4OJV

Crystal structure of unliganded yeast PDE1

Summary for 4OJV

• Entry DOI: 10.2210/pdb4ojv/pdb
• Related: 4OJX
• Descriptor: 3',5'-cyclic-nucleotide phosphodiesterase 1, SULFATE ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total)
• Functional Keywords: phosphodiesterase, cgmp and camp, yeast pde, dual specificity, hydrolase
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Total number of polymer chains: 1
• Total formula weight: 42415.06

Authors

Tian, Y.,Cui, W.,Huang, M.,Robinson, H.,Wan, Y.,Wang, Y.,Ke, H. (deposition date: 2014-01-21, release date: 2014-12-03, Last modification date: 2024-02-28)

Primary citation

Tian, Y.,Cui, W.,Huang, M.,Robinson, H.,Wan, Y.,Wang, Y.,Ke, H.
Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-monophosphate.
Biochemistry, 53:4938-4945, 2014

PubMed Abstract: Cyclic nucleotide phosphodiesterases (PDEs) decompose second messengers cAMP and cGMP that play critical roles in many physiological processes. PDE1 of Saccharomyces cerevisiae has been subcloned and expressed in Escherichia coli. Recombinant yPDE1 has a KM of 110 μM and a kcat of 16.9 s(-1) for cAMP and a KM of 105 μM and a kcat of 11.8 s(-1) for cGMP. Thus, the specificity constant (kcat/KM(cAMP))/(kcat/KM(cGMP)) of 1.4 indicates a dual specificity of yPDE1 for hydrolysis of both cAMP and cGMP. The crystal structures of unliganded yPDE1 and its complex with GMP at 1.31 Å resolution reveal a new structural folding that is different from those of human PDEs but is partially similar to that of some other metalloenzymes such as metallo-β-lactamase. In spite of their different structures and divalent metals, yPDE1 and human PDEs may share a common mechanism for hydrolysis of cAMP and cGMP.

PubMed: 25050706
DOI: 10.1021/bi500406h

Experimental method

X-RAY DIFFRACTION (1.31 Å)