4MIT

Crystal structure of E. histolytica RacC bound to the EhPAK4 PBD

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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Literature

Entamoeba histolytica RacC Selectively Engages p21-Activated Kinase Effectors.

Bosch, D.E., Siderovski, D.P.

(2015) Biochemistry 54: 404-412

  • DOI: 10.1021/bi501226f
  • Primary Citation of Related Structures:  
    4MIT

  • PubMed Abstract: 

    • Rho family GTPases modulate actin cytoskeleton dynamics by signaling through multiple effectors, including the p21-activated kinases (PAKs). The intestinal parasite Entamoeba histolytica expresses ∼20 Rho family GTPases and seven isoforms of PAK, two of which have been implicated in pathogenesis-related processes such as amoebic motility and invasion and host cell phagocytosis ...

    Rho family GTPases modulate actin cytoskeleton dynamics by signaling through multiple effectors, including the p21-activated kinases (PAKs). The intestinal parasite Entamoeba histolytica expresses ∼20 Rho family GTPases and seven isoforms of PAK, two of which have been implicated in pathogenesis-related processes such as amoebic motility and invasion and host cell phagocytosis. Here, we describe two previously unstudied PAK isoforms, EhPAK4 and EhPAK5, as highly specific effectors of EhRacC. A structural model based on 2.35 Å X-ray crystallographic data of a complex between EhRacC(Q65L)·GTP and the EhPAK4 p21 binding domain (PBD) reveals a fairly well-conserved Rho/effector interface despite deviation of the PBD α-helix. A structural comparison with EhRho1 in complex with EhFormin1 suggests likely determinants of Rho family GTPase signaling specificity in E. histolytica. These findings suggest a high degree of Rho family GTPase diversity and specificity in the single-cell parasite E. histolytica. Because PAKs regulate pathogenesis-related processes in E. histolytica, they may be valid pharmacologic targets for anti-amoebiasis drugs.

    Organizational Affiliation: 

    Department of Pharmacology, The University of North Carolina , Chapel Hill, North Carolina 27514, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rho family GTPaseA, B, C, D186Entamoeba histolytica HM-3:IMSSMutation(s): 1 
Gene Names: EhRacC, KM1_331620
EC: 3.6.5.2
UniProt
Find proteins for Q24816 (Entamoeba histolytica)
Explore Q24816 
Go to UniProtKB:  Q24816
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ24816
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine protein kinase PAK, putativeE, F, G, H70Entamoeba histolytica HM-1:IMSS-AMutation(s): 0 
Gene Names: EHI7A_018700, EhPAK4
UniProt
Find proteins for N9UZ59 (Entamoeba histolytica HM-1:IMSS-A)
Explore N9UZ59 
Go to UniProtKB:  N9UZ59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN9UZ59
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
Q [auth C],
U [auth D]		GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
T [auth C],
V [auth D],
W [auth D],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.322α = 90
b = 211.957β = 102.85
c = 49.78γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Database references