3jwp: Difference between revisions

Latest revision as of 06:22, 27 November 2024

Crystal structure of Plasmodium falciparum SIR2A (PF13_0152) in complex with AMP

Structural highlights

3jwp 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 2.65Å
Ligands:	AMP, MSE, PGE, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SIR2A_PLAF7 NAD-dependent protein deacylase (PubMed:21992006). Catalyzes the NAD-dependent hydrolysis of medium and long chain fatty acyl groups from lysine residues (PubMed:21992006). Has weak NAD-dependent protein deacetylase activity (PubMed:17827348, PubMed:18221799, PubMed:18397290, PubMed:18729382, PubMed:20601220, PubMed:21992006). Regulates the endonuclease activity of ALBA3 by deacetylation of 'Lys-23' (PubMed:22006844, PubMed:36947546). Regulates the expression of the surface antigen-coding var genes central to the malaria pathogenesis (PubMed:15820676, PubMed:22379140). Cooperates with Sir2B to mediate silencing and mutual exclusive expression of only 1 of the 60 subtelomeric var genes at a time, coding for functionally different but epitopically variant versions of the erythrocyte membrane protein 1 (PfEMP1) molecule, to evade the detection by host immune surveillance (PubMed:19402747). Involved in recruiting ORC1 to the telomers and subtelomeric repeat regions (TAREs) and promoters of var genes (PubMed:22379140). Can ADP-ribosylate both histones and itself (PubMed:17827348). May also have a role in telomeric end protection (PubMed:18525026).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Freitas-Junior LH, Hernandez-Rivas R, Ralph SA, Montiel-Condado D, Ruvalcaba-Salazar OK, Rojas-Meza AP, Mancio-Silva L, Leal-Silvestre RJ, Gontijo AM, Shorte S, Scherf A. Telomeric heterochromatin propagation and histone acetylation control mutually exclusive expression of antigenic variation genes in malaria parasites. Cell. 2005 Apr 8;121(1):25-36. PMID:15820676 doi:10.1016/j.cell.2005.01.037
↑ Merrick CJ, Duraisingh MT. Plasmodium falciparum Sir2: an unusual sirtuin with dual histone deacetylase and ADP-ribosyltransferase activity. Eukaryot Cell. 2007 Nov;6(11):2081-91. Epub 2007 Sep 7. PMID:17827348 doi:10.1128/EC.00114-07
↑ Chakrabarty SP, Saikumari YK, Bopanna MP, Balaram H. Biochemical characterization of Plasmodium falciparum Sir2, a NAD+-dependent deacetylase. Mol Biochem Parasitol. 2008 Apr;158(2):139-51. doi:, 10.1016/j.molbiopara.2007.12.003. Epub 2007 Dec 15. PMID:18221799 doi:10.1016/j.molbiopara.2007.12.003
↑ Prusty D, Mehra P, Srivastava S, Shivange AV, Gupta A, Roy N, Dhar SK. Nicotinamide inhibits Plasmodium falciparum Sir2 activity in vitro and parasite growth. FEMS Microbiol Lett. 2008 May;282(2):266-72. doi:, 10.1111/j.1574-6968.2008.01135.x. Epub 2008 Apr 2. PMID:18397290 doi:10.1111/j.1574-6968.2008.01135.x
↑ Mancio-Silva L, Rojas-Meza AP, Vargas M, Scherf A, Hernandez-Rivas R. Differential association of Orc1 and Sir2 proteins to telomeric domains in Plasmodium falciparum. J Cell Sci. 2008 Jun 15;121(Pt 12):2046-53. doi: 10.1242/jcs.026427. PMID:18525026 doi:10.1242/jcs.026427
↑ French JB, Cen Y, Sauve AA. Plasmodium falciparum Sir2 is an NAD+-dependent deacetylase and an acetyllysine-dependent and acetyllysine-independent NAD+ glycohydrolase. Biochemistry. 2008 Sep 23;47(38):10227-39. doi: 10.1021/bi800767t. Epub 2008 Aug , 26. PMID:18729382 doi:10.1021/bi800767t
↑ Tonkin CJ, Carret CK, Duraisingh MT, Voss TS, Ralph SA, Hommel M, Duffy MF, Silva LM, Scherf A, Ivens A, Speed TP, Beeson JG, Cowman AF. Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum. PLoS Biol. 2009 Apr 14;7(4):e84. doi: 10.1371/journal.pbio.1000084. PMID:19402747 doi:10.1371/journal.pbio.1000084
↑ Chakrabarty SP, Balaram H. Reversible binding of zinc in Plasmodium falciparum Sir2: structure and activity of the apoenzyme. Biochim Biophys Acta. 2010 Sep;1804(9):1743-50. doi:, 10.1016/j.bbapap.2010.06.010. Epub 2010 Jun 23. PMID:20601220 doi:10.1016/j.bbapap.2010.06.010
↑ Zhu AY, Zhou Y, Khan S, Deitsch KW, Hao Q, Lin H. Plasmodium falciparum Sir2A Preferentially Hydrolyzes Medium and Long Chain Fatty Acyl Lysine. ACS Chem Biol. 2011 Oct 21. PMID:21992006 doi:10.1021/cb200230x
↑ Goyal M, Alam A, Iqbal MS, Dey S, Bindu S, Pal C, Banerjee A, Chakrabarti S, Bandyopadhyay U. Identification and molecular characterization of an Alba-family protein from human malaria parasite Plasmodium falciparum. Nucleic Acids Res. 2012 Feb;40(3):1174-90. PMID:22006844 doi:10.1093/nar/gkr821
↑ Deshmukh AS, Srivastava S, Herrmann S, Gupta A, Mitra P, Gilberger TW, Dhar SK. The role of N-terminus of Plasmodium falciparum ORC1 in telomeric localization and var gene silencing. Nucleic Acids Res. 2012 Jul;40(12):5313-31. PMID:22379140 doi:10.1093/nar/gks202
↑ Banerjee C, Nag S, Goyal M, Saha D, Siddiqui AA, Mazumder S, Debsharma S, Pramanik S, Bandyopadhyay U. Nuclease activity of Plasmodium falciparum Alba family protein PfAlba3. Cell Rep. 2023 Apr 25;42(4):112292. PMID:36947546 doi:10.1016/j.celrep.2023.112292

