Deaminase

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<StructureSection load='1p6o' size='350' side='right' caption='Structure of yeast cytosine deaminase complex with pyrimidine-based inhibitor, acetate, Ca+2 (green) and Zn+2 (grey) ions (PDB entry [[1p6o]])' scene=''>
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<StructureSection load='1p6o' size='350' side='right' caption='Structure of yeast cytosine deaminase complex with pyrimidine-based inhibitor, acetate, Ca+2 (green) and Zn+2 (grey) ions (PDB entry [[1p6o]])' scene='55/551217/Cv/1'>
__TOC__
__TOC__
== Function ==
== Function ==
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* '''L-serine deaminase''' (LSD) converts L-serine to pyruvate.<br />
* '''L-serine deaminase''' (LSD) converts L-serine to pyruvate.<br />
* '''D-serine deaminase''' (DSD) converts D-serine to pyruvate.<br />
* '''D-serine deaminase''' (DSD) converts D-serine to pyruvate.<br />
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* '''Aminofutalosine deaminase''' deaminates aminofutalosine which is an intermediate in the menaquinone biosynthesis in ''Helicobacter pylori'' <ref>PMID:34077175</ref>. <br />
== Relevance ==
== Relevance ==
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== Structural highlights ==
== Structural highlights ==
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The active site of cytosine deaminase contains a catalytically active zinc atom.<ref>PMID:12906827</ref>
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The <scene name='55/551217/Cv/3'>active site of cytosine deaminase contains a catalytically active zinc</scene> atom.<ref>PMID:12906827</ref>
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</StructureSection>
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== 3D Structures of deaminase ==
== 3D Structures of deaminase ==
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[[Deaminase 3D structures]]
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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</StructureSection>
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*Cytidine deaminase
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**[[1r5t]] – yCDA - yeast <BR />
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**[[2a8n]] – AtCDA – ''Agrobacterium tumefaciens'' <BR />
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**[[2g84]] – CDA – ''Nitrosomonas europaea'' <BR />
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**[[2d30]] – CDA – ''Bacillus anthracis'' <BR />
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**[[3dmo]] – CDA – ''Burkholderia pseudomallei'' <BR />
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**[[3ijf]] – MtCDA – ''Mycobacterium tuberculosis'' <BR />
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**[[3mpz]] – CDA – ''Mycobacterium smegmatis'' <BR />
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**[[3r2n]] – CDA – ''Mycobacterium leprae'' <BR />
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**[[4f3w]] – CDA – ''Mycobacterium marinum'' <BR />
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*''Cytidine deaminase complex with nucleoside''
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**[[1ctt]] – EcCDA + dihydro-pyrimidinone – ''Escherichia coli'' <BR />
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**[[1ctu]] – EcCDA + hydroxyl-dihydro-zebularine <BR />
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**[[1af2]] – EcCDA + uridine <BR />
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**[[1aln]] – EcCDA + deazacytidine <BR />
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**[[1jtk]] – BsCDA + tetrahydrodeoxyuridine - ''Bacillus subtilis'' <BR />
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**[[1uwz]], [[1ux0]], [[1ux1]] – BsCDA (mutant) + tetrahydrodeoxyuridine <BR />
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**[[1mq0]] – hCDA + β-ribofuranosyl diazepinone - human <BR />
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**[[1zab]] – mCDA + deazauridine - mouse <BR />
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**[[2fr5]] – mCDA + tetrahydrouridine <BR />
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**[[2fr6]] – mCDA + cytidine + uridine <BR />
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**[[4eg2]] – CDA + uridine - ''Vibrio cholerae'' <BR />
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*Cytosine deaminase
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**[[1k6w]] – EcCDDA <BR />
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**[[1r9x]], [[1r9y]], [[1r9z]], [[1ra0]], [[1ra5]], [[3g77]] – EcCDDA (mutant)<BR />
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**[[1rb7]], [[1uaq]] – yCDDA <BR />
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**[[1ysb]], [[1ysd]] – yCDDA (mutant)<BR />
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*''Cytosine deaminase complex''
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**[[3r0d]] – EcCDDA + Zn <BR />
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**[[3rn6]] – EcCDDA + Zn + iso-guanine<BR />
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**[[1k70]] – EcCDDA + pyrimidine derivative<BR />
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**[[1rak]] – EcCDDA (mutant) + pyrimidine derivative<BR />
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**[[3o7u]] – EcCDDA + Zn + phosphono-cytosine<BR />
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**[[1ox7]] – yCDDA + Zn <BR />
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**[[1p6o]] – yCDDA + pyrimidine derivative<BR />
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**[[2o3k]] – yCDDA (mutant) + pyrimidine derivative<BR />
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**[[4r7w]], [[4r85]], [[4r88]] – CDDA + cytosine derivative – ''Klebsiella pneumoniae''<BR />
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* Deoxycytidylate deaminase
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**[[2hvv]], [[2hvw]] – SmDCMP - ''Streptococcus mutans'' <BR />
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**[[1vq2]] – DCMP - Enterobacteria phage T4 <BR />
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**[[4p9c]] – CyDCMP + deoxyCMP - Cyanophage S-TIM5 <BR />
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**[[4p9d]] – CyDCMP + TMP <BR />
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**[[4p9e]] – CyDCMP <BR />
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**[[2w4l]] – hDCMP<BR />
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*Guanine deaminase
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**[[1tiy]], [[1wkq]] – BsGDA <BR />
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**[[3e0l]] – hGDA<br />
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*''Guanine deaminase complex with nucleoside''
