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| | ==Crystal structure of HypB from Helicobacter pylori in complex with nickel== | | ==Crystal structure of HypB from Helicobacter pylori in complex with nickel== |
| - | <StructureSection load='4lps' size='340' side='right' caption='[[4lps]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='4lps' size='340' side='right'caption='[[4lps]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4lps]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LPS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4lps]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LPS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hypB, HP_0900 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4lps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lps OCA], [http://pdbe.org/4lps PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lps RCSB], [http://www.ebi.ac.uk/pdbsum/4lps PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lps ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4lps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lps OCA], [https://pdbe.org/4lps PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lps RCSB], [https://www.ebi.ac.uk/pdbsum/4lps PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lps ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/HYPB_HELPY HYPB_HELPY]] Plays a role in both the hydrogenase and the urease nickel cofactor insertion step. | + | [https://www.uniprot.org/uniprot/HYPB_HELPY HYPB_HELPY] Plays a role in both the hydrogenase and the urease nickel cofactor insertion step. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[HypA-HypB-HypC-HypD-HypE-HypF|HypA-HypB-HypC-HypD-HypE-HypF]] | + | *[[HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures|HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Campylobacter pylori]] | + | [[Category: Helicobacter pylori 26695]] |
| - | [[Category: Ariyakumaran, R]] | + | [[Category: Large Structures]] |
| - | [[Category: Cavazza, C]] | + | [[Category: Ariyakumaran R]] |
| - | [[Category: Lebrette, H]] | + | [[Category: Cavazza C]] |
| - | [[Category: Sydor, A M]] | + | [[Category: Lebrette H]] |
| - | [[Category: Zamble, D B]] | + | [[Category: Sydor AM]] |
| - | [[Category: Hydrogenase nickel incorporation gtpase]]
| + | [[Category: Zamble DB]] |
| - | [[Category: Metal binding protein]]
| + | |
| Structural highlights
4lps is a 2 chain structure with sequence from Helicobacter pylori 26695. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
HYPB_HELPY Plays a role in both the hydrogenase and the urease nickel cofactor insertion step.
Publication Abstract from PubMed
The pathogen Helicobacter pylori requires two nickel-containing enzymes, urease and [NiFe]-hydrogenase, for efficient colonization of the human gastric mucosa. These enzymes possess complex metallocenters that are assembled by teams of proteins in multistep pathways. One essential accessory protein is the GTPase HypB, which is required for Ni(II) delivery to [NiFe]-hydrogenase and participates in urease maturation. Ni(II) or Zn(II) binding to a site embedded in the GTPase domain of HypB modulates the enzymatic activity, suggesting a mechanism of regulation. In this study, biochemical and structural analyses of H. pylori HypB (HpHypB) revealed an intricate link between nucleotide and metal binding. HpHypB nickel coordination, stoichiometry, and affinity were modulated by GTP and GDP, an effect not observed for zinc, and biochemical evidence suggests that His-107 coordination to nickel toggles on and off in a nucleotide-dependent manner. These results are consistent with the crystal structure of HpHypB loaded with Ni(II), GDP, and Pi, which reveals a nickel site distinct from that of zinc-loaded Methanocaldococcus jannaschii HypB as well as subtle changes to the protein structure. Furthermore, Cys-142, a metal ligand from the Switch II GTPase motif, was identified as a key component of the signal transduction between metal binding and the enzymatic activity. Finally, potassium accelerated the enzymatic activity of HpHypB but had no effect on the other biochemical properties of the protein. Altogether, this molecular level information about HpHypB provides insight into its cellular function and illuminates a possible mechanism of metal ion discrimination.
Relationship between Ni(II) and Zn(II) Coordination and Nucleotide Binding by the Helicobacter pylori [NiFe]-Hydrogenase and Urease Maturation Factor HypB.,Sydor AM, Lebrette H, Ariyakumaran R, Cavazza C, Zamble DB J Biol Chem. 2014 Feb 14;289(7):3828-41. doi: 10.1074/jbc.M113.502781. Epub 2013 , Dec 12. PMID:24338018[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sydor AM, Lebrette H, Ariyakumaran R, Cavazza C, Zamble DB. Relationship between Ni(II) and Zn(II) Coordination and Nucleotide Binding by the Helicobacter pylori [NiFe]-Hydrogenase and Urease Maturation Factor HypB. J Biol Chem. 2014 Feb 14;289(7):3828-41. doi: 10.1074/jbc.M113.502781. Epub 2013 , Dec 12. PMID:24338018 doi:http://dx.doi.org/10.1074/jbc.M113.502781
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