Tuning the substrate selectivity of meta-cleavage product hydrolase by domain swapping

Applied Microbiology and Biotechnology

Volumn 97, Issue 12, 2013, Pages 5343-5350

  Zhou, Hao ^a   Qu, Yuanyuan ^a   Shen, E ^a   Kong, Chunlei ^a   Zhang, Xuwang ^a   Ma, Qiao ^a   Zhou, Jiti ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Domain swapping; meta Cleavage product hydrolase; Molecular simulation; Substrate specificity

Indexed keywords

DOMAIN SWAPPING; META-CLEAVAGE; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; SITE DIRECTED MUTAGENESIS; SUBSTRATE SELECTIVITY; SUBSTRATE SPECIFICITY; THREE-DIMENSIONAL STRUCTURE;

MOLECULAR DYNAMICS; SUBSTRATES;

HYDROLASES;

CARBON; HYDROLASE; META CLEAVAGE PRODUCT HYDROLASE; UNCLASSIFIED DRUG;

CARBON; ENZYME ACTIVITY; HYDROLYSIS; MOLECULAR ANALYSIS; SUBSTRATE; THREE-DIMENSIONAL MODELING;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL STRAIN; DOMAIN SHUFFLING; ENZYME CONFORMATION; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; HYBRID GENE; HYDROLYSIS; MOLECULAR DYNAMICS; NEIGHBOR JOINING METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PLASMID; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN EXPRESSION; SITE DIRECTED MUTAGENESIS; STATIC ELECTRICITY;

BACTERIAL PROTEINS; HYDROLASES; METABOLIC ENGINEERING; RECOMBINANT PROTEINS; RECOMBINATION, GENETIC; SUBSTRATE SPECIFICITY;

EID: 84878680310     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-012-4405-5     Document Type: Article

References (25)

1. Bauer DC, Bodén M, Their R, Gillam EM (2006) STAR: predicting recombination sites from amino acid sequence. BMC Bioinformatics 7:437
2. Carrière F, Thirstrup K, Hjorth S, Ferrato F, Nielsen PF, Withers-Martinez C, Cambillau C, Boel E, Thim L, Verger R (1997) Pancreatic lipase structure-function relationships by domain exchange. Biochemistry 36:239-248
3. Chen Y, Li S, Chen T, Hua H, Lin Z (2009) Random dissection to select for protein split sites and its application in protein fragment complementation. Protein Sci 18:399-409
4. Dunn G, Montgomery MG, Mohammed F, Coker A, Cooper JB, Robertson T, Garcia JL, Bugg TDH, Wood SP (2005) The structure of the C-C bond hydrolase MhpC provides insights into its catalytic mechanism. J Mol Biol 346:253-265
5. Fushinobu S, Saku T, Hidaka M, Jun SY, Nojiri H, Yamane H, Shoun H, Omori T, Wakagi T (2002) Crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products. Protein Sci 11:2184-2195
6. Fushinobu S, Jun SY, Hidaka M, Nojiri H, Yamane H, Shoun H, Omori T, Wakagi T (2005) A series of crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with various cleavage products. Biosci Biotechnol Biochem 69:491-498
7. Gille C, Frömmel C (2001) STRAP: editor for STRuctural Alignments of Proteins. Bioinformatics 17:377-378
8. Goodey NM, Benkovic SJ (2009) Understanding enzyme mechanism through protein chimeragenesis. In: Köhrer C, RakBhandary UL (eds) Protein engineering. Nucleic acids and molecular biology, vol 22. Springer, Berlin, pp 1-27
9. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435-447
10. Horsman GP, Ke J, Dai S, Seah SY, Bolin JT, Eltis LD (2006) Kinetic and structure insight into the mechanism of BphD, a C-C bond hydrolase from the biphenyl degradation pathway. Biochemistry 45:11071-11086
11. Horsman GP, Bhowmik S, Seah SYK, Kumar P, Bolin JT, Eltis LD (2007) The tautomeric half-reaction of BphD, a C-C bond hydrolase. Kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad. J Biol Chem 282:19894-19904
12. Jun SY, Fushinobu S, Nojiri H, Omori T, Shoun H, Wakagi T (2006) Improving the catalytic efficiency of a meta-cleavage product hydrolase (CumD) from Pseudomonas fluorescens IP01. Biochim Biophys Acta 1764:1159-1166
13. Khajamohiddin S, Repalle ER, Pinjari AB, Merrick M, Siddavattam D (2008) Biodegradation of aromatic compound: an overview of meta-fission product hydrolases. Crit Rev Microbiol 34:13-31
14. Lack NA, Yam KC, Lowe ED, Horsman GP, Owen RL, Sim E, Eltis LD (2010) Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. J Biol Chem 285:434-443
15. Li C, Li JJ, Montgomery MG, Wood SP, Bugg TDH (2006) Catalytic role for arginine 188 in the C-C hydrolase catalytic mechanism for Escherichia coli MhpC and Burkholderia xenovorans LB400 BphD. Biochemistry 45:12470-12479
16. Li A, Qu YY, Zhou JT, Ma F, Zhou H, Shi SN (2010) Characterization of a novel meta-fission product hydrolase from Dyella ginsengisoli LA-4. Process Biochem 45:94-100
17. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785-2791
18. Nandhagopal N, Yamada A, Hatta T, Masai E, Fukuda M, Mitsui Y, Senda T (2001) Crystal structure of 2-hydroxyl-6-oxo-6-phenylhexa-2,4-dienoic acid (HPDA) hydrolase (BphD enzyme) from the Rhodococcus sp. strain RHA1 of the PCB degradation pathway. J Mol Biol 309:1139-1151
19. Seah SYK, Terracina G, Bolin JT, Riebel P, Snieckus V, Eltis LD (1998) Purification and preliminary characterization of a serine hydrolase involved in the microbial degradation of polychlorinated biphenyls. J Biol Chem 273:22943-22949
20. Seah SYK, Ke J, Denis G, Horsman GP, Fortin PD, Whiting CJ, Eltis LD (2007) Characterization of a C-C bond hydrolase from Sphingomonas wittichii RW1 with novel specificities towards polychlorinated biphenyl metabolites. J Bacteriol 189:4038-4045
21. Skiøt M, De Maria L, Chatterjee R, Svendsen A, Patkar SA, Ostergaard PR, Brask J (2009) Understanding the plasticity of the alpha/beta hydrolase fold: lid swapping on the Candida antarctica lipase B results in chimeras with interesting biocatalytic properties. ChemBioChem 10:520-527
22. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599
23. Voigt CA, Martinez C, Wang ZG, Mayo SL, Arnold FH (2002) Protein building blocks preserved by recombination. Nat Struct Biol 9:553-558
24. Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40
25. Zhou H, Qu YY, Kong CL, Wu YG, Zhu K, Yang J, Zhou JT (2012) Promiscuous esterase activities of the C-C hydrolases from Dyella ginsengisoli. Biotechnol Lett 34:1107-1113