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6ii7

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Crystal structure of Plasmodium falciparum adenosine deaminase C27Q+L227I mutant co-complexed with Zn ion, hypoxanthine and inosine

Structural highlights

6ii7 is a 1 chain structure with sequence from Plasmodium falciparum 3D7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.48Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ADA_PLAF7 Catalyzes the hydrolytic deamination of adenosine to produce inosine (PubMed:19728741, PubMed:31002765). Unlike mammalian adenosine deaminases, also catalyzes the deamination of 5'-methylthioadenosine (MTA), a by-product of polyamine biosynthesis, to produce 5'-methylthioinosine (MTI) (PubMed:19728741, PubMed:31002765). Plays an essential role in the purine salvage pathway which allows the parasite to use host cell purines for the synthesis of nucleic acids (Probable).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Plasmodium falciparum (Pf), a malarial pathogen, can only synthesize purine nucleotides employing a salvage pathway because it lacks de novo biosynthesis. Adenosine deaminase (ADA), one of the three purine salvage enzymes, catalyzes the irreversible hydrolytic deamination of adenosine to inosine, which is further converted to GMP and AMP for DNA/RNA production. In addition to adenosine conversion, Plasmodium ADA also catalyzes the conversion of 5'-methylthioadenosine, derived from polyamine biosynthesis, into 5'-methylthioinosine whereas the human enzyme is not capable of this function. Here we report the crystal structure of a surface engineered PfADA at a resolution of 2.48A, together with results on kinetic studies of PfADA wild-type and active site variants. The structure reveals a novel inosine binding pocket linked to a distinctive PfADA substructure (residues 172-179) derived from a non-conserved gating helix loop (172-188) in Plasmodium spp. and other ADA enzymes. Variants of PfADA and human (h) ADA active site amino acids were generated in order to study their role in catalysis, including PfADA- Phe136, -Thr174, -Asp176, and -Leu179, and hADA-Met155, equivalent to PfADA-Asp176. PfADA-Leu179His showed no effect on kinetic parameters. However, kinetic results of PfADA-Asp176Met/Ala mutants and hADA-Met155Asp/Ala showed that the mutation reduced adenosine and 5'-methylthioadenosine substrate affinity in PfADA and kcat in hADA, thereby reducing catalytic efficiency of the enzyme. Phe136Leu mutant showed increased Km (>10-fold) for both substrates whereas Thr174Ile/Ala only affected 5'-methylthioadenosine binding affinity. Together, the structure with the novel inosine binding pocket and the kinetic data provide insights for rational design of inhibitors against PfADA.

Crystal structure of Plasmodium falciparum adenosine deaminase reveals a novel binding pocket for inosine.,Jaruwat A, Riangrungroj P, Ubonprasert S, Sae-Ueng U, Kuaprasert B, Yuthavong Y, Leartsakulpanich U, Chitnumsub P Arch Biochem Biophys. 2019 Apr 16;667:6-13. doi: 10.1016/j.abb.2019.04.002. PMID:31002765^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ho MC, Cassera MB, Madrid DC, Ting LM, Tyler PC, Kim K, Almo SC, Schramm VL. Structural and metabolic specificity of methylthiocoformycin for malarial adenosine deaminases. Biochemistry. 2009 Oct 13;48(40):9618-26. PMID:19728741 doi:http://dx.doi.org/10.1021/bi9012484
↑ Jaruwat A, Riangrungroj P, Ubonprasert S, Sae-Ueng U, Kuaprasert B, Yuthavong Y, Leartsakulpanich U, Chitnumsub P. Crystal structure of Plasmodium falciparum adenosine deaminase reveals a novel binding pocket for inosine. Arch Biochem Biophys. 2019 Apr 16;667:6-13. doi: 10.1016/j.abb.2019.04.002. PMID:31002765 doi:http://dx.doi.org/10.1016/j.abb.2019.04.002
↑ Ho MC, Cassera MB, Madrid DC, Ting LM, Tyler PC, Kim K, Almo SC, Schramm VL. Structural and metabolic specificity of methylthiocoformycin for malarial adenosine deaminases. Biochemistry. 2009 Oct 13;48(40):9618-26. PMID:19728741 doi:http://dx.doi.org/10.1021/bi9012484
↑ Jaruwat A, Riangrungroj P, Ubonprasert S, Sae-Ueng U, Kuaprasert B, Yuthavong Y, Leartsakulpanich U, Chitnumsub P. Crystal structure of Plasmodium falciparum adenosine deaminase reveals a novel binding pocket for inosine. Arch Biochem Biophys. 2019 Apr 16;667:6-13. doi: 10.1016/j.abb.2019.04.002. PMID:31002765 doi:http://dx.doi.org/10.1016/j.abb.2019.04.002

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6ii7"

Categories: Large Structures | Plasmodium falciparum 3D7 | Chitnumsub P | Jaruwat A

@@ Line 3: / Line 3: @@
 <StructureSection load='6ii7' size='340' side='right'caption='[[6ii7]], [[Resolution|resolution]] 2.48&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ii7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Plaf7 Plaf7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6II7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6II7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ii7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum_3D7 Plasmodium falciparum 3D7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6II7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6II7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene>, <scene name='pdbligand=NOS:INOSINE'>NOS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.48&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF3D7_1029600 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36329 PLAF7])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene>, <scene name='pdbligand=NOS:INOSINE'>NOS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6ii7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ii7 OCA], [https://pdbe.org/6ii7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ii7 RCSB], [https://www.ebi.ac.uk/pdbsum/6ii7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ii7 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ii7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ii7 OCA], [http://pdbe.org/6ii7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ii7 RCSB], [http://www.ebi.ac.uk/pdbsum/6ii7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ii7 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADA_PLAF7 ADA_PLAF7] Catalyzes the hydrolytic deamination of adenosine to produce inosine (PubMed:19728741, PubMed:31002765). Unlike mammalian adenosine deaminases, also catalyzes the deamination of 5'-methylthioadenosine (MTA), a by-product of polyamine biosynthesis, to produce 5'-methylthioinosine (MTI) (PubMed:19728741, PubMed:31002765). Plays an essential role in the purine salvage pathway which allows the parasite to use host cell purines for the synthesis of nucleic acids (Probable).<ref>PMID:19728741</ref> <ref>PMID:31002765</ref> <ref>PMID:19728741</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 6ii7" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Adenosine deaminase 3D structures|Adenosine deaminase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Adenosine deaminase]]
 [[Category: Large Structures]]
-[[Category: Plaf7]]
+[[Category: Plasmodium falciparum 3D7]]
-[[Category: Chitnumsub, P]]
+[[Category: Chitnumsub P]]
-[[Category: Jaruwat, A]]
+[[Category: Jaruwat A]]
-[[Category: Hydrolase]]
-[[Category: Tim barrel]]

6ii7

From Proteopedia

Current revision

Crystal structure of Plasmodium falciparum adenosine deaminase C27Q+L227I mutant co-complexed with Zn ion, hypoxanthine and inosine

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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