1WC3

Soluble adenylyl cyclase CyaC from S. platensis in complex with alpha, beta-methylene-ATP and Strontium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bicarbonate Activation of Adenylyl Cyclase Via Promotion of Catalytic Active Site Closure and Metal Recruitment

Steegborn, C.Litvin, T.N.Levin, L.R.Buck, J.Wu, H.

(2005) Nat.Struct.Mol.Biol. 12: 32

  • DOI: 10.1038/nsmb880
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In an evolutionarily conserved signaling pathway, 'soluble' adenylyl cyclases (sACs) synthesize the ubiquitous second messenger cyclic adenosine 3',5'-monophosphate (cAMP) in response to bicarbonate and calcium signals. Here, we present crystal struc ...

    In an evolutionarily conserved signaling pathway, 'soluble' adenylyl cyclases (sACs) synthesize the ubiquitous second messenger cyclic adenosine 3',5'-monophosphate (cAMP) in response to bicarbonate and calcium signals. Here, we present crystal structures of a cyanobacterial sAC enzyme in complex with ATP analogs, calcium and bicarbonate, which represent distinct catalytic states of the enzyme. The structures reveal that calcium occupies the first ion-binding site and directly mediates nucleotide binding. The single ion-occupied, nucleotide-bound state defines a novel, open adenylyl cyclase state. In contrast, bicarbonate increases the catalytic rate by inducing marked active site closure and recruiting a second, catalytic ion. The phosphates of the bound substrate analogs are rearranged, which would facilitate product formation and release. The mechanisms of calcium and bicarbonate sensing define a reaction pathway involving active site closure and metal recruitment that may be universal for class III cyclases.


    Organizational Affiliation

    Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENYLATE CYCLASE
A, B
219Arthrospira platensisMutation(s): 0 
Gene Names: cyaC
EC: 4.6.1.1
Find proteins for O32393 (Arthrospira platensis)
Go to UniProtKB:  O32393
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download SDF File 
Download CCD File 
A, B
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
SR
Query on SR

Download SDF File 
Download CCD File 
A, B
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
APCKi: 300000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.672α = 90.00
b = 71.539β = 90.00
c = 99.572γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
MOLREPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance