6ppl

From Proteopedia

(Difference between revisions)

Revision as of 10:26, 26 February 2020

Cryo-EM structure of human NatE complex (NatA/Naa50)

Structural highlights

6ppl is a 3 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Gene:	NAA50, MAK3, NAT13, NAT5 (HUMAN), NAA15, GA19, NARG1, NATH, TBDN100 (HUMAN), NAA10, ARD1, ARD1A, TE2 (HUMAN)
Activity:	N-terminal amino-acid N(alpha)-acetyltransferase NatA, with EC number 2.3.1.255
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[NAA10_HUMAN] Premature aging appearance-developmental delay-cardiac arrhythmia syndrome;Microphthalmia, Lenz type. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.

Function

[NAA50_HUMAN] Probable catalytic component of the NAA11-NAA15 complex which displays alpha (N-terminal) acetyltransferase activity.^[1] [NAA10_HUMAN] Catalytic subunit of the N-terminal acetyltransferase A (NatA) complex which displays alpha (N-terminal) acetyltransferase activity (PubMed:15496142, PubMed:19826488, PubMed:19420222, PubMed:20145209, PubMed:27708256, PubMed:25489052). Acetylates amino termini that are devoid of initiator methionine (PubMed:19420222). The alpha (N-terminal) acetyltransferase activity may be important for vascular, hematopoietic and neuronal growth and development. Without NAA15, displays epsilon (internal) acetyltransferase activity towards HIF1A, thereby promoting its degradation (PubMed:12464182). Represses MYLK kinase activity by acetylation, and thus represses tumor cell migration (PubMed:19826488). Acetylates, and stabilizes TSC2, thereby repressing mTOR activity and suppressing cancer development (PubMed:20145209). Acetylates HSPA1A and HSPA1B at 'Lys-77' which enhances its chaperone activity and leads to preferential binding to co-chaperone HOPX (PubMed:27708256). Acts as a negative regulator of sister chromatid cohesion during mitosis (PubMed:27422821).^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] [NAA15_HUMAN] Auxillary subunit of the N-terminal acetyltransferase A (NatA) complex which displays alpha (N-terminal) acetyltransferase activity. The NAT activity may be important for vascular, hematopoietic and neuronal growth and development. Required to control retinal neovascularization in adult ocular endothelial cells. In complex with XRCC6 and XRCC5 (Ku80), up-regulates transcription from the osteocalcin promoter.^[10] ^[11] ^[12]

Publication Abstract from PubMed

The human N-terminal acetyltransferase E (NatE) contains NAA10 and NAA50 catalytic, and NAA15 auxiliary subunits and associates with HYPK, a protein with intrinsic NAA10 inhibitory activity. NatE co-translationally acetylates the N-terminus of half the proteome to mediate diverse biological processes, including protein half-life, localization, and interaction. The molecular basis for how NatE and HYPK cooperate is unknown. Here, we report the cryo-EM structures of human NatE and NatE/HYPK complexes and associated biochemistry. We reveal that NAA50 and HYPK exhibit negative cooperative binding to NAA15 in vitro and in human cells by inducing NAA15 shifts in opposing directions. NAA50 and HYPK each contribute to NAA10 activity inhibition through structural alteration of the NAA10 substrate-binding site. NAA50 activity is increased through NAA15 tethering, but is inhibited by HYPK through structural alteration of the NatE substrate-binding site. These studies reveal the molecular basis for coordinated N-terminal acetylation by NatE and HYPK.

Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK.,Deng S, McTiernan N, Wei X, Arnesen T, Marmorstein R Nat Commun. 2020 Feb 10;11(1):818. doi: 10.1038/s41467-020-14584-7. PMID:32042062^[13]

