1SNL

NMR Solution Structure of the Calcium-binding Domain of Nucleobindin (CALNUC)

Summary for 1SNL

• Entry DOI: 10.2210/pdb1snl/pdb
• Related: 1a2x 1blq 1CLL 1CMF 1CMG
• NMR Information: BMRB: 6167
• Descriptor: Nucleobindin 1 (1 entity in total)
• Functional Keywords: ef-hand, calcium-binding, metal binding protein
• Biological source: Homo sapiens (human)
• Cellular location: Golgi apparatus, cis-Golgi network membrane; Peripheral membrane protein; Lumenal side (By similarity): Q02818
• Total number of polymer chains: 1
• Total formula weight: 12419.80

Authors

de Alba, E.,Tjandra, N. (deposition date: 2004-03-11, release date: 2004-08-17, Last modification date: 2024-05-22)

Primary citation

De Alba, E.,Tjandra, N.
Structural Studies on the Ca(2+)-binding Domain of Human Nucleobindin (Calnuc).
Biochemistry, 43:10039-10049, 2004

PubMed Abstract: Nucleobindin, also known as calnuc, participates in Ca2+ storage in the Golgi, as well as in other biological processes that involve DNA-binding and protein-protein interactions. We have determined the three-dimensional solution structure of the Ca(2+)-binding domain of nucleobindin by NMR showing that it consists of two EF-hand motifs. The NMR structure indicates that the phi and psi angles of residues in both motifs are very similar, despite the noncanonical sequence of the C-terminal EF-hand, which contains an arginine residue instead of the typical glycine at the sixth position of the 12-residue loop. The relative orientation of the alpha-helices in the N-terminal EF-hand falls within the common arrangement found in most EF-hand structures. In contrast, the noncanonical EF-hand deviates from the average orientation. The two helix-loop-helix moieties are in the open conformation characteristic of the Ca(2+)-bound state. We find that both motifs bind Ca2+ with apparent dissociation constants of 47 and 40 microM for the noncanonical and the canonical EF-hand, respectively. The Ca(2+)-binding domain of nucleobindin is unstructured in the absence of Ca2+ and folds upon Ca2+ addition. NMR relaxation data and structural studies of the folded domain indicate that it undergoes slow dynamics, suggesting that it is floppier and less compact than a globular domain.

PubMed: 15287731
DOI: 10.1021/bi049310a

Experimental method

SOLUTION NMR