Glycosidic bond cleavage
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1 Glycosidases and Glycosyltransferases Introduction to Inverting/Retaining Mechanisms Inhibitor design Chemical Reaction Proposed catalytic mechanisms Multiple slides courtesy of Harry Gilbert with Wells modifications Glycosidic bond cleavage Glycone Aglycone H 2 O Classic example is lysozyme: cleaves N-acetlymuramic acid-β-4-glcnac Discovered by Alexander Fleming in 1920s Sneezed onto his bacterial agar plate Bacteria found to be lysed next day Potential antimicrobial enzyme He discovered a better antimicrobial agent later; what is it? 1
2 Glycosidic bond cleavage in free solution Glycone Aglycone H 2 O Transition state oxocarbenium ion attacked by hydroxyl ion Rate of glycosidic bond cleavage The transition state (positively charged oxocarbenium ion) is a very high energy molecule Geometry changes from chair to half-chair Why? So C1 and ring oxygen are in same plane So positive charge is not just at C1 but shared between C1 and ring oxygen This stabilises positive charge. Need lots of energy to cause change in geometry of sugar O5 C1 2
3 Two different mechanisms of acid-base assisted catalysis Single displacement mechanism Inversion of the anomeric configuration of glycone sugar β-glycosidic bond Bond is equatorial sugar OH is axial Two different mechanisms of acid-base assisted catalysis Double displacement mechanism Retention of the anomeric configuration of glycone sugar β-glycosidic bond Bond is equatorial OH remains equatorial 3
4 Two different mechanisms of acid-base assisted catalysis How does an enzyme generate protons and hydroxyl ions? Two amino acids with carboxylic acid side-chains Glutamate or aspartate Two mechanisms are as follows: Acid-base assisted single displacement mechanism Catalytic acid Catalytic base The acid catalyst Uncharged Hydrogen in the perfect position to be donated to the glycosidic oxygen. The catalytic base Extracts a proton from water Hydroxyl ion in the perfect position to attack C1 of the transition state 4
5 Acid-base assisted double displacement mechanism Catalytic acid-base Catalytic nucleophile Two distinct reactions Glycosylation Formation of a covalent glycosyl-enzyme intermediate (ester bond) The aglycone sugar released from active site Deglycosylation The ester bond between the glycone sugar and the enzyme is hydrolysed and the glycone sugar is released from the active site The first enzyme structure solved The textbook example of enzyme catalyzed glycoside hydrolysis Hydrolyses the glycosidic bond via a retaining mechanism 5
6 And the lysozyme mechanism is revisited: Covalent enzyme intermediate for hen egg white lysozyme Lysozyme (E35Q) Asp52 Vocadlo et al. Nature 412, How can we identify the catalytic amino acids Glycoside hydrolases are grouped in enzyme families based on sequence similarity (i.e. evolved from a common ancestor. Currently 100+ families All members of same family have Evolved from the same progenitor sequence Conserved mechanism Same fold Conserved catalytic apparatus 6
7 CAZY Several families have ancient ancestral relationship Same fold, mechanism and catalytic residues How does CAZY help us? Tells us what the catalytic residues are Tells us the mechanism Tells us the likely substrate specificity Catalytic acid Sequence 1:73 QNGQTVHGHALVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSAN 1 UNIPROT:XYNA_PSEFL 1:73 335:407 QNGQTVHGHALVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSAN 2 UNIPROT:Q9AJR9 1:68 111:178 RHNQQVRGHNLCWHE--ELPTwaSEVngNAKEILIQHIQTVAGRYAGRIQSWDVVNEAILPKDGRPDG UNIPROT:GUX_CELFI 3:66 115:176 --GKELYGHTLVWHS--QLPDWAKNLNGsfESAMVNHVTKVADHFEGKVASWDVVNEAFADG-DGP UNIPROT:Q :61 116:173 --GKELYGHTLVWHS--QLPDWAKNLNGsfESAMVNHVTKVADHFEGKVASWDVVNEAFAD UNIPROT:Q :63 324:391 ENNMTVHGHALVWHSDYQVPnwAGSAE-DFLAALDTHITTIVDHYegNLVSWDVVNEAIDDNS UNIPROT:Q :63 343:409 -NNINVHGHALVWHSDYQVPNFmsGSAADFIAEVEDHVTQVVTHFkgNVVSWDVVNEAINDGS UNIPROT:Q :73 111:180 QNGKQVRGHTLAWHS--QQPGWMQssGSSLRQAMIDHINGVMAHYKGKIVQWDVVNEAFADG--NSGGRRDSN 8 UNIPROT:Q7SI98 1:73 73:142 QNGKQVRGHTLAWHS--QQPGWMQssGSTLRQAMIDHINGVMGHYKGKIAQWDVVNEAFSD--DGSGGRRDSN 