6YP4 | pdb_00006yp4

Putative adenylyl cyclase HpAC1 from Hippeastrum reveals a dominant triphophatase activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal structure and enzymatic characterization of the putative adenylyl cyclase HpAC1 from Hippeastrum reveal dominant triphosphatase activity.

Kleinboelting, S.Miehling, J.Steegborn, C.

(2020) J Struct Biol 212: 107649-107649

  • DOI: https://doi.org/10.1016/j.jsb.2020.107649
  • Primary Citation Related Structures: 
    6YP4

  • PubMed Abstract: 

    HpAC1, a protein from Hippeastrum hybrid cultivars, was previously suggested to be a plant adenylyl cyclase. We describe a structural and enzymatic characterization of HpAC1. A crystal structure of HpAC1 in complex with a non-hydrolyzable GTP analog confirms a generic CYTH architecture, comprising a β-barrel with an internal substrate site. The structure reveals significant active site differences to AC proteins with CYTH fold, however, and we find that HpAC1 lacks measurable AC activity. Instead, HpAC1 has substantial triphosphatase activity, indicating this protective activity or a related activity as the protein's physiological function.


  • Organizational Affiliation
    • Department of Biochemistry, University of Bayreuth, Universitaetsstr. 30, 95447 Bayreuth, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund and Drug Discovery Hub Dortmund (DDHD), Zentrum für Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany.

Macromolecule Content 

  • Total Structure Weight: 24.97 kDa 
  • Atom Count: 1,932 
  • Modeled Residue Count: 210 
  • Deposited Residue Count: 214 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adenylate cyclase214Hippeastrum hybrid cultivarMutation(s): 0 
Gene Names: AC1
UniProt
Find proteins for E1AQY1 (Hippeastrum hybrid cultivar)
Explore E1AQY1 
Go to UniProtKB:  E1AQY1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1AQY1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP
(Subject of Investigation/LOI)

Query on GCP



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
EDO

Query on EDO



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

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.808α = 90
b = 59.808β = 90
c = 146.982γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany236401975

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description