Deaminase

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<StructureSection load='1p6o' size='350' side='right' caption='Structure of cytidine deaminase complex with deazacytosine (PDB entry [[1aln]])' 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'>
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__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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Mutation in adenine deaminase results in deficiency of the enzyme and is the cause of severe combined immunodeficiency (SCID).
Mutation in adenine deaminase results in deficiency of the enzyme and is the cause of severe combined immunodeficiency (SCID).
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</StructureSection>
 
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== 3D Structures of deaminase ==
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== Structural highlights ==
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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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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{{#tree:id=OrganizedByTopic|openlevels=0|
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*Cytidine deaminase
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== 3D Structures of deaminase ==
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[[Deaminase 3D structures]]
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**[[1r5t]] – yCDA - yeast <BR />
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</StructureSection>
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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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