9 UNIPROT:XYNB_THENE 1:62 96:158 KNDMIVHGHTLVWHN--QLPGWLTgsKEELLNILEDHVKTVVSHFRGRVKIWDVVNEAVSDS UNIPROT:Q :62 96:158 KNDMIVHGHTLVWHN--QLPGWLTgsKEELLNILEDHVKTVVSHFRGRVKIWDVVNEAVSDS UNIPROT:AAN :62 96:158 KNDMIVHGHTLVWHN--QLPGWLTgsKEELLNILEDHVKTVVSHFRGRVKIWDVVNEAVSDS UNIPROT:Q7TM36 8:68 2: GHTVVWHGA--VPTWLNasTDDFRAAFENHIRTVADHFRGKVLAWDVVNEAV---ADDGSG UNIPROT:Q7WVV0 1:62 96:158 ENDMIVHGHTLVWHN--QLPGWITgtKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDS UNIPROT:Q7WUM6 1:62 96:158 ENDMIVHGHTLVWHN--QLPGWITgtKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDS UNIPROT:Q9WXS5 1:62 96:158 ENDMIVHGHTLVWHN--QLPGWITgtKEELLNVLEDHIKTVVSHFKGRVKIWDVVNEAVSDS UNIPROT:Q9P973 1:57 120:176 QNGKSIRGHTLIWHS--QLPAWVNnnNAdlRQVIRTHVSTVVGRYKGKIRAWDVVNE UNIPROT:Q9X584 1:63 115:176 QNGKQVRGHTLAWHS--QQPGWMQssGSALRQAMIDHINGVMAHYKGKIAQWDVVNEAFADGS UNIPROT:XYNA_STRLI 1:63 114:175 QNGKQVRGHTLAWHS--QQPGWMQssGSALRQAMIDHINGVMAHYKGKIVQWDVVNEAFADGS UNIPROT:Q8CJQ1 1:63 114:175 QNGKQVRGHTLAWHS--QQPGWMQssGSALRQAMIDHINGVMAHYKGKIVQWDVVNEAFADGS UNIPROT:P :62 93:155 QNGQGLRCHTLIWYS--QLPGWVSSGNWN-RQTLEahIDNVMGHYKGQCYAWDVVNEAVDDN UNIPROT:Q9XDV5 3:71 427:505 --GMKVHGHTLVWHQ--QTPAWMndSGGNirEemRNHIRTVIEHFGDKVISWDVVNEAMSDNPSNpdWRGS-- 22 UNIPROT:Q8GJ37 3:71 427:505 --GMKVHGHTLVWHQ--QTPAWMndSGGNirEemRNHIRTVIEHFGDKVISWDVVNEAMSDNPSNpdWRGS-- 23 UNIPROT:Q7X2C9 1:63 27:88 QNGKQVRGHTLAWHS--QQPGWMQssGSSLRQAMIDHINGVMNHSKGKIAQWDVVNEAFADGS UNIPROT:Q9RJ91 3:61 105:162 --GMDVRGHTLVWHS--QLPSWVSPLGadLRTAMNAHINGLMGHYKGEIHSWDVVNEAFQD UNIPROT:Q :61 119:176 --GMKVRGHTLVWHS--QLPGWVSPLAadLRSAMNNHITQVMTHYKGKIHSWDVVNEAFQD UNIPROT:Q9RMM5 1:61 113:172 QNGKEVRGHTLAWHS--QQPYWMQssGSDLRQAMIDHINGVMNHYKGKIAQWDVVNEAFED UNIPROT:BAD :61 113:172 QNGKEVRGHTLAWHS--QQPYWMQssGSDLRQAMIDHINGVMNHYKGKIAQWDVVNEAFED
8 Inhibitors of glycoside hydrolases Glycoside hydrolase activities contribute to significant diseases Flu Type II diabetes Possibly Cancer and Aids To combat diseases need to develop inhibitors Designing glycoside hydrolase inhibitors What comprises a good inhibitor? Mechanistic covalent inhibitors not used Very high affinity non-covalent competitive inhibitors Transition state inhibitors 8
9 glycosylation Transition state has a positive charged nature as leaving group departure precedes nucleophile attack deglycosylation TS-based inhibitors that mimic charge distribution deoxynojirimycin Glucosidase Inhibitors isofagamine Both have nm K i values. Affinities are about one million times higher than substrate Why are they transition state mimics? Contains a positive charge 9
10 Mimicking the half-chair Insert a double-bond to enforce planarity Drugs that mainly mimic the half chair All picomolar affinities fold tighter binders than substrates HIV drug: prevents glycosylation in mammalian cells AIDs virus surface proteins are not glycosylated and thus can t evade the immune system Type II diabetes (inhibits human Amylase) Anti-flu drugs 10
11 Annual Reviews Two folds Both have two Rossman domains GTA strongly linked may look like a single β- sheet GT-B has two separate domains Requirement of nucleotide binding limits number of folds greatly 11
12 Inverting GT Retaining GT Inverting GT Retaining GT 12
13 Take Home Points CAZY Inverting/Retaining Mechanisms Mechanistic Based Inhibitors 13
14 References Cantarel et al (2008) Nucleic Acid Res 37:D233-8 (CAZY) Vocadlo at al. (2001) Nature 412: (Mechanistic inhibitors of glycoside hydrolases) Lairson et al. (2008) Ann. Rev. Biochem. 77: (glycosyltransferases) Rye and Withers (2000) Curr. Opin. Chem. Biol. 4: (glycoside hydrolases) Tailford (2008) Nature Chem. Biol. Nat. 4: (Transition state geometry) 14
15 A. B. C. D. E. F. α3 α3 β4 β3 Ser/Thr β4 β3 Asn Asn Ser/Thr Asn α3 β4 β3 β6 Ser/Thr G. H. I. J. K. β3 Ser/Thr Ser/Thr Asn Asn Asn 15
A. B. C. D. E. F. G. H. I. J. K. Ser/Thr. Ser/Thr. Ser/Thr. Ser/Thr. Ser/Thr. Asn. Asn. Asn. Asn. Asn. Asn
A. B. C. D. E. F. "3 "3!4!3 Ser/Thr "3!4!3!4 Asn Asn Ser/Thr Asn!3!6 Ser/Thr G. H. I. J. K.!3 Ser/Thr Ser/Thr 4 4 2 2 6 3 6 Asn Asn Asn Glycosidases and Glycosyltransferases Introduction to Inverting/Retaining
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