User:Brian Boyle/Sandbox 1

From Proteopedia

Current revision

spinqualitylabelsall models Apo BRPF1 Bromodomain solved via solution NMR. (PDB entry 2d9e) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Contents 1 Overview 2 PZP Domain 3 Bromodomain Structure & Acetyllysine Recognition 4 PWWP Domain Overview Peregrin, also known as Bromodomain and PHD Finger-containing 1 (BRPF1) is a 137 kDa protein that plays a versatile role in epigenetic signaling events. It contains three chromatin reader domains, including a , (two PHD fingers separated by a Zinc Knuckle), and proline-tryptophan-tryptophan-proline () domain (from N to C terminus)[1]. Through these three domains, it is capable of recognizing both modified and unmodified histones, as well as non-specifically binding DNA [2],[3]. BRPF1 carries out its function as a component of the MOZ (monocytic leukemic zinc-finger protein) histone acetyltransferase (HAT) complex [4]. This complex is involved in the regulation of gene expression, particularly those involved with skeletal development, hematopoiesis, and neurodevelopmental processes [5],[6],[2]. Accordingly, it has the greatest tissue distribution in the bone marrow and brain. PZP Domain The PZP domain of BRPF1 is located at its N-terminus and has been shown to [2]. Three residues in the H3 peptide undergo unique interactions with the binding pocket. These are , , and .[2]. In addition to its binding to the histone H3 N-terminus, the PZP domain can associate non-specifically with DNA. It is thought that this interaction is mediated by lys-383, lys-390, and arg-392[2]. These residues form a in the second PHD finger that can interact with the negative DNA backbone. Interestingly, the DNA- and histone H3-binding capabilities of the PZP domain seem to work in tandem, as is associates much stronger with the nucleosome core particle than it does with the H3 tail alone[7]. Bromodomain Structure & Acetyllysine Recognition Consistent with other bromodomains, the BRPF1 bromodomain consists of a four α-helical bundle. These helices are termed (from N to C terminus)[8]. There are present in its structure. The ZA loop links together the αZ and αA helices, while the BC loop links αB and αC[8]. BRPF1 Asn-83 forms a hydrogen bond with the carbonyl moiety of the acetyllysine residue. The bromodomain is shown in green. The H4K12ac peptide is shown in cyan. (PDB entry 4QYD) The BRPF1 bromodomain has been shown to recognize and bind to various acetylated lysine marks on the N-terminal tails of histones tails [3]. It preferentially binds to histone H4 acetylated at positions K5 (2rs9), K8, and K12 (4qyd) as well as H3 and H2A ((4qyl) at position K14 and K5, respectively[4],[3]. Interestingly, the BRPF1 bromodomain has also been shown to bind di-acetylated histone peptides as a monomer with high affinity, including H4K5acK8ac and H4K5acK12ac [4]. Acetyllysine recognition is coordinated by a number of residues in the bromodomain's binding pocket. Using NMR chemical shift perturbation experiments, Glass et al. reported several the undergo conformational changes upon histone H4 ligand binding (I27, L34, E36, V37, N83, and I88)[4]. Notably, asparagine 83 was among these. The interaction between the amide nitrogen of asparagine with the carbonyl of the acetyllysine group is conserved in all bromodomains and is necessary for binding to occur [4],[8]. Furthermore, the tyrosine 40 and isoleucine 27 stabilize the acetyllysine residue through water-mediated hydrogen bonds[8]. PWWP Domain PWWP domains are a weakly conserved protein module that often contain a proline-tryptophan-tryptophan-proline motif and have been show to recognize methylated histones[9]. The BRPF1 PWWP domain has high selectivity for histone H3 Lys-36 (2x4w) that has been trimethylated (H3K36me3)[10]. The trimethyl mark at H3K36 has gained a lot attention due to its established roles is RNA splicing and developmental disorders[11],[12]. Recognition of H3K36me3 is strongly dependent on the , which consists of Tyr-1096, Tyr-1099, and Phe-1147.

BRPF1 Association with the MOZ HAT Complex

The MOZ Histone Acetyltransferase Complex is a tetramer consisting of MEAF6, ING5, BRPF1 and MOZ or MORF^[2]. Within BRPF1, there are two non-chromatin-binding modules surrounding the PZP domain that are responsible for its association with the MOZ HAT Complex. On the N-terminal side of the PZP, lies the MOZ/MORF binding domain^[13]. On the other side of the PZP domain, there is a small module involved in binding to ING5 and MEAF6^[14]. BRPF1 seems to be required for the formation of the MOZ HAT complex, as it acts as a bridge associating MOZ or MORF with ING5 and MEAF6^[14].

Sequential and Structural Conservation in BRPF1

Sequence alignment of family IV bromodomains by Clustal Omega.

