Structural and Functional Studies of a Polygalacturonase from the Phytopathogen Burkholderia cepacia
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(19) . This thesis is submitted in partial fulfillment of the requirements for the academic title of Doctor Philosophiae at the International School for Advanced Studies (Trieste, Italy). The work was carried out under the supervision of Dr. Doriano Lamba and Dr. Cristiana Campa within the PhD program in Structural and Functional Genomics, at the Structural Biology Laboratory, Elettra, Synchrotron Light Facility (Trieste, Italy), at the Bacteriology Group Laboratory, I
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(541) * & D. endoPGI__A_niger. -----------------------ASTCTFTS---ASEASESI---SSCSDVVLSS-IEVP 30. endoPG__A_aculeatus endoPGII__A_niger endoPG__F_moniliforme endoPG__S_purpureum endoPG__E_carotovora. -----------------------ATTCTFSGSNGASSASKSK---TSCSTIVLSN-VAVP ------------------------DSCTFTT---AAAAKAGK---AKCSTITLNN-IEVP ------------------------DPCSVTE---YSGLATAV---SSCKNIVLNG-FQVP ------------------------ATCTVKS----VDDAKDI---AGCSAVTLNG-FTVP SDSRTVSEPKTPSSCTTLKADSSTATSTIQKALNNCDQGKAVRLSAGSTSVFLSGPLSLP ..:. : .. : *.. . :*. 33 29 29 28 60. endoPGI__A_niger endoPG__A_aculeatus endoPGII__A_niger endoPG__F_moniliforme endoPG__S_purpureum endoPG__E_carotovora. AGETLDLSD-----AADGSTITFEGTTSFGYKEWKGP-------LIRFGGKDLT----VT SGTTLDLTK-----LNDGTHVIFSGETTFGYKEWSGP-------LISVSGSDLT----IT AGTTLDLTG-----LTSGTKVIFEGTTTFQYEEWAGP-------LISMSGEHIT----VT TGKQLDLSS-----LQNDSTVTFKGTTTFATTADNDFN------PIVISGSNIT----IT AGNTLVLN------PDKGATVTMAGDITFAKTTLDGP-------LFTIDGTGIN----FV SGVSLLIDKGVTLRAVNNAKSFENAPSSCGVVDKNGKGCDAFITAVSTTNSGIYGPGTID :* * : ..: . : . . . : .. 74 77 73 74 71 120. endoPGI__A_niger endoPG__A_aculeatus endoPGII__A_niger endoPG__F_moniliforme endoPG__S_purpureum endoPG__E_carotovora. MADGAVIDGDGSRWWDSKGTNGG-KTKPKFMYIHDVE---DSTFKGINIKNTPVQAISVQ GASGHSINGDGSRWWDGEGGNGG-KTKPKFFAAHSLT---NSVISGLKIVNSPVQVFSVA GASGHLINCDGARWWDGKGTSG--KKKPKFFYAHGLD---SSSITGLNIKNTPLMAFSVQ GASGHVIDGNGQAYWDGKGSNSNSNQKPDHFIVVQKTTG-NSKITNLNIQNWPVHCFDIT GAD-HIFDGNGALYWDGKGTNNG-THKPHPFLKIKGS----GTYKKFEVLNSPAQAISVG GQGGVKLQDKKVSWWELAADAKVKKLKQNTPRLIQINKSKNFTLYNVSLINSPNFHVVFS . :: . :*: . . * . ..: * * . .. 130 133 128 133 125 180. .
(542) endoPGI__A_niger endoPG__A_aculeatus endoPGII__A_niger endoPG__F_moniliforme endoPG__S_purpureum endoPG__E_carotovora. ATN--VHLNDFTIDNSDGDDN--------GGHNTDGFDISESTGVYISGATVKNQDDCIA GSDY-LTLKDITIDNSDGDDN--------GGHNTDAFDIGTSTYVTISGATVYNQDDCVA AND--ITFTDVTINNADGDTQ--------GGHNTDAFDVGNSVGVNIIKPWVHNQDDCLA GSSQ-LTISGLILDNRAGDKPNAKSGSLPAAHNTDGFDISSSDHVTLDNNHVYNQDDCVA PTDAHLTLDGITVDDFAGDTKN-------LGHNTDGFDVSAN-NVTIQNCIVKNQDDCIA DGDG-FTAWKTTIKTPS------------TARNTDGIDPMSSKNITIAYSNIATGDDNVA .. .. :.. .:***.:*. .. : :. 180 184 178 192 177 227. : . ** :*. endoPGI__A_niger endoPG__A_aculeatus endoPGII__A_niger endoPG__F_moniliforme endoPG__S_purpureum endoPG__E_carotovora. INSGE------SISFTGGTCSGGHGLSIGSVGGRDDNTVKNVTISDSTVSNSANGVRIKT VNSGE------NIYFSGGYCSGGHGLSIGSVGGRSDNTVKNVTFVDSTIINSDNGVRIKT VNSGE------NIWFTGGTCIGGHGLSIGSVGDRSNNVVKNVTIEHSTVSNSENAVRIKT VTSGT------NIVVSNMYCSGGHGLSIGSVGGKSDNVVDGVQFLSSQVVNSQNGCRIKS INDGN------NIRFENNQCSGGHGISIGSIATG--KHVSNVVIKGNTVTRSMYGVRIKA IKAYKGRAETRNISILHNDFGTGHGMSIGSETMG----VYNVTVDDLKMNGTTNGLRIKS :. .* . ***:**** * .* . : : . ***:. 234 238 232 246 229 283. endoPGI__A_niger endoPG__A_aculeatus endoPGII__A_niger endoPG__F_moniliforme endoPG__S_purpureum endoPG__E_carotovora. I-YKETGDVSEITYSNIQLSGITDYGIVIEQDYENGSPTGTPSTGIPITDVTVDG--VTG N-IDTTGSVSDVTYKDITLTSIAKYGIVVQQNY--GDTSSTPTTGVPITDFVLDN--VHG I-SGATGSVSEITYSNIVMSGISDYGVVIQQDYEDGKPTGKPTNGVTIQDVKLES--VTG N-SGATGTINNVTYQNIALTNISTYGVDVQQDYLNGGPTGKPTNGVKISNIKFIK--VTG QRTATSASVSGVTYDANTISGIAKYGVLISQSYP--DDVGNPGTGAPFSDVNFTGGATTI D-KSAAGVVNGVRYSNVVMKNVAKP-IVIDTVYEKKEGSNVP----DWSDITFKD----:. :. : *. :..:: : :. * . * :. .. 291 293 289 303 287 332. endoPGI__A_niger endoPG__A_aculeatus endoPGII__A_niger endoPG__F_moniliforme endoPG__S_purpureum endoPG__E_carotovora. TLEDDATQVYILCGDGSCSDWTWSGVDLSGGKTSDKCENVPSGASC--SVVSSGTNILISCGSGSCSDWTWTDVSVSGGKTSSKCTNVPSGASC--SVDSGATEIYLLCGSGSCSDWTWDDVKVTGGKKSTACKNFPSVASC--TVASSAQDWFILCGDGSCSGFTFSGNAITGGGKTSSCNYPTNTCPS--KVNNAATRVTVECGN-CSGNWNWSQLTVTGGKAGTIKSDKAKITGGQYL -VTSETKGVVVLNGENAKKPIEVTMKNVKLTSDSTWQIKNVNVKK---: .. :. *. .. :.. 337 339 335 349 335 376. .. & DHL
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