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**[[2i9u]] – GDA + guanine – ''Clostridium acetobutylicum'' <BR />
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**[[2ood]] – GDA + guanine – ''Bradrhizobium japonicum'' <BR />
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**[[2uz9]] – hGDA + xanthine <BR />
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**[[4aql]] – hGDA + valacyclovir <BR />
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*Adenine deaminase
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**[[2ics]] – ADA - ''Enterococcus faecalis''<BR />
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**[[3nqb]], [[3t81]], [[3t8l]] – AtADA <BR />
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*Adenosine deaminase See [[Adenosine deaminase]]
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*Glucosamine 6-phosphate deaminase
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**[[1dea]], [[1cd5]], [[1fs6]], [[1fsf]] – EcGPD <BR />
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**[[1jt9]] – EcGPD (mutant) <BR />
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**[[2ri0]] – SmGPD – ''Streptococcus mutans'' <BR />
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**[[3hn6]] – GPD – ''Borrelia burgdorferi''<br />
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**[[1j5x]] – GPD – ''Thermotoga maritima''<br />
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**[[2bkv]] – BsGPD <br />
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**[[2bkx]] – BsGPD + fructose 6-phosphate<BR />
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**[[4r7t]] – VcGPD <br />
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**[[1hor]] – EcGPD + deoxy-amino glucitol-phosphate<BR />
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**[[1hot]], [[1frz]], [[1fs5]], [[2wu1]] – EcGPD + N-acetyl-glucosamine-6-phosphate<BR />
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**[[1fqo]] – EcGPD + fructose 6-phosphate<BR />
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**[[2ri1]] – SmGPD + glucosamine-6-phosphate<BR />
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*1-aminocyclopropane-1-carboxylate (ACC) deaminase
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**[[1f2d]] – WsACCD + PLP – ''Williopsis saturnus''<BR />
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**[[1j0c]] – WsACCD (mutant) + PLP <BR />
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**[[1j0d]] – WsACCD (mutant) + inhibitor<BR />
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**[[1j0e]] – WsACCD (mutant) + PLP + ACC<BR />
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**[[1j0a]] – PhACCD + PLP + 2-propanol – ''Pyrococcus horikoshii''<BR />
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**[[1j0b]] – PhACCD + inhibitor<BR />
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**[[1tyz]] – PsACCD + PLP - ''Pseudomonas''<BR />
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**[[1rqx]] – PsACCD + PLP + inhibitor <BR />
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**[[1tz2]] – PsACCD + PLP + ACC<BR />
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**[[1tzj]] – PsACCD + PLP + vinylglycine<BR />
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**[[1tzk]] – PsACCD + PLP + α-ketobutyrate<BR />
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**[[1tzm]] – PsACCD + PLP + chloroalanine<BR />
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*dCTP deaminase
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**[[2qlp]] – MtCTPD <BR />
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**[[3km3]] – CTPD – ''Anaplasma phagocytophilum''<br />
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**[[4dhk]] – CTPD - ''Burkholderia thailandensis''<BR />
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*''dCTP deaminase complex''
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**[[1xs1]] – EcCTPD + dUTP<BR />
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**[[1xs4]] – EcCTPD (mutant) + dCTP<BR />
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**[[2j4h]] – EcCTPD (mutant) + dCDP<BR />
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**[[1xs6]], [[2v9x]] – EcCTPD (mutant) + dUTP<BR />
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**[[2j4q]] – EcCTPD (mutant) + dTTP + dTDP<BR />
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**[[2qxx]] – MtCTPD + dTTP<BR />
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*dCTP deaminase-dUTPase
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**[[2hxb]], [[1ogh]], [[1pkh]], [[3gf0]] – MjDCD-DUT – ''Methanocaldococcus jannaschii'' <BR />
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**[[1pkj]] – MjDCD-DUT + dUTP<BR />
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**[[2hxd]] – MjDCD-DUT (mutant) + dUTP derivative<BR />
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**[[1pkk]] – MjDCD-DUT + dCTP<BR />
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*Porphobilinogen deaminase See [[Porphobilinogen Deaminase]]
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*Blasticidin-S deaminase
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**[[1wn5]], [[2z3g]] – AtBSD – ''Aspergillus terreus'' <BR />
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**[[2z3j]] – AtBSD (mutant) <BR />
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**[[3oj6]] – BSD – Coccidioides immitis <BR />
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**[[1wn6]] – AtBSD + blasticidin-S intermediate<BR />
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**[[2z3h]] – AtBSD + deaminohydroxy blasticidin-S <BR />
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**[[2z3i]] – AtBSD (mutant) + blasticidin-S <BR />
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*Threonine deaminase
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**[[1tdj]] – EcTHD + PLP <BR />
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**[[2gn0]], [[2gn1]] – StTHD + PLP derivative – ''Salmonella typhimurium''<BR />
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**[[2gn2]] – StTHD + PLP derivative + CMP<BR />
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**[[3iau]] – THD + PLP derivative – tomato<BR />
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**[[1ve5]] – THD + PLP – ''Thermus thermophilus''<BR />
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*L-serine deaminase
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**[[1pwe]] – rLSD - rat <BR />
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**[[1p5j]], [[2rkb]] – hLSD (mutant) + PLP <BR />
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**[[1pwh]] – rLSD + PLP derivative <BR />
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*D-serine deaminase
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**[[3r0x]], [[3r0z]] – DSD – ''Salmonella enterica''<BR />
 
