2LHI

Solution structure of Ca2+/CNA1 peptide-bound yCaM

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

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Literature

Solution structures of yeast Saccharomyces cerevisiae calmodulin in calcium- and target peptide-bound states reveal similarities and differences to vertebrate calmodulin.

Ogura, K., Kumeta, H., Takahasi, K., Kobashigawa, Y., Yoshida, R., Itoh, H., Yazawa, M., Inagaki, F.

(2012) Genes Cells 17: 159-172

  • DOI: 10.1111/j.1365-2443.2012.01580.x
  • Primary Citation of Related Structures:  
    2LHH, 2LHI

  • PubMed Abstract: 

    • We determined the solution structures of the calmodulin (CaM) isoform from yeast Saccharomyces cerevisiae (yCaM) in the calcium-bound form and in complex with a target peptide using NMR spectroscopy and small-angle X-ray scattering (SAXS). yCaM shows a number of unique features distinct from the vertebrate CaM isoforms: (i) it has only approximately 60% sequence identity to vertebrate CaM; (ii) its fourth Ca(2+)-binding domain is inactivated by amino acid substitution ...

    We determined the solution structures of the calmodulin (CaM) isoform from yeast Saccharomyces cerevisiae (yCaM) in the calcium-bound form and in complex with a target peptide using NMR spectroscopy and small-angle X-ray scattering (SAXS). yCaM shows a number of unique features distinct from the vertebrate CaM isoforms: (i) it has only approximately 60% sequence identity to vertebrate CaM; (ii) its fourth Ca(2+)-binding domain is inactivated by amino acid substitution. As NMR analyses of Ca(2+)-bound full-length yCaM implied that the fourth EF-hand motif region (EF4) presents a disordered conformation, we determined the solution structure of an EF4-deletion mutant of Ca(2+)-bound yCaM. The deletion mutant showed a compact globular structure, with the target recognition sites of the N-terminal domain and the third EF-hand region bound to each other. Furthermore, we determined the solution structure of Ca(2+)-bound yCaM complexed with a calcineurin-derived peptide. Interestingly, the structure closely resembled that of the vertebrate CaM-calcineurin complex, with the EF4 region in cooperation with the peptide binding. Moreover, the results of SAXS analyses were consistent with the NMR solution structures and showed the conformational changes of yCaM in three functional stages. These unique structural characteristics of yCaM are closely related to Ca(2+)-mediated signal transduction in yeast.

    Organizational Affiliation: 

    Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Kita 21 Nishi 11, Kita-ku, Sapporo 001-0021, Japan.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin,Serine/threonine-protein phosphatase 2B catalytic subunit A1A176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CMD1, YBR109C, YBR0904, CMP1, CNA1, L9753.6, YLR433C
EC: 3.1.3.16
UniProt
Find proteins for P06787 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06787 
Go to UniProtKB:  P06787
Find proteins for P23287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23287 
Go to UniProtKB:  P23287
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP23287P06787
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 
  • OLDERADO: 2LHI Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Data collection, Database references, Source and taxonomy, Structure summary