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

References

↑ Arnesen T, Anderson D, Torsvik J, Halseth HB, Varhaug JE, Lillehaug JR. Cloning and characterization of hNAT5/hSAN: an evolutionarily conserved component of the NatA protein N-alpha-acetyltransferase complex. Gene. 2006 Apr 26;371(2):291-5. Epub 2006 Feb 28. PMID:16507339 doi:http://dx.doi.org/S0378-1119(05)00749-3
↑ Jeong JW, Bae MK, Ahn MY, Kim SH, Sohn TK, Bae MH, Yoo MA, Song EJ, Lee KJ, Kim KW. Regulation and destabilization of HIF-1alpha by ARD1-mediated acetylation. Cell. 2002 Nov 27;111(5):709-20. PMID:12464182
↑ Arnesen T, Anderson D, Baldersheim C, Lanotte M, Varhaug JE, Lillehaug JR. Identification and characterization of the human ARD1-NATH protein acetyltransferase complex. Biochem J. 2005 Mar 15;386(Pt 3):433-43. doi: 10.1042/BJ20041071. PMID:15496142 doi:http://dx.doi.org/10.1042/BJ20041071
↑ Arnesen T, Van Damme P, Polevoda B, Helsens K, Evjenth R, Colaert N, Varhaug JE, Vandekerckhove J, Lillehaug JR, Sherman F, Gevaert K. Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans. Proc Natl Acad Sci U S A. 2009 May 19;106(20):8157-62. doi:, 10.1073/pnas.0901931106. Epub 2009 May 6. PMID:19420222 doi:http://dx.doi.org/10.1073/pnas.0901931106
↑ Shin DH, Chun YS, Lee KH, Shin HW, Park JW. Arrest defective-1 controls tumor cell behavior by acetylating myosin light chain kinase. PLoS One. 2009 Oct 14;4(10):e7451. doi: 10.1371/journal.pone.0007451. PMID:19826488 doi:10.1371/journal.pone.0007451
↑ Kuo HP, Lee DF, Chen CT, Liu M, Chou CK, Lee HJ, Du Y, Xie X, Wei Y, Xia W, Weihua Z, Yang JY, Yen CJ, Huang TH, Tan M, Xing G, Zhao Y, Lin CH, Tsai SF, Fidler IJ, Hung MC. ARD1 stabilization of TSC2 suppresses tumorigenesis through the mTOR signaling pathway. Sci Signal. 2010 Feb 9;3(108):ra9. doi: 10.1126/scisignal.2000590. PMID:20145209 doi:http://dx.doi.org/10.1126/scisignal.2000590
↑ Myklebust LM, Van Damme P, Stove SI, Dorfel MJ, Abboud A, Kalvik TV, Grauffel C, Jonckheere V, Wu Y, Swensen J, Kaasa H, Liszczak G, Marmorstein R, Reuter N, Lyon GJ, Gevaert K, Arnesen T. Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Hum Mol Genet. 2015 Apr 1;24(7):1956-76. doi: 10.1093/hmg/ddu611. Epub 2014 Dec, 8. PMID:25489052 doi:http://dx.doi.org/10.1093/hmg/ddu611
↑ Rong Z, Ouyang Z, Magin RS, Marmorstein R, Yu H. Opposing Functions of the N-terminal Acetyltransferases Naa50 and NatA in Sister-chromatid Cohesion. J Biol Chem. 2016 Sep 2;291(36):19079-91. doi: 10.1074/jbc.M116.737585. Epub 2016, Jul 15. PMID:27422821 doi:http://dx.doi.org/10.1074/jbc.M116.737585
↑ Seo JH, Park JH, Lee EJ, Vo TT, Choi H, Kim JY, Jang JK, Wee HJ, Lee HS, Jang SH, Park ZY, Jeong J, Lee KJ, Seok SH, Park JY, Lee BJ, Lee MN, Oh GT, Kim KW. ARD1-mediated Hsp70 acetylation balances stress-induced protein refolding and degradation. Nat Commun. 2016 Oct 6;7:12882. doi: 10.1038/ncomms12882. PMID:27708256 doi:http://dx.doi.org/10.1038/ncomms12882
↑ Gendron RL, Good WV, Adams LC, Paradis H. Suppressed expression of tubedown-1 in retinal neovascularization of proliferative diabetic retinopathy. Invest Ophthalmol Vis Sci. 2001 Nov;42(12):3000-7. PMID:11687548
↑ Willis DM, Loewy AP, Charlton-Kachigian N, Shao JS, Ornitz DM, Towler DA. Regulation of osteocalcin gene expression by a novel Ku antigen transcription factor complex. J Biol Chem. 2002 Oct 4;277(40):37280-91. Epub 2002 Jul 26. PMID:12145306 doi:http://dx.doi.org/10.1074/jbc.M206482200
↑ Arnesen T, Anderson D, Baldersheim C, Lanotte M, Varhaug JE, Lillehaug JR. Identification and characterization of the human ARD1-NATH protein acetyltransferase complex. Biochem J. 2005 Mar 15;386(Pt 3):433-43. doi: 10.1042/BJ20041071. PMID:15496142 doi:http://dx.doi.org/10.1042/BJ20041071
↑ Deng S, McTiernan N, Wei X, Arnesen T, Marmorstein R. Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK. Nat Commun. 2020 Feb 10;11(1):818. doi: 10.1038/s41467-020-14584-7. PMID:32042062 doi:http://dx.doi.org/10.1038/s41467-020-14584-7