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**[[3ss7]], [[3ss9]] – EcDSD + PLP <BR />
 
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**[[3gwq]] – DSD - ''Burkholderia xenovorans''<BR />
 
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}}
 
== References ==
== References ==
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

Structure of yeast cytosine deaminase complex with pyrimidine-based inhibitor, acetate, Ca+2 (green) and Zn+2 (grey) ions (PDB entry 1p6o)

Drag the structure with the mouse to rotate

References

  1. ↑ Bransteitter R, Pham P, Scharff MD, Goodman MF. Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase. Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):4102-7. Epub 2003 Mar 21. PMID:12651944 doi:http://dx.doi.org/10.1073/pnas.0730835100
  2. ↑ Egeblad L, Welin M, Flodin S, Graslund S, Wang L, Balzarini J, Eriksson S, Nordlund P. Pan-Pathway Based Interaction Profiling of FDA-Approved Nucleoside and Nucleobase Analogs with Enzymes of the Human Nucleotide Metabolism. PLoS One. 2012;7(5):e37724. Epub 2012 May 25. PMID:22662200 doi:10.1371/journal.pone.0037724
  3. ↑ Feng M, Harijan RK, Harris LD, Tyler PC, Frohlich RFG, Brown M, Schramm VL. Aminofutalosine Deaminase in the Menaquinone Pathway of Helicobacter pylori. Biochemistry. 2021 Jun 22;60(24):1933-1946. doi: 10.1021/acs.biochem.1c00215., Epub 2021 Jun 2. PMID:34077175 doi:http://dx.doi.org/10.1021/acs.biochem.1c00215
  4. ↑ Negroni L, Samson M, Guigonis JM, Rossi B, Pierrefite-Carle V, Baudoin C. Treatment of colon cancer cells using the cytosine deaminase/5-fluorocytosine suicide system induces apoptosis, modulation of the proteome, and Hsp90beta phosphorylation. Mol Cancer Ther. 2007 Oct;6(10):2747-56. PMID:17938268 doi:http://dx.doi.org/10.1158/1535-7163.MCT-07-0040
  5. ↑ Ireton GC, Black ME, Stoddard BL. The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy. Structure. 2003 Aug;11(8):961-72. PMID:12906827

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Michal Harel, Alexander Berchansky

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