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OCA, Michael B. Goshe, Shiva Akhlaghi

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-{{User:Michael_B._Goshe/Template_BCH455_555}}
+{{User:Michael_B._Goshe/Template_BCH455_555}}<Structure load='1QSO' size='350' frame='true' align='right' caption='3D Model of Hpa2. Clicking links in the test will highlighted : chains A,B,C,D, β-sheets, main chain, side chain, and residues 100-104.' scene='Insert optional scene name here' />
+=Histone Acetyltransferase Hpa2=
 <!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
-<Structure load='1QSO' size='350' frame='true' align='right' caption='3D Model of Hpa2, showing: chains A,B,C,D, β-sheets, main chain, side chain, and residues 100-104.' scene='Insert optional scene name here' />
-=Histone Acetyltransferase Hpa2=
 Histone Acetyltransferase Hpa2 is a member of the GNAT (Gcn5-related N-acetyltransferases) super-family of enzymes that are found spread out across nature and use acyl-CoA's to acylate their cognate substrates.<ref name=desperate>"Histone Acetyltransferase HPA2 from Saccharomyces Cerevisiae." Protein Data Bank. EMDataBank, n.d. Web. 17 Nov. 2013.[http://www.rcsb.org/pdb/explore/explore.do?structureId=1QSO RCSB.org]</ref> GNAT is a catalytic subunit of ADA and SAGA histone acetyltransferase complexes. <ref>"GCN5/YGR252W Summary." YeastGenome.org. Standford University, n.d. Web. 26 Nov. 2013. [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=gcn5 YeastGenome.org]</ref>Hpa2 is found in the organism Saccharomyces Cerevisiae, which is more commonly known as Baker's Yeast.<ref>"Q06592 (HPA2_YEAST) Reviewed, UniProtKB/Swiss-Prot." Unitprot.org. UniProtKB, 13 Nov. 2013. Web. 16 Nov. 2013.[http://www.uniprot.org/uniprot/Q06592 UnitPro.org]</ref> It was also discovered in other organisms, such as Pelagibacterium halotolerans B2 - a marine halotolerant bacterium in the East China Sea. <ref>Huo. "Complete Genome Sequence of Pelagibacterium Halotolerans B2(T)." J. Bacteriol 197.8 (2012): 1. Web. 26 Nov. 2013. [http://www.ncbi.nlm.nih.gov/pubmed/22156395 NCBI.nlm.nih.gov]</ref> In vitro, Hpa2 serves to acetylate histone H3 'Lys-4' and 'Lys-14' and histone H4 'Lys-5' and 'Lys-12.' The acetylation of the e-amino group of lysines on the histone N terminal tails and core regions cause changes in the chromatin structure and dynamics, which often times leads to transcriptional activation.<ref>Sampath, el al. "Enzymology: Biochemical Characterization of Hpa2 and Hpa3-two Small Closely Related Acetyltransferases from S. Cerevisiae." Journal of Biological Chemistry (2013): 2-17. Web. 17 Nov. 2013. [http://www.jbc.org/content/early/2013/06/17/jbc.M113.486274.full.pdf JBC.org]</ref> In solution, Hpa2 forms a dimer, and upon binding with AcCoA forms a tetramer.<ref name=desperate/><ref name=Shiva/> It is classified as a [[transferase]].<ref name=Shiva>Angus-Hill, et al. "Crystal Structure of the Histone Acetyltransferase Hpa2: a Tetrameric Member of the Gcn5-related N-acetyltransferase Superfamily." J. Mol. Biol. 1999.3338 (1999): 1-14. Web. 18 Nov. 2013.</ref>
 =Structure=
-Has a four chain structure (<scene name='56/564050/Chain_a/1' target=0>A</scene>, <scene name='56/564050/Chain_b/1' target=0>B</scene>, <scene name='56/564050/Chain_c/1' target=0>C</scene>, <scene name='56/564050/Chain_d/1' target=0>D</scene>) with 2.4 A resolution, and 2.9 A resolution with a co-factor (acetyl-CoA). Core fold features include four conserved sequence motifs of the GNAT family, and comprises a central highly curved five stranded <scene name='56/564050/Beta_sheets/1' target=0>β-sheet</scene> surrounded on both sides by helical segments.<ref name=Shiva/>