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='6ppl' size='340' side='right'caption='[[6ppl]], [[Resolution|resolution]] 3.02&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ppl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PPL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ppl]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PPL FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NAA50, MAK3, NAT13, NAT5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NAA15, GA19, NARG1, NATH, TBDN100 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NAA10, ARD1, ARD1A, TE2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-terminal_amino-acid_N(alpha)-acetyltransferase_NatA N-terminal amino-acid N(alpha)-acetyltransferase NatA], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.255 2.3.1.255] </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=6ppl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ppl OCA], [http://pdbe.org/6ppl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ppl RCSB], [http://www.ebi.ac.uk/pdbsum/6ppl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ppl ProSAT]</span></td></tr>
@@ Line 13: / Line 14: @@
 == Function ==
 [[http://www.uniprot.org/uniprot/NAA50_HUMAN NAA50_HUMAN]] Probable catalytic component of the NAA11-NAA15 complex which displays alpha (N-terminal) acetyltransferase activity.<ref>PMID:16507339</ref>  [[http://www.uniprot.org/uniprot/NAA10_HUMAN NAA10_HUMAN]] Catalytic subunit of the N-terminal acetyltransferase A (NatA) complex which displays alpha (N-terminal) acetyltransferase activity (PubMed:15496142, PubMed:19826488, PubMed:19420222, PubMed:20145209, PubMed:27708256, PubMed:25489052). Acetylates amino termini that are devoid of initiator methionine (PubMed:19420222). The alpha (N-terminal) acetyltransferase activity may be important for vascular, hematopoietic and neuronal growth and development. Without NAA15, displays epsilon (internal) acetyltransferase activity towards HIF1A, thereby promoting its degradation (PubMed:12464182). Represses MYLK kinase activity by acetylation, and thus represses tumor cell migration (PubMed:19826488). Acetylates, and stabilizes TSC2, thereby repressing mTOR activity and suppressing cancer development (PubMed:20145209). Acetylates HSPA1A and HSPA1B at 'Lys-77' which enhances its chaperone activity and leads to preferential binding to co-chaperone HOPX (PubMed:27708256). Acts as a negative regulator of sister chromatid cohesion during mitosis (PubMed:27422821).<ref>PMID:12464182</ref> <ref>PMID:15496142</ref> <ref>PMID:19420222</ref> <ref>PMID:19826488</ref> <ref>PMID:20145209</ref> <ref>PMID:25489052</ref> <ref>PMID:27422821</ref> <ref>PMID:27708256</ref>  [[http://www.uniprot.org/uniprot/NAA15_HUMAN NAA15_HUMAN]] Auxillary subunit of the N-terminal acetyltransferase A (NatA) complex which displays alpha (N-terminal) acetyltransferase activity. The NAT activity may be important for vascular, hematopoietic and neuronal growth and development. Required to control retinal neovascularization in adult ocular endothelial cells. In complex with XRCC6 and XRCC5 (Ku80), up-regulates transcription from the osteocalcin promoter.<ref>PMID:11687548</ref> <ref>PMID:12145306</ref> <ref>PMID:15496142</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The human N-terminal acetyltransferase E (NatE) contains NAA10 and NAA50 catalytic, and NAA15 auxiliary subunits and associates with HYPK, a protein with intrinsic NAA10 inhibitory activity. NatE co-translationally acetylates the N-terminus of half the proteome to mediate diverse biological processes, including protein half-life, localization, and interaction. The molecular basis for how NatE and HYPK cooperate is unknown. Here, we report the cryo-EM structures of human NatE and NatE/HYPK complexes and associated biochemistry. We reveal that NAA50 and HYPK exhibit negative cooperative binding to NAA15 in vitro and in human cells by inducing NAA15 shifts in opposing directions. NAA50 and HYPK each contribute to NAA10 activity inhibition through structural alteration of the NAA10 substrate-binding site. NAA50 activity is increased through NAA15 tethering, but is inhibited by HYPK through structural alteration of the NatE substrate-binding site. These studies reveal the molecular basis for coordinated N-terminal acetylation by NatE and HYPK.
+Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK.,Deng S, McTiernan N, Wei X, Arnesen T, Marmorstein R Nat Commun. 2020 Feb 10;11(1):818. doi: 10.1038/s41467-020-14584-7. PMID:32042062<ref>PMID:32042062</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6ppl" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
 [[Category: Large Structures]]
 [[Category: Deng, S]]

6ppl

From Proteopedia

Revision as of 10:26, 26 February 2020

Cryo-EM structure of human NatE complex (NatA/Naa50)

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox