4u9v: Difference between revisions

Revision as of 08:10, 22 March 2023

Crystal structure of NatD (Naa40p) bound to acetyl CoA

Structural highlights

4u9v is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ACO
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAA40_HUMAN Responsible for the acetylation of the N-terminal residues of histones H4 and H2A.^[1]

Publication Abstract from PubMed

N-terminal acetylation is among the most common protein modifications in eukaryotes and is mediated by evolutionarily conserved N-terminal acetyltransferases (NATs). NatD is among the most selective NATs; its only known substrates are histones H4 and H2A, containing the N-terminal sequence SGRGK in humans. Here we characterize the molecular basis for substrate-specific acetylation by NatD by reporting its crystal structure bound to cognate substrates and performing related biochemical studies. A novel N-terminal segment wraps around the catalytic core domain to make stabilizing interactions, and the alpha1-alpha2 and beta6-beta7 loops adopt novel conformations to properly orient the histone N termini in the binding site. Ser1 and Arg3 of the histone make extensive contacts to highly conserved NatD residues in the substrate binding pocket, and flanking glycine residues also appear to contribute to substrate-specific binding by NatD, together defining a Ser-Gly-Arg-Gly recognition sequence. These studies have implications for understanding substrate-specific acetylation by NAT enzymes.

The Molecular Basis for Histone H4- and H2A-Specific Amino-Terminal Acetylation by NatD.,Magin RS, Liszczak GP, Marmorstein R Structure. 2015 Feb 3;23(2):332-41. doi: 10.1016/j.str.2014.10.025. Epub 2015 Jan, 22. PMID:25619998^[2]

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

References

↑ Hole K, Van Damme P, Dalva M, Aksnes H, Glomnes N, Varhaug JE, Lillehaug JR, Gevaert K, Arnesen T. The human N-alpha-acetyltransferase 40 (hNaa40p/hNatD) is conserved from yeast and N-terminally acetylates histones H2A and H4. PLoS One. 2011;6(9):e24713. doi: 10.1371/journal.pone.0024713. Epub 2011 Sep 15. PMID:21935442 doi:https://dx.doi.org/10.1371/journal.pone.0024713
↑ Magin RS, Liszczak GP, Marmorstein R. The Molecular Basis for Histone H4- and H2A-Specific Amino-Terminal Acetylation by NatD. Structure. 2015 Feb 3;23(2):332-41. doi: 10.1016/j.str.2014.10.025. Epub 2015 Jan, 22. PMID:25619998 doi:https://dx.doi.org/10.1016/j.str.2014.10.025

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Hole K, Van Damme P, Dalva M, Aksnes H, Glomnes N, Varhaug JE, Lillehaug JR, Gevaert K, Arnesen T. The human N-alpha-acetyltransferase 40 (hNaa40p/hNatD) is conserved from yeast and N-terminally acetylates histones H2A and H4. PLoS One. 2011;6(9):e24713. doi: 10.1371/journal.pone.0024713. Epub 2011 Sep 15. PMID:21935442 doi:https://dx.doi.org/10.1371/journal.pone.0024713

[2] Magin RS, Liszczak GP, Marmorstein R. The Molecular Basis for Histone H4- and H2A-Specific Amino-Terminal Acetylation by NatD. Structure. 2015 Feb 3;23(2):332-41. doi: 10.1016/j.str.2014.10.025. Epub 2015 Jan, 22. PMID:25619998 doi:https://dx.doi.org/10.1016/j.str.2014.10.025

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='4u9v' size='340' side='right'caption='[[4u9v]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4u9v]] is a 1 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=4U9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U9V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4u9v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U9V 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></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4u9w|4u9w]], [[4u9x|4u9x]], [[4ua3|4ua3]]</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=4u9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u9v OCA], [https://pdbe.org/4u9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u9v RCSB], [https://www.ebi.ac.uk/pdbsum/4u9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u9v ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NAA40, NAT11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4u9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u9v OCA], [http://pdbe.org/4u9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4u9v RCSB], [http://www.ebi.ac.uk/pdbsum/4u9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4u9v ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NAA40_HUMAN NAA40_HUMAN]] Responsible for the acetylation of the N-terminal residues of histones H4 and H2A.<ref>PMID:21935442</ref>
+[https://www.uniprot.org/uniprot/NAA40_HUMAN NAA40_HUMAN] Responsible for the acetylation of the N-terminal residues of histones H4 and H2A.<ref>PMID:21935442</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Liszczak, G P]]
+[[Category: Liszczak GP]]
-[[Category: Magin, R S]]
+[[Category: Magin RS]]
-[[Category: Marmorstein, R]]
+[[Category: Marmorstein R]]
-[[Category: Acetyl-coa]]
-[[Category: Acetyltransferase]]
-[[Category: Gnat fold]]
-[[Category: N-terminal acetylation]]
-[[Category: Transferase]]

4u9v: Difference between revisions

Revision as of 08:10, 22 March 2023

Crystal structure of NatD (Naa40p) bound to acetyl CoA

Structural highlights

Function

Publication Abstract from PubMed

References

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