2GL0

Structure of PAE2307 in complex with adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.170 

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This is version 1.3 of the entry. See complete history


Literature

The Structure of an Ancient Conserved Domain Establishes a Structural Basis for Stable Histidine Phosphorylation and Identifies a New Family of Adenosine-specific Kinases.

Lott, J.S.Paget, B.Johnston, J.M.Delbaere, L.T.Sigrell-Simon, J.A.Banfield, M.J.Baker, E.N.

(2006) J Biol Chem 281: 22131-22141

  • DOI: https://doi.org/10.1074/jbc.M603062200
  • Primary Citation of Related Structures:  
    1WVQ, 2GL0

  • PubMed Abstract: 

    Phosphorylation of both small molecules and proteins plays a central role in many biological processes. In proteins, phosphorylation most commonly targets the oxygen atoms of Ser, Thr, and Tyr. In contrast, stably phosphorylated His residues are rarely found, due to the lability of the N-P bond, and histidine phosphorylation features most often in transient processes. Here we present the crystal structure of a protein of previously unknown function, which proves to contain a stably phosphorylated histidine residue. The protein is the product of open reading frame PAE2307, from the hyperthermophilic archaeon Pyrobaculum aerophilum, and is representative of a highly conserved protein family found in archaea and bacteria. The crystal structure of PAE2307, solved at 1.45-A resolution (R = 0.208, R(free) = 0.227), forms a remarkably tightly associated hexamer. The phosphorylated histidine at the proposed active site, pHis85, occupies a cavity that is at the interface between two subunits and contains a number of fully conserved residues. Stable phosphorylation is attributed to favorable hydrogen bonding of the phosphoryl group and a salt bridge with pHis85 that provides electronic stabilization. In silico modeling suggested that the protein may function as an adenosine kinase, a conclusion that is supported by in vitro assays of adenosine binding, using fluorescence spectroscopy, and crystallographic visualization of an adenosine complex of PAE2307 at 2.25-A resolution.


  • Organizational Affiliation

    Laboratory of Structural Biology, Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds St., Private Bag 92-019, Auckland, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
conserved hypothetical protein
A, B, C, D, E
A, B, C, D, E, F
167Pyrobaculum aerophilum str. IM2Mutation(s): 0 
Gene Names: PAE2307
EC: 2.7.1.20
UniProt
Find proteins for Q8ZVF7 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2))
Explore Q8ZVF7 
Go to UniProtKB:  Q8ZVF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZVF7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ADN Binding MOAD:  2GL0 Kd: 1.50e+4 (nM) from 1 assay(s)
PDBBind:  2GL0 Kd: 1.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.862α = 90
b = 109.825β = 90
c = 112.484γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description