9PCQ | pdb_00009pcq

Phosphorylation of a Conserved Aspartate at the Eukaryotic Elongation Factor 2 Kinase Catalytic Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.243 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Phosphorylation of a conserved aspartate in the catalytic site of eukaryotic elongation factor 2 kinase.

Piserchio, A.Isiorho, E.A.Abzalimov, R.Dalby, K.N.Ghose, R.

(2026) Protein Sci 35: e70442-e70442

  • DOI: https://doi.org/10.1002/pro.70442
  • Primary Citation Related Structures: 
    9PCQ

  • PubMed Abstract: 

    Eukaryotic elongation factor 2 kinase (eEF-2K) is a member of the α-kinase family of atypical serine/threonine kinases. eEF-2K, the only calmodulin-activated α-kinase, phosphorylates the ribosome-associated GTPase, eukaryotic elongation factor 2 (eEF-2), suppressing translational elongation. α-kinases, including eEF-2K, possess catalytic site geometries that are distinct from those of typical kinases, suggesting possible divergence in their phospho-transfer mechanisms. Unlike typical protein kinases, where chemistry is known to proceed through a sequential mechanism involving a ternary kinase-substrate-ATP•Mg 2+ complex, the nature of the chemical step catalyzed by α-kinases remains poorly defined. Here, multiple orthogonal lines of evidence, including a crystal structure and solution-state mass spectrometry data, suggest phosphorylation of a catalytically essential aspartate residue (D284) at the eEF-2K active site. Previous crystallographic evidence of the presence of a phospho-aspartate at an equivalent position (D766) in the related Dictyostelium α-kinase MHCK-A strongly suggests that this species represents a conserved active-site feature in α-kinase family members, despite their disparate modes of activation. This observation, together with existing kinetics data on eEF-2K, raises the possibility that phospho-transfer chemistry in α-kinases occurs via an ordered stepwise mechanism involving a phospho-enzyme intermediate, contrasting with typical protein kinases.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA.

Macromolecule Content 

  • Total Structure Weight: 78.22 kDa 
  • Atom Count: 5,139 
  • Modeled Residue Count: 614 
  • Deposited Residue Count: 678 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic elongation factor 2 kinase531Homo sapiensMutation(s): 0 
Gene Names: EEF2K
EC: 2.7.11.20
UniProt & NIH Common Fund Data Resources
Find proteins for O00418 (Homo sapiens)
Explore O00418 
Go to UniProtKB:  O00418
PHAROS:  O00418
GTEx:  ENSG00000103319 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00418
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Calmodulin-1B [auth B00A]147Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B00A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth B00A],
H [auth B00A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
PHD
Query on PHD
A
L-PEPTIDE LINKINGC4 H8 N O7 PASP
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.464α = 90
b = 88.632β = 90
c = 154.872γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM123252

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-04
    Type: Initial release