NCS-constrained Exhaustive Search Using Oligomeric Models

Overview

Journal Acta Crystallogr D Biol Crystallogr

Specialty Chemistry

Date 2007 Dec 21

PMID 18094472

Citations 11

Authors

Michail N Isupov

Andrey A Lebedev

Affiliations

Soon will be listed here.

Abstract

The efficiency of the cross-rotation function step of molecular replacement (MR) is intrinsically limited as it uses only a fraction of the Patterson vectors. Along with general techniques extending the boundaries of the method, there are approaches that utilize specific features of a given structure. In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted. In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search. Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.

Citing Articles

The Isoenzymic Diketocamphane Monooxygenases of ATCC 17453-An Episodic History and Still Mysterious after 60 Years.

Willetts A Microorganisms. 2021; 9(12).

PMID: 34946195 PMC: 8706424. DOI: 10.3390/microorganisms9122593.

Characterised Flavin-Dependent Two-Component Monooxygenases from the CAM Plasmid of ATCC 17453 (NCIMB 10007): ketolactonases by Another Name.

Willetts A Microorganisms. 2018; 7(1).

PMID: 30577535 PMC: 6352141. DOI: 10.3390/microorganisms7010001.

Reply to the Comment by Littlechild and Isupov.

Willetts A, Kelly D Microorganisms. 2017; 5(3).

PMID: 28878173 PMC: 5620646. DOI: 10.3390/microorganisms5030055.

Comments to Article by Willetts A. et al., Microorganisms 2016, 4, 38.

Littlechild J, Isupov M Microorganisms. 2017; 5(3).

PMID: 28878152 PMC: 5620645. DOI: 10.3390/microorganisms5030054.

The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer-Villiger monooxygenase.

Isupov M, Schroder E, Gibson R, Beecher J, Donadio G, Saneei V Acta Crystallogr D Biol Crystallogr. 2015; 71(Pt 11):2344-53.

PMID: 26527149 PMC: 4631483. DOI: 10.1107/S1399004715017939.

References

Vagin A, Teplyakov A . An approach to multi-copy search in molecular replacement. Acta Crystallogr D Biol Crystallogr. 2000; 56(Pt 12):1622-4. DOI: 10.1107/s0907444900013780. View

Tong L . How to take advantage of non-crystallographic symmetry in molecular replacement: 'locked' rotation and translation functions. Acta Crystallogr D Biol Crystallogr. 2001; 57(Pt 10):1383-9. DOI: 10.1107/s0907444901012446. View

Jones K, Smith R, Trudgill P . Diketocamphane enantiomer-specific 'Baeyer-Villiger' monooxygenases from camphor-grown Pseudomonas putida ATCC 17453. J Gen Microbiol. 1993; 139(4):797-805. DOI: 10.1099/00221287-139-4-797. View

Tanner J, Miller M, Wilson K, Tu S, Krause K . Structure of bacterial luciferase beta 2 homodimer: implications for flavin binding. Biochemistry. 1997; 36(4):665-72. DOI: 10.1021/bi962511x. View

Schuermann J, Tanner J . MRSAD: using anomalous dispersion from S atoms collected at Cu Kalpha wavelength in molecular-replacement structure determination. Acta Crystallogr D Biol Crystallogr. 2003; 59(Pt 10):1731-6. DOI: 10.1107/s0907444903015725. View

Read R . Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr D Biol Crystallogr. 2001; 57(Pt 10):1373-82. DOI: 10.1107/s0907444901012471. View

Shevtsov M, Chen Y, Gollnick P, Antson A . Crystal structure of Bacillus subtilis anti-TRAP protein, an antagonist of TRAP/RNA interaction. Proc Natl Acad Sci U S A. 2005; 102(49):17600-5. PMC: 1308913. DOI: 10.1073/pnas.0508728102. View

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

Leonard P, Brzozowski A, Lebedev A, Marshall C, Smith D, Verma C . The 1.8 A resolution structure of hydroxycinnamoyl-coenzyme A hydratase-lyase (HCHL) from Pseudomonas fluorescens, an enzyme that catalyses the transformation of feruloyl-coenzyme A to vanillin. Acta Crystallogr D Biol Crystallogr. 2006; 62(Pt 12):1494-501. DOI: 10.1107/S0907444906039199. View

10.

Esnouf R . An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph Model. 1997; 15(2):132-4, 112-3. DOI: 10.1016/S1093-3263(97)00021-1. View

11.

Asojo O, Boulegue C, Hoover D, Lu W, Lubkowski J . Structures of thymus and activation-regulated chemokine (TARC). Acta Crystallogr D Biol Crystallogr. 2003; 59(Pt 7):1165-73. DOI: 10.1107/s0907444903009454. View

12.

Matthews B . Solvent content of protein crystals. J Mol Biol. 1968; 33(2):491-7. DOI: 10.1016/0022-2836(68)90205-2. View

13.

Wittmann J, Rudolph M . Pseudo-merohedral twinning in monoclinic crystals of human orotidine-5'-monophosphate decarboxylase. Acta Crystallogr D Biol Crystallogr. 2007; 63(Pt 6):744-9. DOI: 10.1107/S0907444907016605. View

14.

Keillor J, Lherbet C, Castonguay R, Lapierre D, Martinez-Oyanedel J, Fothergill-Gilmore L . Expression, purification, crystallization and preliminary crystallographic analysis of Trypanosoma brucei phosphofructokinase. Acta Crystallogr D Biol Crystallogr. 2003; 59(Pt 3):532-4. DOI: 10.1107/s0907444902023478. View

15.

Antson A, Dodson E, Dodson G, Greaves R, Chen X, Gollnick P . Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Nature. 1999; 401(6750):235-42. DOI: 10.1038/45730. View

16.

Fleming T, Jones C, Piper P, Cowan D, Isupov M, Littlechild J . Characterization, crystallization and preliminary X-ray investigation of glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 4):671-4. DOI: 10.1107/s0907444997018076. View

17.

Krissinel E, Henrick K . Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr. 2004; 60(Pt 12 Pt 1):2256-68. DOI: 10.1107/S0907444904026460. View

18.

Potterton L, McNicholas S, Krissinel E, Gruber J, Cowtan K, Emsley P . Developments in the CCP4 molecular-graphics project. Acta Crystallogr D Biol Crystallogr. 2004; 60(Pt 12 Pt 1):2288-94. DOI: 10.1107/S0907444904023716. View

19.

Keegan R, Winn M . Automated search-model discovery and preparation for structure solution by molecular replacement. Acta Crystallogr D Biol Crystallogr. 2007; 63(Pt 4):447-57. DOI: 10.1107/S0907444907002661. View

20.

Trapani S, Abergel C, Gutsche I, Horcajada C, Fita I, Navaza J . Combining experimental data for structure determination of flexible multimeric macromolecules by molecular replacement. Acta Crystallogr D Biol Crystallogr. 2006; 62(Pt 5):467-75. DOI: 10.1107/S0907444906005361. View