Heidi Hu/Sandbox 2: Difference between revisions
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One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]. | One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]. | ||
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<applet load='3A44' size='[ | <applet load='3A44' size='[450,438]' frame='true' align='right' | ||
caption='Structures of | caption='Structures of HypA (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=2kdx 2KDX]), (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A43 3A43]), and (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A44 3A44])' /> | ||
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== Introduction == | == Introduction == | ||
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Accessory proteins HypABCDEF and UreIEFGH facilitate | Accessory proteins HypABCDEF and UreIEFGH facilitate the maturation of [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''H<sub>2</sub>ase''] and [http://en.wikipedia.org/wiki/Urease ''urease''] respectively<ref>PMID:9252185</ref>. HypA is a nickel metallochaperone normally associated with the maturation of [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''H<sub>2</sub>ase'']<ref name="NiTraff">PMID:22970729</ref>. In H. pylori, however, it is also require for the full activy of urease, despite the presence of the urease-specific Ni-chaperone, UreE<ref>PMID:11123699</ref>. | ||
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The [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori'']HypA (''Hp''HypA) is a 13.2kDa Ni-chaperone with both a nickel binding site and and structural zinc site. Zn(II) is coordinated by two CXXC motif each with a flanking histidine, whereas the Ni(II) is known to bind to the N-terminus MHE motif<ref name="bob">PMID:20662514</ref>. The ''Hp''HypA protein has also been characterized as a monomer and a homodimer. The <scene name='Heidi_Hu/Sandbox_2/Hphypa/2'>N-terminal modified monomeric structure</scene> (N-terminal tag colored in red) has been solved by NMR (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=2KDX 2KDX])<ref>PMID:19621959</ref>. The monomeric structure shows an <scene name='Heidi_Hu/Sandbox_2/Hphypa_2nd_structure/1'>alpha/beta lobe</scene> containing the N- and C-termini well separated from the <scene name='Heidi_Hu/Sandbox_2/Hphypa_2nd_structure/2'>zinc binding lobe</scene>. The homodimeric ''Hp''HypA has been characterized by NMR to have the similar overall structure with discrepancies to the metal binding sites<ref name="bob"/>. The metal sites in ''Hp''HypA have been characterized by [http://en.wikipedia.org/wiki/X-ray_absorption_spectroscopy ''X-ray absorption spectroscopy''] (XAS) at pH 6.3 and 7.2 to similate the internal pH of [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] under acid shock or at neutral pH conditions<ref name="bob"/> respectively. While the Ni(II) site is 6-coordinate N/O under both pH conditions, the Zn(II) coordination changes from Cys<sub>4</sub> at neutral pH to Cys<sub>2</sub>His<sub>2</sub> at acidic pH with nickel-bound<ref name="bob"/> (Fig. 1). Changes to the coordination of structural Zinc site in response to pH has been hypothesized to be linked to changes in HypA conformations and protein interaction partners<ref name="bob"/>. | |||
[[Image:HypA-pH-Ni-Change.png|200 px|thumb|Fig. 1: Diagram of Ni- and pH-dependent structural changes to Zn(II) site of ''Hp''HypA (adapted figure<ref name="bob"/>)]] | |||
The crystal structure of <scene name='Heidi_Hu/Sandbox_2/Hypa_monomer/1'>monomeric</scene> (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A43 3A43]) and <scene name='Heidi_Hu/Sandbox_2/Dimeric_hypa/1'>homodimeric</scene> (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A44 3A44]) HypA from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis ''Thermococcus kodakarensis''] has been solved<ref>PMID:19769985</ref>. The HypA homodimer from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis ''T. kodakarensis''] shows a switch dimer, where one beta strand of each alpha/beta lobe comes from the opposite subunit. Additionally, each <scene name='Heidi_Hu/Sandbox_2/Dimeric_zinc_site/1'>Zn(II) site</scene> is coordinated by CXXC motifs from a different subunit. These observations were consistent with the [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] homodimeric HypA NMR data<ref name="bob"/>. | The crystal structure of <scene name='Heidi_Hu/Sandbox_2/Hypa_monomer/1'>monomeric</scene> (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A43 3A43]) and <scene name='Heidi_Hu/Sandbox_2/Dimeric_hypa/1'>homodimeric</scene> (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A44 3A44]) HypA from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis ''Thermococcus kodakarensis''] has been solved<ref>PMID:19769985</ref>. The HypA homodimer from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis ''T. kodakarensis''] shows a switch dimer, where one beta strand of each alpha/beta lobe comes from the opposite subunit. Additionally, each <scene name='Heidi_Hu/Sandbox_2/Dimeric_zinc_site/1'>Zn(II) site</scene> is coordinated by CXXC motifs from a different subunit. These observations were consistent with the [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] homodimeric HypA NMR data<ref name="bob"/>. | ||
== Research Interests == | == Research Interests == | ||