Godzik A

References (6)

Title : Novel putative polyethylene terephthalate (PET) plastic degrading enzymes from the environmental metagenome - Karunatillaka_2021_Proteins__
Author(s) : Karunatillaka I , Jaroszewski L , Godzik A
Ref : Proteins , : , 2021
Abstract : Several plastic degrading enzymes have been described in the literature, most notably PETases that are capable of hydrolyzing polyethylene terephthalate (PET) plastic. One of them, the PETase from Ideonella sakaiensis, a bacterium isolated from environmental samples within a PET bottle recycling site, was a subject of extensive studies. To test how widespread PETase functionality is in other bacterial communities, we used a cascade of BLAST searches in the JGI metagenomic datasets and showed that close homologs of I. sakaiensis PETase can also be found in other metagenomic environmental samples from both human-affected and relatively pristine sites. To confirm their classification as putative PETases, we verified that the newly identified proteins have the PETase sequence signatures common to known PETases and that phylogenetic analyses group them with the experimentally characterized PETases. Additionally, docking analysis was performed in order to further confirm the functional assignment of the putative environmental PETases.
ESTHER : Karunatillaka_2021_Proteins__
PubMedSearch : Karunatillaka_2021_Proteins__
PubMedID: 34553433

Title : Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution -
Author(s) : Zubieta C , Krishna SS , McMullan D , Miller MD , Abdubek P , Agarwalla S , Ambing E , Astakhova T , Axelrod HL , Carlton D , Chiu HJ , Clayton T , Deller M , DiDonato M , Duan L , Elsliger MA , Grzechnik SK , Hale J , Hampton E , Han GW , Haugen J , Jaroszewski L , Jin KK , Klock HE , Knuth MW , Koesema E , Kumar A , Marciano D , Morse AT , Nigoghossian E , Oommachen S , Reyes R , Rife CL , van den Bedem H , Weekes D , White A , Xu Q , Hodgson KO , Wooley J , Deacon AM , Godzik A , Lesley SA , Wilson IA
Ref : Proteins , 68 :999 , 2007
PubMedID: 17546672
Gene_locus related to this paper: bacce-BC4730

Title : Crystal structure of an alpha\/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution -
Author(s) : Arndt JW , Schwarzenbacher R , Page R , Abdubek P , Ambing E , Biorac T , Canaves JM , Chiu HJ , Dai X , Deacon AM , DiDonato M , Elsliger MA , Godzik A , Grittini C , Grzechnik SK , Hale J , Hampton E , Han GW , Haugen J , Hornsby M , Klock HE , Koesema E , Kreusch A , Kuhn P , Jaroszewski L , Lesley SA , Levin I , McMullan D , McPhillips TM , Miller MD , Morse A , Moy K , Nigoghossian E , Ouyang J , Peti WS , Quijano K , Reyes R , Sims E , Spraggon G , Stevens RC , van den Bedem H , Velasquez J , Vincent J , von Delft F , Wang X , West B , White A , Wolf G , Xu Q , Zagnitko O , Hodgson KO , Wooley J , Wilson IA
Ref : Proteins , 58 :755 , 2005
PubMedID: 15624212
Gene_locus related to this paper: yeast-YDR428C

Title : Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs - Okazaki_2002_Nature_420_563
Author(s) : Okazaki Y , Furuno M , Kasukawa T , Adachi J , Bono H , Kondo S , Nikaido I , Osato N , Saito R , Suzuki H , Yamanaka I , Kiyosawa H , Yagi K , Tomaru Y , Hasegawa Y , Nogami A , Schonbach C , Gojobori T , Baldarelli R , Hill DP , Bult C , Hume DA , Quackenbush J , Schriml LM , Kanapin A , Matsuda H , Batalov S , Beisel KW , Blake JA , Bradt D , Brusic V , Chothia C , Corbani LE , Cousins S , Dalla E , Dragani TA , Fletcher CF , Forrest A , Frazer KS , Gaasterland T , Gariboldi M , Gissi C , Godzik A , Gough J , Grimmond S , Gustincich S , Hirokawa N , Jackson IJ , Jarvis ED , Kanai A , Kawaji H , Kawasawa Y , Kedzierski RM , King BL , Konagaya A , Kurochkin IV , Lee Y , Lenhard B , Lyons PA , Maglott DR , Maltais L , Marchionni L , McKenzie L , Miki H , Nagashima T , Numata K , Okido T , Pavan WJ , Pertea G , Pesole G , Petrovsky N , Pillai R , Pontius JU , Qi D , Ramachandran S , Ravasi T , Reed JC , Reed DJ , Reid J , Ring BZ , Ringwald M , Sandelin A , Schneider C , Semple CA , Setou M , Shimada K , Sultana R , Takenaka Y , Taylor MS , Teasdale RD , Tomita M , Verardo R , Wagner L , Wahlestedt C , Wang Y , Watanabe Y , Wells C , Wilming LG , Wynshaw-Boris A , Yanagisawa M , Yang I , Yang L , Yuan Z , Zavolan M , Zhu Y , Zimmer A , Carninci P , Hayatsu N , Hirozane-Kishikawa T , Konno H , Nakamura M , Sakazume N , Sato K , Shiraki T , Waki K , Kawai J , Aizawa K , Arakawa T , Fukuda S , Hara A , Hashizume W , Imotani K , Ishii Y , Itoh M , Kagawa I , Miyazaki A , Sakai K , Sasaki D , Shibata K , Shinagawa A , Yasunishi A , Yoshino M , Waterston R , Lander ES , Rogers J , Birney E , Hayashizaki Y
Ref : Nature , 420 :563 , 2002
Abstract : Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
ESTHER : Okazaki_2002_Nature_420_563
PubMedSearch : Okazaki_2002_Nature_420_563
PubMedID: 12466851
Gene_locus related to this paper: mouse-1lipg , mouse-1llip , mouse-1plrp , mouse-3neur , mouse-ABH15 , mouse-abhd4 , mouse-abhd5 , mouse-Abhd8 , mouse-Abhd11 , mouse-abhda , mouse-acot4 , mouse-adcl4 , mouse-AI607300 , mouse-BAAT , mouse-bphl , mouse-C87498 , mouse-Ldah , mouse-Ces1d , mouse-Ces2e , mouse-CMBL , mouse-DGLB , mouse-dpp9 , mouse-ES10 , mouse-F135A , mouse-FASN , mouse-hslip , mouse-hyes , mouse-Kansl3 , mouse-LIPH , mouse-LIPK , mouse-lipli , mouse-LIPM , mouse-lypla1 , mouse-lypla2 , mouse-MEST , mouse-MGLL , mouse-ndr4 , mouse-OVCA2 , mouse-pafa , mouse-pcp , mouse-ppce , mouse-Ppgb , mouse-PPME1 , mouse-q3uuq7 , mouse-Q8BLF1 , mouse-ACOT6 , mouse-Q8C1A9 , mouse-Q9DAI6 , mouse-Q80UX8 , mouse-Q8BGG9 , mouse-Q8C167 , mouse-rbbp9 , mouse-SERHL , mouse-tssp

Title : The Aspergillus nidulans cysA gene encodes a novel type of serine O-acetyltransferase which is homologous to homoserine O-acetyltransferases - Grynberg_2000_Microbiology_146 ( Pt 10)_2695
Author(s) : Grynberg M , Topczewski J , Godzik A , Paszewski A
Ref : Microbiology , 146 ( Pt 10) :2695 , 2000
Abstract : The Aspergillus nidulans cysA gene was cloned by functional complementation of the cysA1 mutation that impairs the synthesis of O:-acetylserine. The molecular nature of cysA1 and cysA103 alleles was characterized; a nucleotide substitution and a frame shift were found in the former and a deletion mutation in the latter. The CYSA protein is 525 amino acids long and is encoded by an uninterrupted open reading frame. Expression of the cysA gene appears not to be regulated by sulfur, carbon and nitrogen sources. Protein sequence analysis reveals extensive similarity to homoserine O:-acetyltransferases, particularly the bacterial ones, and no homology with known serine O:-acetyltransferases. The authors propose that the CYSA protein is analogous to serine O:-acetyltransferases, i.e. it catalyses the same reaction but has an independent evolutionary origin.
ESTHER : Grynberg_2000_Microbiology_146 ( Pt 10)_2695
PubMedSearch : Grynberg_2000_Microbiology_146 ( Pt 10)_2695
PubMedID: 11021945
Gene_locus related to this paper: emeni-CYSC

Title : Functional analysis of the Escherichia coli genome for members of the alpha\/beta hydrolase family - Zhang_1998_Fold.Des_3_535
Author(s) : Zhang L , Godzik A , Skolnick J , Fetrow JS
Ref : Fold Des , 3 :535 , 1998
Abstract : BACKGROUND: Database-searching methods based on sequence similarity have become the most commonly used tools for characterizing newly sequenced proteins. Due to the often underestimated functional diversity in protein families and superfamilies, however, it is difficult to make the characterization specific and accurate. In this work, we have extended a method for active-site identification from predicted protein structures.
RESULTS: The structural conservation and variation of the active sites of the alpha/beta hydrolases with known structures were studied. The similarities were incorporated into a three-dimensional motif that specifies essential requirements for the enzymatic functions. A threading algorithm was used to align 651 Escherichia coli open reading frames (ORFs) to one of the members of the alpha/beta hydrolase fold family. These ORFs were then screened according to our three-dimensional motif and with an extra requirement that demands conservation of the key active-site residues among the proteins that bear significant sequence similarity to the ORFs. 17 ORFs from E. coli were predicted to have hydrolase activity and their putative active-site residues were identified. Most were in agreement with the experiments and results of other database-searching methods. The study further suggests that YHET_ECOLI, a hypothetical protein classified as a member of the UPF0017 family (an uncharacterized protein family), bears all the hallmarks of the alpha/beta hydrolase family.
CONCLUSIONS: The novel feature of our method is that it uses three-dimensional structural information for function prediction. The results demonstrate the importance and necessity of such a method to fill the gap between sequence alignment and function prediction; furthermore, the method provides a way to verify the structure predictions, which enables an expansion of the applicable scope of the threading algorithms.
ESTHER : Zhang_1998_Fold.Des_3_535
PubMedSearch : Zhang_1998_Fold.Des_3_535
PubMedID: 9889164