+Has a four chain structure (<scene name='56/564050/Chain_a/1' target=0>A</scene>, <scene name='56/564050/Chain_b/1' target=0>B</scene>, <scene name='56/564050/Chain_c/1' target=0>C</scene>, <scene name='56/564050/Chain_d/1' target=0>D</scene>) with 2.4 Å resolution, and 2.9 Å resolution with a co-factor (acetyl-CoA). Core fold features include four conserved sequence motifs of the GNAT family, and comprises a central, highly curved five stranded <scene name='56/564050/Beta_sheets/1' target=0>β-sheet</scene> surrounded on both sides by helical segments.<ref name=Shiva/>
-Each monomer has a similar and compact α-β structure. The structure's core contains a central mixed five-stranded sheet structure from sheets β1 to β5. Strands β1 to β4, however, are organized in an anti-parallel arrangement while β4 and β5 are parallel, but only at their amino-terminal ends. At the other end of the parallel β4 and β5 strands, they are spread apart because of a β bulge in strand β4 caused by residue N74 of strand β3 as well as N91 and D92 of β4. The central sheet is accompanied on each side by two α-helices. Helices α1 and α2 are on one side of the sheet with α1 lying nearly flat against and perpendicular to other direction of the strands, while helices α3 and α4 are on the opposite side of the sheet with helix α3 cupped within the curved face of the sheet. <ref name=Shiva/> The method used to determine the structure was [[X-ray crystallography]]. Sedimentation and crystal structure analysis clearly shows that Hpa2 is dimeric in solution and tetramerizes in the unit crystal. The crystal structure of the oligomer reveals that two Hpa2 dimers are held together by interaction between the bound acetyl-CoA molecules. The average B-factor value of the <scene name='56/564050/Bakhbone_mainechain/1' target=0>main chain</scene> is 23.9  with a 25.4 <scene name='56/564050/Sidechain/2' target=0>side chain</scene>. The R-factor is 0.19. <ref name=Shiva/>
+Each monomer has a similar and compact α-β structure. The structure's core contains a central mixed five-stranded sheet structure from sheets β1 to β5. Strands β1 to β4, however, are organized in an anti-parallel arrangement while β4 and β5 are parallel, but only at their amino-terminal ends. At the other end of the parallel β4 and β5 strands, they are spread apart because of a β bulge in strand β4 caused by residue N74 of strand β3 as well as N91 and D92 of β4. The central sheet is accompanied on each side by two α-helices. Helices α1 and α2 are on one side of the sheet with α1 lying nearly flat against and perpendicular to the other direction of the strands, while helices α3 and α4 are on the opposite side of the sheet with helix α3 cupped within the curved face of the sheet. <ref name=Shiva/> The method used to determine the structure was [[X-ray crystallography]]. Sedimentation and crystal structure analysis clearly shows that Hpa2 is dimeric in solution and tetramerizes in the unit crystal. The crystal structure of the oligomer reveals that two Hpa2 dimers are held together by interaction between the bound acetyl-CoA molecules. The average B-factor value of the <scene name='56/564050/Bakhbone_mainechain/1' target=0>main chain</scene> is 23.9  with a 25.4 <scene name='56/564050/Sidechain/2' target=0>side chain</scene>. The R-factor is 0.19. <ref name=Shiva/> [[Image:Chain.jpg.png | thumb | '''Figure 1.''' Sequence of Hpa2.]]
-[[Image:Chain.jpg.png | thumb | '''Figure 1.''' Sequence of Hpa2.]]
