Heidi Hu/Sandbox 2: Difference between revisions

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='[400,388]' frame='true' align='right'

caption='Structures of H. pylori 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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[http://en.wikipedia.org/wiki/Helicobacter_pylori ''Helicobacter pylori''] is a pathogenic bacterium that colonizes the human gastric mucosa, which can cause peptic ulcers and has been linked to stomach cancers.<ref>PMID:9146793</ref>  [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] requires the activity of nickel-dependent enzymes, [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''Hydrogenase''] (H₂ase) and [http://en.wikipedia.org/wiki/Urease ''urease''], to survive in the acidic environment of the stomach.<ref>PMID:2050411</ref><ref>PMID:8063376</ref><ref>PMID:12459589</ref>  Thus nickel is an important nutrient for H. pylori.

Accessory proteins HypABCDEF and UreIEFGH facilitate in the maturation of [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''H₂ase''] 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 ''H₂ase'']<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>.  

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 or 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 similating the internal pH of H. pylori under acid shock or at neutral pH conditions<ref name="bob"/>.  Whereas the Ni(II) site is 6-coordinate N/O under both pH conditions, the Zn(II) coordination changes from Cys₄ at neutral pH to Cys₂His₂ at acidic pH with nickel-bound<ref name="bob"/> (Fig. 1).  Changes in the coordination of structural Zinc site in response to pH has been hypothesized to be linked to altered HypA structures and protein interaction partners<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 ==

The Ni- and pH-dependent changes in the [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] HypA structural zinc site suggests multiple conformations of this protein.  Thus HypA is likely interfacing between the maturation of [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''H₂ase''] and/or [http://en.wikipedia.org/wiki/Urease ''urease''] in [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] in a pH-dependent manner, as it is required for the full activation of both of these nickel enzymes. The [http://people.chem.umass.edu/mmaroney/ Maroney Lab] at the University of Massachusetts Amherst is interested in characterizing the conformational changes in HypA and its interaction partners under neutral and acid shock conditions.