2BFR | pdb_00002bfr

The Macro domain is an ADP-ribose binding module

• PDB DOI: https://doi.org/10.2210/pdb2BFR/pdb

• Classification: MACRO_H2A DOMAIN/HYDROLASE
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-10 Released: 2004-12-16 
• Deposition Author(s): Karras, G.I., Buhecha, H.R., Allen, M.D., Pugieux, C., Sait, F., Bycroft, M., Ladurner, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.237 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

The Macro Domain is an Adp-Ribose Binding Module.

Karras, G.I., Kustatscher, G., Buhecha, H.R., Allen, M.D., Pugieux, C., Sait, F., Bycroft, M., Ladurner, A.G.

(2005) EMBO J 24: 1911

• PubMed: 15902274 
• DOI: https://doi.org/10.1038/sj.emboj.7600664
• Primary Citation Related Structures: 
  2BFQ, 2BFR


• PubMed Abstract: 
  

  The ADP-ribosylation of proteins is an important post-translational modification that occurs in a variety of biological processes, including DNA repair, transcription, chromatin biology and long-term memory formation. Yet no protein modules are known that specifically recognize the ADP-ribose nucleotide. We provide biochemical and structural evidence that macro domains are high-affinity ADP-ribose binding modules. Our structural analysis reveals a conserved ligand binding pocket among the macro domain fold. Consistently, distinct human macro domains retain their ability to bind ADP-ribose. In addition, some macro domain proteins also recognize poly-ADP-ribose as a ligand. Our data suggest an important role for proteins containing macro domains in the biology of ADP-ribose.

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Organizational Affiliation: 
• Gene Expression Programme and Structural & Computational Biology Programme, European Molecular Biology Laboratory, Heidelberg, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 21.46 kDa 
• Atom Count: 1,543 
• Modeled Residue Count: 192 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL PROTEIN AF1521	A	192	Archaeoglobus fulgidus	Mutation(s): 0  EC: 3.2.2
UniProt
Find proteins for O28751 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28751  Go to UniProtKB:  O28751

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	A	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.237 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.84	α = 90
b = 87.84	β = 90
c = 61.069	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-16 
Deposition Author(s): Karras, G.I., Buhecha, H.R., Allen, M.D., Pugieux, C., Sait, F., Bycroft, M., Ladurner, A.G.

Revision History  

• Version 1.0: 2004-12-16
  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: 2019-04-10
  Changes: Data collection, Derived calculations, Other, Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary