PDBsum entry: 2bw7

Lyase

PDB id: 2bw7

Contents

Protein chains

198 a.a. *

Ligands

APC ×4

ECS ×2

Metals

_CA ×4

_MG ×4

Waters ×139

* Residue conservation analysis

PDB id:

2bw7

Name:

Lyase

Title:

A novel mechanism for adenylyl cyclase inhibition from the crystal structure of its complex with catechol estrogen

Structure:

Adenylate cyclase. Chain: a, b, c, d. Fragment: catalytic domain, residues 1005-1199. Synonym: soluble adenylyl cyclase cyac. Engineered: yes

Source:

Spirulina platensis. Organism_taxid: 118562. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.30Å R-factor: 0.207 R-free: 0.257

Authors:

C.Steegborn,T.N.Litvin,K.C.Hess,A.B.Capper,R.Taussig,J.Buck, L.R.Levin,H.Wu

Key ref:

C.Steegborn et al. (2005). A novel mechanism for adenylyl cyclase inhibition from the crystal structure of its complex with catechol estrogen. J Biol Chem, 280, 31754-31759. PubMed id: 16002394 DOI: 10.1074/jbc.M507144200

Date:

12-Jul-05 Release date: 20-Jul-05

Protein chains

O32393  (O32393_SPIPL) -  Adenylate cyclase

Seq: 1202 a.a.

Struc: 198 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.6.1.1 - Adenylate cyclase.
• Reaction: ATP = 3',5'-cyclic AMP + diphosphate

ATP = 3',5'-cyclic AMP (Bound ligand (Het Group name = APC) matches with 70.00% similarity) + diphosphate

• Cofactor: Pyridoxal 5'-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: cyclic nucleotide biosynthetic process (1 term)
• Biochemical function: phosphorus-oxygen lyase activity (1 term)

reference

DOI no: 10.1074/jbc.M507144200

J Biol Chem 280:31754-31759 (2005)

PubMed id: 16002394

A novel mechanism for adenylyl cyclase inhibition from the crystal structure of its complex with catechol estrogen.

C.Steegborn, T.N.Litvin, K.C.Hess, A.B.Capper, R.Taussig, J.Buck, L.R.Levin, H.Wu.

ABSTRACT

Catechol estrogens are steroid metabolites that elicit physiological responses through binding to a variety of cellular targets. We show here that catechol estrogens directly inhibit soluble adenylyl cyclases and the abundant trans-membrane adenylyl cyclases. Catechol estrogen inhibition is non-competitive with respect to the substrate ATP, and we solved the crystal structure of a catechol estrogen bound to a soluble adenylyl cyclase from Spirulina platensis in complex with a substrate analog. The catechol estrogen is bound to a newly identified, conserved hydrophobic patch near the active center but distinct from the ATP-binding cleft. Inhibitor binding leads to a chelating interaction between the catechol estrogen hydroxyl groups and the catalytic magnesium ion, distorting the active site and trapping the enzyme substrate complex in a non-productive conformation. This novel inhibition mechanism likely applies to other adenylyl cyclase inhibitors, and the identified ligand-binding site has important implications for the development of specific adenylyl cyclase inhibitors.

Selected figure(s)

Figure 1.
FIG. 1. Chemical structures of estrogen and its metabolites. The catechol derivatives 2-CE, 4-CE, and 2-hydroxyestrone are major catabolites of the steroid hormones estrogen and estrone. The hydroxyl group added to the sterol scaffold is needed for subsequent conjugation and decomposition reactions.

Figure 3.
FIG. 3. Structure of CyaC in complex with CE. A, kinetic mechanism for the inhibition of CyaC by 2-CE. AC activities determined at varying substrate and inhibitor concentrations are displayed in a double reciprocal plot. The linear extrapolations intersect on the x-axis, indicating that CE inhibition is non-competitive with the substrate ATP. B, overall structure of CyaC in complex with the substrate analog , -Me-ATP and the inhibitor 2-CE. The two monomers of the homodimer are shown in red and blue, respectively. Two inhibitor molecules occupy the center of the dimer, whereas the active sites are still occupied by the substrate analog and two metal ions. C, detailed view of the interactions between CyaC and the inhibitor 2-CE bound next to the active site, which harbors the substrate analog , -Me-ATP and two divalent metal ions (one magnesium ion colored cyan, and one calcium ion in gray). F[o] - F[c] omit electron density for the inhibitor is shown contoured at 2.5 . Single letter amino acid abbreviations are presented with position numbers. D, electrostatic surface of the 2-CE binding site showing its mainly hydrophobic nature (blue, positively charged; red, negatively charged). The hydroxyl groups of the inhibitor chelate the catalytic magnesium ion (ion A), removing it from its normal binding site (indicated in gray).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 31754-31759) copyright 2005.

Figures were selected by an automated process.