General Information

Database Accession: DI1100030

Name: Proteinase A complexed with IA3 peptide inhibitor

PDB ID: 1dpj PDB

Experimental method: X-ray (1.80 Å)

Source organism: Saccharomyces cerevisiae

Proof of disorder: Confirmed

Primary publication of the structure:

Li M, Phylip LH, Lees WE, Winther JR, Dunn BM, Wlodawer A, Kay J, Gustchina A
The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix.

(2000) Nat. Struct. Biol. 7: 113-7

PMID: 10655612 PubMed


Aspartic proteinase A from yeast is specifically and potently inhibited by a small protein called IA3 from Saccharomyces cerevisiae. Although this inhibitor consists of 68 residues, we show that the inhibitory activity resides within the N-terminal half of the molecule. Structures solved at 2.2 and 1.8 A, respectively, for complexes of proteinase A with full-length IA3 and with a truncated form consisting only of residues 2-34, reveal an unprecedented mode of inhibitor-enzyme interactions. Neither form of the free inhibitor has detectable intrinsic secondary structure in solution. However, upon contact with the enzyme, residues 2-32 become ordered and adopt a near-perfect alpha-helical conformation. Thus, the proteinase acts as a folding template, stabilizing the helical conformation in the inhibitor, which results in the potent and specific blockage of the proteolytic activity.

Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function: not assigned

Biological process:

cellular protein catabolic process The chemical reactions and pathways resulting in the breakdown of a protein by individual cells. GeneOntology

Cellular component:

vacuole A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GeneOntology

protein complex A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. GeneOntology

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 2 distinct polypeptide molecules

Chains: B, A

Notes: No modifications of the original PDB file.

Chain B

Name: Protease A inhibitor 3 Disordered Confirmed

Source organism: Saccharomyces cerevisiae

Length: 29 residues


UniProtKB AC: P01094 (positions: 3-31) UniProt Coverage: 42.6%

UniRef90 AC: UniRef90_P01094 (positions: 3-31) UniRef90

Chain A

Name: Saccharopepsin Ordered

Source organism: Saccharomyces cerevisiae

Length: 329 residues


UniProtKB AC: P07267 (positions: 77-405) UniProt Coverage: 81.2%

UniRef90 AC: UniRef90_P07267 (positions: 77-405) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Chain B: Disordered Confirmed

The 1-68 region described in DisProt entry DP00179 cover 100% of the sequence present in the structure.

Chain A: Ordered

The aspartyl protease domain involved in the interaction is known to adopt a stable structure in isolation (see Pfam domain PF00026). A solved monomeric structure of the domain is represented by PDB ID 2jxr.

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

There are 2 related structures in the Protein Data Bank:

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