 ==Co-factor==
 Most of the hydrogen bonding between Hpa2 and its co-factor AcCoA are highly conserved and occur via the main-chain groups, not the side-chains. This explains the uniformity of the binds with the co-factors, despite the low degree of sequence conservation. The conserved main-chain contacts seen in a segment of Motif A forms a loop before and around the first turn of the helix in Motif A. This is found in residues
-<scene name='56/564050/Residues_100-104/3' target=0>100-104</scene>. Most of the residues in this loop contribute to a series of hydrogen bonds between the α and β phosphate oxygen atoms via main-chain groups. This includes a conserved solvent molecule interaction. This loops was not located within Hpa2 in the absence of its co-factor, indicating that this region is formed upon <scene name='56/564050/Test/1' target=1>co-factor</scene> binding. It appears that this  area of interactions is a vital determinant for the binding of AcCoA. <ref name=Shiva/> The pantetheine arm of CoA interacts with the backbone amide and carbonyl groups of β4, and is wedged between the spread apart areas on the strands of β4 and β5. The loop connecting β4 and α3 provides five amide
+<scene name='56/564050/Residues_100-104/3' target=0>100-104</scene>. Most of the residues in this loop contribute to a series of hydrogen bonds between the α and β phosphate oxygen atoms via main-chain groups. This includes a conserved solvent molecule interaction. This loop was not located within Hpa2 in the absence of its co-factor, indicating that this region is formed upon <scene name='56/564050/Test/1' target=1>co-factor</scene> binding. It appears that this  area of interactions is a vital determinant for the binding of AcCoA. <ref name=Shiva/> The pantetheine arm of CoA interacts with the backbone amide and carbonyl groups of β4, and is wedged between the spread apart areas on the strands of β4 and β5. The loop connecting β4 and α3 provides five amide
 <scene name='56/564050/Backbone/1' target=1>backbone</scene> hydrogen bonds to the pyrophosphate group of the bound CoA. <ref name=Akhlaghi/>
 ==Active Site==
-The region around the <scene name='56/564050/Active_sites_zoom/1' target=1>active site</scene> has potential consequences for substrate binding. For Hpa2, there exists a pocket adjacent to the active site which is sealed off on two sides by the second Hpa2 monomer in each dimer. This pocket restricts the conformation of a polypeptide backbone in the vicinity of the active site. Therefore, Hpa2 is able to distinguish between potential substrate, whereby the only lysine side-chains that may enter the active site are those with surrounding polypeptides that can adopt a conformation with the ability to fit through the pocket. <ref name=Shiva/>
+The region around the <scene name='56/564050/Active_sites_zoom/1' target=1>active site</scene> has potential consequences for substrate binding. For Hpa2, there exists a pocket adjacent to the active site which is sealed off on two sides by the second Hpa2 monomer in each dimer. This pocket restricts the conformation of a polypeptide backbone in the vicinity of the active site. Therefore, Hpa2 is able to distinguish between potential substrate, whereby the only lysine side-chains that may enter the active site are those with surrounding polypeptides that can adopt a conformation with the ability to fit through the pocket. <ref name=Shiva/> <Structure load='1QSM' size='350' frame='true' align='right' caption='Hpa2 + AcCoA, Clicking links in the test will highlighted : co-factor, backbone, β-strands, active site, α-helices.' scene='Insert optional scene name here' />
-<Structure load='1QSM' size='350' frame='true' align='right' caption='Hpa2 + AcCoA, showing: co-factor, backbone, β-strands, active site, α-helices.' scene='Insert optional scene name here' />
 =Secondary Structure=
-Most of the secondary structure elements of the monomer contribute residues involved in dimer contacts. A large part of the interface is formed by two projections from the core part of the monomer structure. The first projection is formed by the C-terminal end of strand β3, turn β3-β4, and the N-terminal end of strand β4, while the second is formed by strand β7. Together with strands β5 and β6 they form a barrel-like structure containing ten strands in which the component strands of the barrel locked together.<ref name=Shiva/> Most importantly, strand b7 from each monomer interacts between strands β5 and β6 of the opposite monomer, which also extends the central sheet structure by two strands. Also, the two projections interact with residues from helices α1 and α2, turn α1 α2, turn α2 β2, and helices α3 and α4 of the opposite monomer. There are eight <scene name='56/564050/Beta_strands/2' target=1>β-strands</scene>, four <scene name='56/564050/Alpha_helices/2'>α-helices</scene>, and ten turns. Thirty-three percent of the secondary structure is helical (5 helices and 50 residues), while thirty-one percent consists of β-sheets (6 strands and 47 residues). <ref name=desperate/>
+Most of the secondary structure elements of the monomer contribute residues involved in dimer contacts. A large part of the interface is formed by two projections from the core part of the monomer structure. The first projection is formed by the C-terminal end of strand β3, turn β3-β4, and the N-terminal end of strand β4, while the second is formed by strand β7. Together with strands β5 and β6 they form a barrel-like structure containing ten strands in which the component strands of the barrel are locked together.<ref name=Shiva/> Most importantly, strand β7 from each monomer interacts between strands β5 and β6 of the opposite monomer, which also extends the central sheet structure by two strands. Also, the two projections interact with residues from helices α1 and α2, turn α1 α2, turn α2 β2, and helices α3 and α4 of the opposite monomer. There are eight <scene name='56/564050/Beta_strands/2' target=1>β-strands</scene>, four <scene name='56/564050/Alpha_helices/2'>α-helices</scene>, and ten turns. Thirty-three percent of the secondary structure is helical (5 helices and 50 residues), while thirty-one percent consists of β-sheets (6 strands and 47 residues). <ref name=desperate/>
 =Mechanism=
@@ Line 50: / Line 44: @@
 =Implications=
-The analysis of a loss-of-function mutant of the hpa2 gene suggests that the hpa2 affects bacterial proliferation in host plants and a hypersensitive response in nonhost plants. As this is the first of such enzyme activity identified in the Hrp protein family, we speculate that the Hpa2 contributes to the assembly of the TTSS by enlarging gaps in the peptidoglycan meshwork of bacterial cell walls.<ref>Zhang, et al. "A Conserved Hpa2 Protein Has Lytic Activity Against the Bacterial Cell Wall in Phytopathogenic Xanthomonas Oryzae." Appl. Microbiol. Biotechnology 79.4 (2008): 1. Web. 19 Nov. 2013. [http://www.ncbi.nlm.nih.gov/pubmed/18431569 NCBI.nlm.nih.gov]</ref> Members of the GNAT family have been found in E. Coli, a common organism with some strands that cause sickness to humans. Three other GNAT's have been attributed to acetylating three ribosomal proteins: S5, S18, and L12. <ref name=Akhlaghi/> Hpa2 also plays a role in governing gene expression through its effects on chromatin structure and assembly. Additionally, it affects gene regulation, antibiotic resistance, and hormonal regulation of circadian rhythms.<ref name=Shiva/> It was also found that in head and neck carcinoma patients, Hpa2 expression was noticeably elevated, which correlated with prolonged time to disease recurrence, as well as inversely correlated with tumor cell spreading within lymph nodes. This would make it appear that Hpa2 restrains tumor metastasis, most likely by constricting heparanese enzymatic activity, granting a favorable outcome to the head and neck cancer patients.<ref>Levy-Adam. "Heparanase 2 Interacts with Heparan Sulfate with High Affinity and Inhibits Heparanase Activity." Journal of Biological Chemistry 285.36 (2010): 1-19. Web. 4 Dec. 2013. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2934666/ NCBI.nlm.nih.gov]</ref>
+The analysis of a loss-of-function mutant of the Hpa2 gene suggests that the Hpa2 affects bacterial proliferation in host plants and a hypersensitive response in nonhost plants. As this is the first of such enzyme activity identified in the Hrp protein family, it is speculated that the Hpa2 contributes to the assembly of the TTSS by enlarging gaps in the peptidoglycan meshwork of bacterial cell walls.<ref>Zhang, et al. "A Conserved Hpa2 Protein Has Lytic Activity Against the Bacterial Cell Wall in Phytopathogenic Xanthomonas Oryzae." Appl. Microbiol. Biotechnology 79.4 (2008): 1. Web. 19 Nov. 2013. [http://www.ncbi.nlm.nih.gov/pubmed/18431569 NCBI.nlm.nih.gov]</ref> Members of the GNAT family have been found in E. Coli, a common organism with some strands that cause sickness to humans. Three other GNAT's have been attributed to acetylating three ribosomal proteins: S5, S18, and L12. <ref name=Akhlaghi/> Hpa2 also plays a role in governing gene expression through its effects on chromatin structure and assembly. Additionally, it affects gene regulation, antibiotic resistance, and hormonal regulation of circadian rhythms.<ref name=Shiva/> It was also found that in head and neck carcinoma patients, Hpa2 expression was noticeably elevated, which correlated with prolonged time to disease recurrence, as well as inversely correlated with tumor cell spreading within lymph nodes. This would make it appear that Hpa2 restrains tumor metastasis, most likely by constricting heparanese enzymatic activity, granting a favorable outcome to the head and neck cancer patients.<ref>Levy-Adam. "Heparanase 2 Interacts with Heparan Sulfate with High Affinity and Inhibits Heparanase Activity." Journal of Biological Chemistry 285.36 (2010): 1-19. Web. 4 Dec. 2013. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2934666/ NCBI.nlm.nih.gov]</ref>
 =References=
 <references/>