title: Sequence, Structure, and Binding Analysis of Cyclodextrinase (TK1770) from T. kodakarensis (KOD1) Using an In Silico Approach.
abstract: Thermostable cyclodextrinase (Tk1770 CDase) from hyperthermophilic archaeon Thermococcus kodakarensis (KOD1) hydrolyzes cyclodextrins into linear dextrins. The sequence of Tk1770 CDase retrieved from UniProt was aligned with sequences of sixteen CD hydrolyzing enzymes and a phylogenetic tree was constructed using Bayesian inference. The homology model of Tk1770 CDase was constructed and optimized with Modeller v9.14 program. The model was validated with ProSA server and PROCHECK analysis. Four conserved regions and the catalytic triad consisting of Asp411, Glu437, and Asp502 of GH13 family were identified in catalytic site. Also an additional fifth conserved region downstream to the fourth region was also identified. The structure of Tk1770 CDase consists of an additional N'-domain and a helix-loop-helix motif that is conserved in all archaeal CD hydrolyzing enzymes. The N'-domain contains an extended loop region that forms a part of catalytic domain and plays an important role in stability and substrate binding. The docking of substrate into catalytic site revealed the interactions with different conserved residues involved in substrate binding and formation of enzyme-substrate complex.
authors.affiliation: Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan.
authors.forename: Ramzan
authors.initials: R
authors.lastname: Ali
authors.affiliation: Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan.
authors.forename: Muhammad Imtiaz
authors.initials: MI
authors.lastname: Shafiq
mesh_terms: D020816:Amino Acid Motifs; D020134:Catalytic Domain; D003198:Computer Simulation; D017124:Conserved Sequence; D003505:Cyclodextrins / Q000378:metabolism; D006026:Glycoside Hydrolases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D010802:Phylogeny; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D019712:Thermococcus / Q000201:enzymology* / Q000235:genetics
chemical_list: D003505:Cyclodextrins; D006026:Glycoside Hydrolases; C048745:cyclomaltodextrinase
references.citation: Lett Appl Microbiol. 2013 Oct;57(4):336-43
references.pmid: 23789737
references.citation: J Biotechnol. 2009 Mar 25;140(3-4):184-93
references.pmid: 19428713
references.citation: Bioinformatics. 2012 Apr 15;28(8):1166-7
references.pmid: 22368248
references.citation: Protein Eng Des Sel. 2006 Dec;19(12):555-62
references.pmid: 17085431
references.citation: J Comput Chem. 2009 Dec;30(16):2785-91
references.pmid: 19399780
references.citation: Curr Opin Chem Biol. 2002 Apr;6(2):151-60
references.pmid: 12038998
references.citation: FEBS J. 2005 Nov;272(21):5497-513
references.pmid: 16262690
references.citation: Biochim Biophys Acta. 2008 Dec;1784(12):2004-11
references.pmid: 18824139
references.citation: Microbiol Mol Biol Rev. 2001 Mar;65(1):1-43
references.pmid: 11238984
references.citation: Curr Opin Biotechnol. 1998 Apr;9(2):141-5
references.pmid: 9588002
references.citation: Bioinformatics. 2003 Aug 12;19(12):1572-4
references.pmid: 12912839
references.citation: Appl Environ Microbiol. 2014 Feb;80(3):1108-15
references.pmid: 24296501
references.citation: FEMS Microbiol Lett. 2000 Feb 1;183(1):55-61
references.pmid: 10650202
references.citation: Biochim Biophys Acta. 2013 Jan;1834(1):380-6
references.pmid: 22902546
references.citation: Cell Res. 2009 Feb;19(2):271-3
references.pmid: 19153597
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W407-10
references.pmid: 17517781
references.citation: Braz J Microbiol. 2010 Oct;41(4):850-61
references.pmid: 24031565
references.citation: Bioresour Technol. 2003 Aug;89(1):17-34
references.pmid: 12676497
references.citation: Archaea. 2015;2015:397924
references.pmid: 25688178
references.citation: J Biol Chem. 2012 Mar 9;287(11):7979-89
references.pmid: 22223643
references.citation: Appl Microbiol Biotechnol. 2010 Feb;85(5):1241-9
references.pmid: 19908036
references.citation: Curr Protoc Protein Sci. 2007 Nov;Chapter 2:Unit 2.9
references.pmid: 18429317
references.citation: Biochim Biophys Acta. 2000 May 23;1478(2):165-85
references.pmid: 10825529