID: 27644504109     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.051783005     Document Type: Article

References (25)

1. Alfonzo, J.D., Thiemann, O.H., and Simpson, L. 1998. Purification and characterization of MAR1: A mitochondrial associated ribonuclease from Leishmania tarentolae. J. Biol. Chem. 273: 30003-30011.
2. Beitz, E. 2000. TeXshade: Shading and labeling of multiple sequence alignments using LaTeX2e. Bioinformatics 16: 135-139.
3. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54: 905-921.
4. Chayen, N.E., Shaw Stewart, P.D., and Blow, D.M. 1992. Microbatch crystallization under oil: A new technique allowing many small-volume crystallization trials. J. Crystal Growth 122: 176-180.
5. Collaborative Computational Project, Number 4 (CCP4). 1994. The CCP4 Suite: Programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50: 760-763.
6. Colovos, C., Cascio, D., and Yeates, T.O. 1998. The 1.8 Å crystal structure of the ycaC gene product from Escherichia coli reveals an octameric hydrolase of unknown specificity. Structure 10: 1329-1337.
7. Deng, J., Davies, D.R., Wisedchaisri, G., Wu, M., Hol, W.G., and Mehlin, C. 2004. An improved protocol for rapid freezing of protein samples for long-term storage. Acta Crystallogr. D Biol. Crystallogr. 60: 203-204.
8. Guda, C., Lu, S., Scheeff, E.D., Bourne, P.E., and Shindyalov, I.N. 2004. CE-MC: A multiple protein structure alignment server. Nucleic Acids Res. 32: W100-W103.
9. Holton, J.M. and Alber, T. 2004. Automated protein crystal structure determination using ELVES. Proc. Natl. Acad. Sci. 101: 1537-1542.
10. Kissinger, C.R., Gehlhaar, D.K., and Fogel, D.B. 1999. Rapid automated molecular replacement by evolutionary search. Acta Crystallogr. D Biol. Crystallogr. 55: 484-491.
11. Kleywegt, G.J. and Jones, T.A. 1997. Detecting folding motifs and similarities in protein structures. Methods Enzymol. 277: 525-545.
12. Krupka, H.I., Rupp, B., Segelke, W., Lekin, T., Wright, D., Wu, H.C., Todd, P., and Azarani, A. 2002. The high-speed Hydra-Plus-One system for automated high-throughput protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 58: 1523-1566.
13. Leslie, A.G.W. 1992. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography, No. 26.
14. Leslie, A.G.W., Brick, P., and Wonacott, A. 1986. Recent changes to the MOSFLM package for processing film and image plate data. Daresbury Lab. Inf. Quart. Protein Crystallogr. 18: 33-39.
15. Luft, J.R., Collins, R.J., Fehrman, N.A., Lauricella, A.M., Veatch, C.K., and DeTitta, G.T. 2003. A deliberate approach to screening for initial crystallization conditions of biological macromolecules. J. Struct. Biol. 142: 170-179.
16. McRee, D.E. 1999. XtalView/Xfit: A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125: 156-165.
17. Mehlin, C., Boni, E.E., Andreyka, J., and Terry, R.W. 2004. Cloning grills: High throughput cloning for structural genomics. J. Struct. Funct. Genomics 5: 59-61.
18. Murshudov, G.N., Vagin, A.A., and Dodson, E.J. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53: 240-255.
19. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
20. Otwinowski, Z. and Minor, W. 1997. Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.
21. Parsons, J.F., Calabrese, K., Eisenstein, E., and Ladner, J.E. 2003. Structure and mechanism of Pseudomonas aeruginosa PhzD: An isochorismatase from the phenazine biosynthetic pathway. Biochemistry 42: 5684-5693.
22. Romao, M.J., Turk, D., Gomis-Ruth, F.X., Huber, R., Schumacher, G., Mollering, H., and Russmann, L. 1992. Crystal structure analysis, refinement and enzymatic reaction mechanism of N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. at 2.0 Å resolution. J. Mol. Biol. 226: 1111-1130.
23. Steller, I., Bolotovsky, R., and Rossmann, M., 1998. The use of partial reflections for scaling and averaging x-ray area-detector data. J. Appl. Crystallogr. 30: 1036-1040.
24. Terwilliger, T.C. and Berendzen, J. 1999. Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55: 849-861.
25. Zajc, A., Romao, M.J., Turk, B., and Huber, R. 1996. Crystallographic and fluorescence studies of ligand binding to N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. J. Mol. Biol. 263: 269-283.