2GVZ

Crystal Structure of Complex of Gs- with The Catalytic Domains of Mammalian Adenylyl Cyclase: Complex with MANT-ATP and Mn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.275 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Broad specificity of Mammalian adenylyl cyclase for interaction with 2',3'-substituted purine- and pyrimidine nucleotide inhibitors.

Mou, T.-C.Gille, A.Suryanarayana, S.Richter, M.Seifert, R.Sprang, S.R.

(2006) Mol.Pharmacol. 70: 878-886

  • DOI: 10.1124/mol.106.026427
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Membrane adenylyl cyclases (mACs) play an important role in signal transduction and are therefore potential drug targets. Earlier, we identified 2',3'-O-(N-methylanthraniloyl) (MANT)-substituted purine nucleotides as a novel class of highly potent co ...

    Membrane adenylyl cyclases (mACs) play an important role in signal transduction and are therefore potential drug targets. Earlier, we identified 2',3'-O-(N-methylanthraniloyl) (MANT)-substituted purine nucleotides as a novel class of highly potent competitive mAC inhibitors (Ki values in the 10 nM range). MANT nucleotides discriminate among various mAC isoforms through differential interactions with a binding pocket localized at the interface between the C1 and C2 domains of mAC. In this study, we examine the structure/activity relationships for 2',3'-substituted nucleotides and compare the crystal structures of mAC catalytic domains (VC1:IIC2) bound to MANT-GTP, MANT-ATP, and 2',3'-(2,4,6-trinitrophenyl) (TNP)-ATP. TNP-substituted purine and pyrimidine nucleotides inhibited VC1:IIC2 with moderately high potency (Ki values in the 100 nM range). Elongation of the linker between the ribosyl group and the MANT group and substitution of N-adenine atoms with MANT reduces inhibitory potency. Crystal structures show that MANT-GTP, MANT-ATP, and TNP-ATP reside in the same binding pocket in the VC1:IIC2 protein complex, but there are substantial differences in interactions of base, fluorophore, and polyphosphate chain of the inhibitors with mAC. Fluorescence emission and resonance transfer spectra also reflect differences in the interaction between MANT-ATP and VC1:IIC2 relative to MANT-GTP. Our data are indicative of a three-site mAC pharmacophore; the 2',3'-O-ribosyl substituent and the polyphosphate chain have the largest impact on inhibitor affinity and the nucleotide base has the least. The mAC binding site exhibits broad specificity, accommodating various bases and fluorescent groups at the 2',3'-O-ribosyl position. These data should greatly facilitate the rational design of potent, isoform-selective mAC inhibitors.


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenylate cyclase type 5
A
225Canis lupus familiarisMutation(s): 1 
Gene Names: ADCY5
EC: 4.6.1.1
Find proteins for P30803 (Canis lupus familiaris)
Go to Gene View: ADCY5
Go to UniProtKB:  P30803
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Adenylate cyclase type 2
B
212Rattus norvegicusMutation(s): 0 
Gene Names: Adcy2
EC: 4.6.1.1
Find proteins for P26769 (Rattus norvegicus)
Go to UniProtKB:  P26769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(s), alpha subunit
C
394Bos taurusMutation(s): 0 
Gene Names: GNAS (GNAS1)
Find proteins for P04896 (Bos taurus)
Go to Gene View: GNAS
Go to UniProtKB:  P04896
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FKP
Query on FKP

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Download CCD File 
A
METHYLPIPERAZINOFORSKOLIN
C30 H50 N2 O7
UNNWBVSRDSMIDQ-QAMJDCALSA-N
 Ligand Interaction
GSP
Query on GSP

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Download CCD File 
C
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
 Ligand Interaction
ONA
Query on ONA

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Download CCD File 
A
3'-O-[2-(METHYLAMINO)BENZOYL]ADENOSINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
2'(3')-O-(N-METHYLANTHRANILOYL)-ADENOSINE 5'-TRIPHOSPHATE
C18 H23 N6 O14 P3
YAPJXKKTHXODSV-LSCFUAHRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ONAKi: 130 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.275 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 116.800α = 90.00
b = 132.100β = 90.00
c = 69.600γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation