Solution structure of HypA protein

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Structure of a nickel chaperone, HypA, from Helicobacter pylori reveals two distinct metal binding sites

Xia, W.Li, H.Sze, K.-H.Sun, H.

(2009) J Am Chem Soc 131: 10031-10040

  • DOI: https://doi.org/10.1021/ja900543y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Metallochaperones bind metals and ensure the safe delivery of metals to the targets. They are required for the activation and maturation of nickel-containing enzymes [Ni,Fe]-hydrogenase and urease. Metallochaperone HypA was found to be essential to facilitate nickel delivery to hydrogenase together with its partner HypB, although the detailed mechanism is not clear. In this study, we have cloned hypA gene from Helicobacter pylori (strain 26695), overexpressed, and purified the protein. The zinc-bound HypA (Zn-HypA) exists as a monomer in solution, and its solution structure was determined by NMR spectroscopy together with molecular dynamics simulated annealing. Zn-HypA folds into two domains, including a zinc domain and a nickel domain with a mixed alpha/beta structure. The former houses a rigid zinc-binding site possibly with the role of structural stabilization, whereas the latter harbors a nickel-binding site at the N-terminus. Zinc binds to the four conserved cysteines tetrahedrally as evidenced by (113)Cd NMR spectroscopy, and nickel coordinates with four nitrogens of the protein probably in a square-planar geometry. Low coordination number of Ni(2+) may allow the metal to be readily transferred to its downstream receptors. Our studies may shed light on how the metallochaperone exerts its functions in intracellular nickel delivery.

  • Organizational Affiliation

    Department of Chemistry and Open Laboratory of Chemical Biology, University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogenase/urease nickel incorporation protein hypA119Helicobacter pylori 26695Mutation(s): 0 
Gene Names: HP_0869hypA
Find proteins for P0A0U4 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P0A0U4 
Go to UniProtKB:  P0A0U4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A0U4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary
  • Version 1.3: 2023-06-14
    Changes: Database references, Derived calculations, Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references