Bromodomains are categorized into several families based on sequence and structural similarity. The BRPF1 bromodomain belongs to family IV of bromodomains^[15]. Out of these bromodomain proteins, the BRPF3 bromodomain has the highest sequence identity with that of BRPF1 (66.2%). A specific asparagine residue is conserved across all bromodomains due to its integral role in acetyllysine recognition.

PWWP domains have very low sequence and structural conservation. In fact, BRPF1 actually contains a PSYP motif rather than the canonical PWWP motif, however this change doesn't impact its ability to recognize methylated lysine. Furthermore, while many PWWP domains contain a β-barrel, there are significant differences in other structural aspects among PWWP domains^[16]. The aromatic cage in the β-barrel is a conserved structure and is necessary for methyllysine binding^[16].

Links to Human Disease

BRPF1 has been implicated in the progression of several cancers. Chromosomal translocations of the gene encoding MOZ (a subunit in the MOZ HAT complex) have been linked to the development of acute myeloid leukemia ^[4]. The crucial role of BRPF1 in this complex has made it the subject of many studies in order to understand how this mutation leads to cancer. Another study reported an association between upregulation of the BRPF1 gene and poor survival rates in hepatocellular carcinoma patients ^[17].

Mutations within the gene itself have been associated with neurological disorders and widespread reduced histone acetylation ^[1].

Available Structures

The following are some, but not all, of the available structures containing domains of BRPF1:

Bromodomain (apo): 2d92 Bromodomain w/ histone peptides: 4qyl, 4qyd, 5ffv, 5ffw Bromodomain w/ inhibitors: 6ekq, 5ov8, 5o5h, 5o5f, 5o5a, 5o55 PZP (apo): 5erc PZP w/ histone H3 peptide: 6u04 PWWP (apo): 2x35 PWWP w/ H3K36me3: 2x4w, 2x4y, 2x4x

References

1. ↑ ^{1.0 1.1} Yan K, Rousseau J, Littlejohn RO, Kiss C, Lehman A, Rosenfeld JA, Stumpel CT, Stegmann AP, Robak L, Scaglia F, Nguyen TT, Fu H, Ajeawung NF, Camurri MV, Li L, Gardham A, Panis B, Almannai M, Sacoto MJ, Baskin B, Ruivenkamp C, Xia F, Bi W, Cho MT, Potjer TP, Santen GW, Parker MJ, Canham N, McKinnon M, Potocki L, MacKenzie JJ, Roeder ER, Campeau PM, Yang XJ. Mutations in the Chromatin Regulator Gene BRPF1 Cause Syndromic Intellectual Disability and Deficient Histone Acetylation. Am J Hum Genet. 2017 Jan 5;100(1):91-104. doi: 10.1016/j.ajhg.2016.11.011. Epub, 2016 Dec 8. PMID:27939640 doi:http://dx.doi.org/10.1016/j.ajhg.2016.11.011
2. ↑ ^{2.0 2.1 2.2 2.3 2.4 2.5} Klein BJ, Cox KL, Jang SM, Cote J, Poirier MG, Kutateladze TG. Molecular Basis for the PZP Domain of BRPF1 Association with Chromatin. Structure. 2019 Nov 6. pii: S0969-2126(19)30355-7. doi:, 10.1016/j.str.2019.10.014. PMID:31711755 doi:http://dx.doi.org/10.1016/j.str.2019.10.014
3. ↑ ^{3.0 3.1 3.2} Poplawski A, Hu K, Lee W, Natesan S, Peng D, Carlson S, Shi X, Balaz S, Markley JL, Glass KC. Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain. J Mol Biol. 2014 Apr 17;426(8):1661-76. doi: 10.1016/j.jmb.2013.12.007. Epub 2013, Dec 12. PMID:24333487 doi:http://dx.doi.org/10.1016/j.jmb.2013.12.007
4. ↑ ^{4.0 4.1 4.2 4.3 4.4 4.5} Obi JO, Lubula MY, Cornilescu G, Henrickson A, McGuire K, Evans CM, Phillips M, Boyson SP, Demeler B, Markley JL, Glass KC. The BRPF1 bromodomain is a molecular reader of di-acetyllysine. Curr Res Struct Biol. 2020;2:104-115. doi: 10.1016/j.crstbi.2020.05.001. Epub, 2020 May 12. PMID:33554132 doi:http://dx.doi.org/10.1016/j.crstbi.2020.05.001
5. ↑ Hibiya K, Katsumoto T, Kondo T, Kitabayashi I, Kudo A. Brpf1, a subunit of the MOZ histone acetyl transferase complex, maintains expression of anterior and posterior Hox genes for proper patterning of craniofacial and caudal skeletons. Dev Biol. 2009 May 15;329(2):176-90. doi: 10.1016/j.ydbio.2009.02.021. Epub 2009 , Feb 27. PMID:19254709 doi:http://dx.doi.org/10.1016/j.ydbio.2009.02.021
6. ↑ You L, Li L, Zou J, Yan K, Belle J, Nijnik A, Wang E, Yang XJ. BRPF1 is essential for development of fetal hematopoietic stem cells. J Clin Invest. 2016 Sep 1;126(9):3247-62. doi: 10.1172/JCI80711. Epub 2016 Aug 8. PMID:27500495 doi:http://dx.doi.org/10.1172/JCI80711
7. ↑ Klein BJ, Muthurajan UM, Lalonde ME, Gibson MD, Andrews FH, Hepler M, Machida S, Yan K, Kurumizaka H, Poirier MG, Cote J, Luger K, Kutateladze TG. Bivalent interaction of the PZP domain of BRPF1 with the nucleosome impacts chromatin dynamics and acetylation. Nucleic Acids Res. 2015 Nov 30. pii: gkv1321. PMID:26626149 doi:http://dx.doi.org/10.1093/nar/gkv1321
8. ↑ ^{8.0 8.1 8.2 8.3} Lubula MY, Eckenroth BE, Carlson S, Poplawski A, Chruszcz M, Glass KC. Structural insights into recognition of acetylated histone ligands by the BRPF1 bromodomain. FEBS Lett. 2014 Sep 30. pii: S0014-5793(14)00705-4. doi:, 10.1016/j.febslet.2014.09.028. PMID:25281266 doi:http://dx.doi.org/10.1016/j.febslet.2014.09.028
9. ↑ Qiu C, Sawada K, Zhang X, Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat Struct Biol. 2002 Mar;9(3):217-24. PMID:11836534 doi:10.1038/nsb759
10. ↑ Vezzoli A, Bonadies N, Allen MD, Freund SM, Santiveri CM, Kvinlaug BT, Huntly BJ, Gottgens B, Bycroft M. Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nat Struct Mol Biol. 2010 May;17(5):617-9. Epub 2010 Apr 18. PMID:20400950 doi:10.1038/nsmb.1797
11. ↑ Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet. 2009 Mar;41(3):376-81. doi: 10.1038/ng.322. Epub 2009 Feb 1. PMID:19182803 doi:http://dx.doi.org/10.1038/ng.322
12. ↑ Nimura K, Ura K, Shiratori H, Ikawa M, Okabe M, Schwartz RJ, Kaneda Y. A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf-Hirschhorn syndrome. Nature. 2009 Jul 9;460(7252):287-91. doi: 10.1038/nature08086. Epub 2009 May 31. PMID:19483677 doi:http://dx.doi.org/10.1038/nature08086
13. ↑ Lalonde ME, Avvakumov N, Glass KC, Joncas FH, Saksouk N, Holliday M, Paquet E, Yan K, Tong Q, Klein BJ, Tan S, Yang XJ, Kutateladze TG, Cote J. Exchange of associated factors directs a switch in HBO1 acetyltransferase histone tail specificity. Genes Dev. 2013 Sep 15;27(18):2009-24. doi: 10.1101/gad.223396.113. PMID:24065767 doi:http://dx.doi.org/10.1101/gad.223396.113
14. ↑ ^{14.0 14.1} Ullah M, Pelletier N, Xiao L, Zhao SP, Wang K, Degerny C, Tahmasebi S, Cayrou C, Doyon Y, Goh SL, Champagne N, Cote J, Yang XJ. Molecular architecture of quartet MOZ/MORF histone acetyltransferase complexes. Mol Cell Biol. 2008 Nov;28(22):6828-43. doi: 10.1128/MCB.01297-08. Epub 2008 Sep , 15. PMID:18794358 doi:10.1128/MCB.01297-08
15. ↑ Lloyd JT, Glass KC. Biological function and histone recognition of family IV bromodomain-containing proteins. J Cell Physiol. 2018 Mar;233(3):1877-1886. doi: 10.1002/jcp.26010. Epub 2017 Jun , 13. PMID:28500727 doi:http://dx.doi.org/10.1002/jcp.26010
16. ↑ ^{16.0 16.1} Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J. Structural and Histone Binding Ability Characterizations of Human PWWP Domains. PLoS One. 2011;6(6):e18919. Epub 2011 Jun 20. PMID:21720545 doi:10.1371/journal.pone.0018919
17. ↑ Cheng CL, Tsang FH, Wei L, Chen M, Chin DW, Shen J, Law CT, Lee D, Wong CC, Ng IO, Wong CM. Bromodomain-containing protein BRPF1 is a therapeutic target for liver cancer. Commun Biol. 2021 Jul 20;4(1):888. doi: 10.1038/s42003-021-02405-6. PMID:34285329 doi:http://dx.doi.org/10.1038/s42003-021-02405-6