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Freitas-Junior LH, Hernandez-Rivas R, Ralph SA, Montiel-Condado D, Ruvalcaba-Salazar OK, Rojas-Meza AP, Mancio-Silva L, Leal-Silvestre RJ, Gontijo AM, Shorte S, Scherf A. Telomeric heterochromatin propagation and histone acetylation control mutually exclusive expression of antigenic variation genes in malaria parasites. Cell. 2005 Apr 8;121(1):25-36. PMID:15820676 doi:10.1016/j.cell.2005.01.037

[2] Merrick CJ, Duraisingh MT. Plasmodium falciparum Sir2: an unusual sirtuin with dual histone deacetylase and ADP-ribosyltransferase activity. Eukaryot Cell. 2007 Nov;6(11):2081-91. Epub 2007 Sep 7. PMID:17827348 doi:10.1128/EC.00114-07

[3] Chakrabarty SP, Saikumari YK, Bopanna MP, Balaram H. Biochemical characterization of Plasmodium falciparum Sir2, a NAD+-dependent deacetylase. Mol Biochem Parasitol. 2008 Apr;158(2):139-51. doi:, 10.1016/j.molbiopara.2007.12.003. Epub 2007 Dec 15. PMID:18221799 doi:10.1016/j.molbiopara.2007.12.003

[4] Prusty D, Mehra P, Srivastava S, Shivange AV, Gupta A, Roy N, Dhar SK. Nicotinamide inhibits Plasmodium falciparum Sir2 activity in vitro and parasite growth. FEMS Microbiol Lett. 2008 May;282(2):266-72. doi:, 10.1111/j.1574-6968.2008.01135.x. Epub 2008 Apr 2. PMID:18397290 doi:10.1111/j.1574-6968.2008.01135.x

[5] Mancio-Silva L, Rojas-Meza AP, Vargas M, Scherf A, Hernandez-Rivas R. Differential association of Orc1 and Sir2 proteins to telomeric domains in Plasmodium falciparum. J Cell Sci. 2008 Jun 15;121(Pt 12):2046-53. doi: 10.1242/jcs.026427. PMID:18525026 doi:10.1242/jcs.026427

[6] French JB, Cen Y, Sauve AA. Plasmodium falciparum Sir2 is an NAD+-dependent deacetylase and an acetyllysine-dependent and acetyllysine-independent NAD+ glycohydrolase. Biochemistry. 2008 Sep 23;47(38):10227-39. doi: 10.1021/bi800767t. Epub 2008 Aug , 26. PMID:18729382 doi:10.1021/bi800767t

[7] Tonkin CJ, Carret CK, Duraisingh MT, Voss TS, Ralph SA, Hommel M, Duffy MF, Silva LM, Scherf A, Ivens A, Speed TP, Beeson JG, Cowman AF. Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum. PLoS Biol. 2009 Apr 14;7(4):e84. doi: 10.1371/journal.pbio.1000084. PMID:19402747 doi:10.1371/journal.pbio.1000084

[8] Chakrabarty SP, Balaram H. Reversible binding of zinc in Plasmodium falciparum Sir2: structure and activity of the apoenzyme. Biochim Biophys Acta. 2010 Sep;1804(9):1743-50. doi:, 10.1016/j.bbapap.2010.06.010. Epub 2010 Jun 23. PMID:20601220 doi:10.1016/j.bbapap.2010.06.010

[9] Zhu AY, Zhou Y, Khan S, Deitsch KW, Hao Q, Lin H. Plasmodium falciparum Sir2A Preferentially Hydrolyzes Medium and Long Chain Fatty Acyl Lysine. ACS Chem Biol. 2011 Oct 21. PMID:21992006 doi:10.1021/cb200230x

[10] Goyal M, Alam A, Iqbal MS, Dey S, Bindu S, Pal C, Banerjee A, Chakrabarti S, Bandyopadhyay U. Identification and molecular characterization of an Alba-family protein from human malaria parasite Plasmodium falciparum. Nucleic Acids Res. 2012 Feb;40(3):1174-90. PMID:22006844 doi:10.1093/nar/gkr821

[11] Deshmukh AS, Srivastava S, Herrmann S, Gupta A, Mitra P, Gilberger TW, Dhar SK. The role of N-terminus of Plasmodium falciparum ORC1 in telomeric localization and var gene silencing. Nucleic Acids Res. 2012 Jul;40(12):5313-31. PMID:22379140 doi:10.1093/nar/gks202

[12] Banerjee C, Nag S, Goyal M, Saha D, Siddiqui AA, Mazumder S, Debsharma S, Pramanik S, Bandyopadhyay U. Nuclease activity of Plasmodium falciparum Alba family protein PfAlba3. Cell Rep. 2023 Apr 25;42(4):112292. PMID:36947546 doi:10.1016/j.celrep.2023.112292

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@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3jwp.jpg|left|200px]]
-<!--
+==Crystal structure of Plasmodium falciparum SIR2A (PF13_0152) in complex with AMP==
-The line below this paragraph, containing "STRUCTURE_3jwp", creates the "Structure Box" on the page.
+<StructureSection load='3jwp' size='340' side='right'caption='[[3jwp]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3jwp]] 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=3JWP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JWP FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3jwp|  PDB=3jwp  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3jwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jwp OCA], [https://pdbe.org/3jwp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jwp RCSB], [https://www.ebi.ac.uk/pdbsum/3jwp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jwp ProSAT]</span></td></tr>
+</table>
-===Crystal structure of Plasmodium falciparum SIR2A (PF13_0152) in complex with AMP===
+== Function ==
+[https://www.uniprot.org/uniprot/SIR2A_PLAF7 SIR2A_PLAF7] NAD-dependent protein deacylase (PubMed:21992006). Catalyzes the NAD-dependent hydrolysis of medium and long chain fatty acyl groups from lysine residues (PubMed:21992006). Has weak NAD-dependent protein deacetylase activity (PubMed:17827348, PubMed:18221799, PubMed:18397290, PubMed:18729382, PubMed:20601220, PubMed:21992006). Regulates the endonuclease activity of ALBA3 by deacetylation of 'Lys-23' (PubMed:22006844, PubMed:36947546). Regulates the expression of the surface antigen-coding var genes central to the malaria pathogenesis (PubMed:15820676, PubMed:22379140). Cooperates with Sir2B to mediate silencing and mutual exclusive expression of only 1 of the 60 subtelomeric var genes at a time, coding for functionally different but epitopically variant versions of the erythrocyte membrane protein 1 (PfEMP1) molecule, to evade the detection by host immune surveillance (PubMed:19402747). Involved in recruiting ORC1 to the telomers and subtelomeric repeat regions (TAREs) and promoters of var genes (PubMed:22379140). Can ADP-ribosylate both histones and itself (PubMed:17827348). May also have a role in telomeric end protection (PubMed:18525026).<ref>PMID:15820676</ref> <ref>PMID:17827348</ref> <ref>PMID:18221799</ref> <ref>PMID:18397290</ref> <ref>PMID:18525026</ref> <ref>PMID:18729382</ref> <ref>PMID:19402747</ref> <ref>PMID:20601220</ref> <ref>PMID:21992006</ref> <ref>PMID:22006844</ref> <ref>PMID:22379140</ref> <ref>PMID:36947546</ref>
+== Evolutionary Conservation ==
-==About this Structure==
+[[Image:Consurf_key_small.gif|200px|right]]
-JWP is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JWP OCA].
+Check<jmol>
-[[Category: Plasmodium falciparum]]
+  <jmolCheckbox>
-[[Category: Allali-Hassanali, A.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jw/3jwp_consurf.spt"</scriptWhenChecked>
-[[Category: Arrowsmith, C H.]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
-[[Category: Bountra, C.]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: Brand, V.]]
+  </jmolCheckbox>
-[[Category: Cossar, D.]]
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3jwp ConSurf].
-[[Category: Edwards, A M.]]
+<div style="clear:both"></div>
-[[Category: Hui, R.]]
+== References ==
-[[Category: Hutchinson, A.]]
+<references/>
-[[Category: Kozieradzki, I.]]
+__TOC__
-[[Category: Lin, Y H.]]
+</StructureSection>
-[[Category: MacKenzie, F.]]
+[[Category: Large Structures]]
-[[Category: Qiu, W.]]
+[[Category: Plasmodium falciparum 3D7]]
-[[Category: Ravichandran, M.]]
+[[Category: Allali-Hassanali A]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Arrowsmith CH]]
-[[Category: Schapira, M.]]
+[[Category: Bountra C]]
-[[Category: Senisterra, G.]]
+[[Category: Brand V]]
-[[Category: Vedadi, M.]]
+[[Category: Cossar D]]
-[[Category: Weigelt, J.]]
+[[Category: Edwards AM]]
-[[Category: Wernimont, A K.]]
+[[Category: Hui R]]
-[[Category: Zhao, Y.]]
+[[Category: Hutchinson A]]
-[[Category: Malaria]]
+[[Category: Kozieradzki I]]
-[[Category: Sgc]]
+[[Category: Lin YH]]
-[[Category: Structural genomic]]
+[[Category: MacKenzie F]]
-[[Category: Structural genomics consortium]]
+[[Category: Qiu W]]
-[[Category: Transcription regulation]]
+[[Category: Ravichandran M]]
+[[Category: Schapira M]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 21 10:42:17 2009''
+[[Category: Senisterra G]]
+[[Category: Vedadi M]]
+[[Category: Weigelt J]]
+[[Category: Wernimont AK]]
+[[Category: Zhao Y]]

3jwp: Difference between revisions

Latest revision as of 06:22, 27 November 2024

Crystal structure of Plasmodium falciparum SIR2A (PF13_0152) in complex with AMP

Structural highlights

Function

Evolutionary Conservation

References

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