2VUW | pdb_00002vuw

Structure of human haspin kinase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.169 (Depositor), 0.175 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history

Literature

Structure and Functional Characterization of the Atypical Human Kinase Haspin.

Eswaran, J.Patnaik, D.Filippakopoulos, P.Wang, F.Stein, R.L.Murray, J.W.Higgins, J.M.G.Knapp, S.

(2009) Proc Natl Acad Sci U S A 106: 20198

  • DOI: https://doi.org/10.1073/pnas.0901989106
  • Primary Citation Related Structures: 
    2VUW, 3DLZ, 3IQ7

  • PubMed Abstract: 

    The protein kinase haspin/Gsg2 plays an important role in mitosis, where it specifically phosphorylates Thr-3 in histone H3 (H3T3). Its protein sequence is only weakly homologous to other protein kinases and lacks the highly conserved motifs normally required for kinase activity. Here we report structures of human haspin in complex with ATP and the inhibitor iodotubercidin. These structures reveal a constitutively active kinase conformation, stabilized by haspin-specific inserts. Haspin also has a highly atypical activation segment well adapted for specific recognition of the basic histone tail. Despite the lack of a DFG motif, ATP binding to haspin is similar to that in classical kinases; however, the ATP gamma-phosphate forms hydrogen bonds with the conserved catalytic loop residues Asp-649 and His-651, and a His651Ala haspin mutant is inactive, suggesting a direct role for the catalytic loop in ATP recognition. Enzyme kinetic data show that haspin phosphorylates substrate peptides through a rapid equilibrium random mechanism. A detailed analysis of histone modifications in the neighborhood of H3T3 reveals that increasing methylation at Lys-4 (H3K4) strongly decreases substrate recognition, suggesting a key role of H3K4 methylation in the regulation of haspin activity.


  • Organizational Affiliation
    • Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom. jeyanthy.eswaran@sgc.ox.ac.uk

Macromolecule Content 

  • Total Structure Weight: 39.39 kDa 
  • Atom Count: 3,113 
  • Modeled Residue Count: 329 
  • Deposited Residue Count: 336 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE HASPIN336Homo sapiensMutation(s): 0 
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TF76 (Homo sapiens)
Explore Q8TF76 
Go to UniProtKB:  Q8TF76
PHAROS:  Q8TF76
GTEx:  ENSG00000177602 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TF76
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5ID

Query on 5ID



Download:Ideal Coordinates CCD File
C [auth A](2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL
C11 H13 I N4 O4
WHSIXKUPQCKWBY-IOSLPCCCSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
B [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
MPD

Query on MPD



Download:Ideal Coordinates CCD File
F [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
DMS

Query on DMS



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

Query on NI



Download:Ideal Coordinates CCD File
D [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.169 (Depositor), 0.175 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.661α = 90
b = 78.775β = 90
c = 79.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 2.0: 2024-05-01
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.1: 2024-11-06
    Changes: Structure summary