Sandbox Reserved 774: Difference between revisions
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=Structure= | =Structure= | ||
Has a four chain structure (<scene name='56/564050/Chain_a/1' target=0>A</scene>, <scene name='56/564050/Chain_d/1' target=0>D</scene>, <scene name='56/564050/Chain_c/1' target=0>C</scene>, <scene name='56/564050/Chain_b/1' target=0>B</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> | Has a four chain structure (<scene name='56/564050/Chain_a/1' target=0>A</scene>, <scene name='56/564050/Chain_d/1' target=0>D</scene>, <scene name='56/564050/Chain_c/1' target=0>C</scene>, <scene name='56/564050/Chain_b/1' target=0>B</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-sheets</scene> surrounded on both sides by helical segments.<ref name=Shiva/> | ||
Each monomer has a similar and compact | 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 is 23.9 (<scene name='56/564050/Bakhbone_mainechain/1' target=0>main chain</scene>) 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.]] | ||
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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 | 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 | <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/Backbone/1' target=1>backbone</scene> hydrogen bonds to the pyrophosphate group of the bound CoA. <ref name=Akhlaghi/> | <scene name='56/564050/Backbone/1' target=1>backbone</scene> hydrogen bonds to the pyrophosphate group of the bound CoA. <ref name=Akhlaghi/> | ||
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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=' | <Structure load='1QSM' size='350' frame='true' align='right' caption='Hpa2 + AcCoA' scene='Insert optional scene name here' /> | ||
=Secondary Structure= | =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 | 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 β-strands, 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= | =Mechanism= | ||
