5FSX

Crystal structure of Trypanosoma brucei macrodomain in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb5FSX/pdb

• Classification: HYDROLASE
• Organism(s): Trypanosoma brucei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-08 Released: 2016-04-20 
• Deposition Author(s): Haikarainen, T., Lehtio, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.253 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Proximal Adp-Ribose Hydrolysis in Trypanosomatids is Catalyzed by a Macrodomain.

Haikarainen, T., Lehtio, L.

(2016) Sci Rep 6: 24213

• PubMed: 27064071 
• DOI: https://doi.org/10.1038/srep24213
• Primary Citation of Related Structures:  
  5FSU, 5FSV, 5FSX, 5FSY, 5FSZ


• PubMed Abstract: 
  

  ADP-ribosylation is a ubiquitous protein modification utilized by both prokaryotes and eukaryotes for several cellular functions, such as DNA repair, proliferation, and cell signaling. Higher eukaryotes, such as humans, utilize various enzymes to reverse the modification and to regulate ADP-ribose dependent signaling. In contrast, some lower eukaryotes, including trypanosomatids, lack many of these enzymes and therefore have a much more simplified ADP-ribose metabolism. Here we identified and characterized ADP-ribose hydrolases from Trypanosoma brucei and Trypanosoma cruzi, which are homologous to human O-acetyl-ADP-ribose deacetylases MacroD1 and MacroD2. The enzymes are capable for hydrolysis of protein linked ADP-ribose and a product of sirtuin-mediated lysine deacetylation, O-acetyl-ADP-ribose. Crystal structures of the trypanosomatid macrodomains revealed a conserved catalytic site with distinct differences to human MacroD1 and MacroD2.

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Organizational Affiliation: 

Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.3 kDa 
• Atom Count: 3,717 
• Modelled Residue Count: 465 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MACRODOMAIN	A, B	266	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for C9ZP98 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972)) Explore C9ZP98  Go to UniProtKB:  C9ZP98

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ADP	Binding MOAD:  5FSX	Ka: 540 (M^-1) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.253 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.957	α = 90
b = 115.59	β = 93.81
c = 70.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Haikarainen, T., Lehtio, L.

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Data collection
• Version 2.0: 2019-10-23
  Changes: Atomic model, Data collection, Other
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description