4CLZ | pdb_00004clz

Crystal structure of human soluble Adenylyl Cyclase with Inhibitor 4, 4'-Diisothiocyano-2,2'-stilbenedisulfonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.199 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Crystal Structures of Human Soluble Adenylyl Cyclase Reveal Mechanisms of Catalysis and of its Activation Through Bicarbonate.

Kleinboelting, S.Diaz, A.Moniot, S.Van Den Heuvel, J.Weyand, M.Levin, L.R.Buck, J.Steegborn, C.

(2014) Proc Natl Acad Sci U S A 111: 3727

  • DOI: https://doi.org/10.1073/pnas.1322778111
  • Primary Citation Related Structures: 
    4CLF, 4CLK, 4CLL, 4CLP, 4CLS, 4CLT, 4CLU, 4CLW, 4CLY, 4CLZ, 4CM0, 4CM2

  • PubMed Abstract: 

    cAMP is an evolutionary conserved, prototypic second messenger regulating numerous cellular functions. In mammals, cAMP is synthesized by one of 10 homologous adenylyl cyclases (ACs): nine transmembrane enzymes and one soluble AC (sAC). Among these, only sAC is directly activated by bicarbonate (HCO3(-)); it thereby serves as a cellular sensor for HCO3(-), carbon dioxide (CO2), and pH in physiological functions, such as sperm activation, aqueous humor formation, and metabolic regulation. Here, we describe crystal structures of human sAC catalytic domains in the apo state and in complex with substrate analog, products, and regulators. The activator HCO3(-) binds adjacent to Arg176, which acts as a switch that enables formation of the catalytic cation sites. An anionic inhibitor, 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid, inhibits sAC through binding to the active site entrance, which blocks HCO3(-) activation through steric hindrance and trapping of the Arg176 side chain. Finally, product complexes reveal small, local rearrangements that facilitate catalysis. Our results provide a molecular mechanism for sAC catalysis and cellular HCO3(-) sensing and a basis for targeting this system with drugs.


  • Organizational Affiliation
    • Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany.

Macromolecule Content 

  • Total Structure Weight: 56.53 kDa 
  • Atom Count: 4,116 
  • Modeled Residue Count: 458 
  • Deposited Residue Count: 475 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ADENYLATE CYCLASE TYPE 10475Homo sapiensMutation(s): 0 
EC: 4.6.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PN6 (Homo sapiens)
Explore Q96PN6 
Go to UniProtKB:  Q96PN6
PHAROS:  Q96PN6
GTEx:  ENSG00000143199 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96PN6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4DS

Query on 4DS



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A],
N [auth A]
4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid
C16 H10 N2 O6 S4
YSCNMFDFYJUPEF-OWOJBTEDSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
O [auth A],
P [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.199 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.51α = 90
b = 100.51β = 90
c = 97.41γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-03-26
    Changes: Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary