Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 53.18 kDa 
• Atom Count: 4146 
• Modelled Residue Count: 452 
• Deposited Residue Count: 470 
• Unique protein chains: 1

2DXU

Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Complexed with Biotinyl-5'-AMP, Mutation R48A

• PDB DOI: 10.2210/pdb2DXU/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-08-30 Released: 2007-03-01 
• Deposition Author(s): Bagautdinov, B., Taketa, M., Matsuura, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.233 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate

Bagautdinov, B., Matsuura, Y., Bagautdinova, S., Kunishima, N.

(2008) J Biol Chem 283: 14739-14750

• PubMed: 18372281 
• DOI: 10.1074/jbc.M709116200
• Primary Citation of Related Structures:  
  1X01, 2D5D, 2DXU, 2DZC, 2E41, 2E64, 2EJF, 2EJG, 2EVB, 2ZGW


• PubMed Abstract: 
  

Biotin protein ligase (BPL) catalyzes the biotinylation of the biotin carboxyl carrier protein (BCCP) only at a special lysine residue. Here we report the first structure of BPL.BCCP complex crystals, which are prepared using two BPL mutants: R48A and R48A/K111A. From a detailed structural characterization, it is likely that the mutants retain functionality as enzymes but have a reduced activity to produce the reaction intermediate biotinyl-5'-AMP. The observed biotin and partly disordered ATP in the mutant structures may act as a non-reactive analog of the substrates or biotinyl-5'-AMP, thereby providing the complex crystals. The four crystallographically independent BPL.BCCP complexes obtained can be classified structurally into three groups: the formation stages 1 and 2 with apo-BCCP and the product stage with biotinylated holo-BCCP. Residues responsible for the complex formation as well as for the biotinylation reaction have been identified. The C-terminal domain of BPL shows especially large conformational changes to accommodate BCCP, suggesting its functional importance. The formation stage 1 complex shows the closest distance between the carboxyl carbon of biotin and the special lysine of BCCP, suggesting its relevance to the unobserved reaction stage. Interestingly, bound ATP and biotin are also seen in the product stage, indicating that the substrates may be recruited into the product stage complex before the release of holo-BCCP, probably for the next reaction cycle. The existence of formation and product stages before and after the reaction stage would be favorable to ensure both the reaction efficiency and the extreme substrate specificity of the biotinylation reaction.

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Organizational Affiliation: 

RIKEN SPring-8 Center, Harima Institute, Sayo-Gun, Hyogo, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
biotin--[acetyl-CoA-carboxylase] ligase	A, B	235	Pyrococcus horikoshii	Mutation(s): 1  Gene Names: birA EC: 6.3.4.15
UniProt
Find proteins for O57883 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57883  Go to UniProtKB:  O57883

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BT5	C [auth B], D [auth B]	BIOTINYL-5-AMP C20 H28 N7 O9 P S UTQCSTJVMLODHM-RHCAYAJFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.233 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.236	α = 90
b = 82.851	β = 101.37
c = 72.354	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-30 
• Released Date: 2007-03-01 
Deposition Author(s): Bagautdinov, B., Taketa, M., Matsuura, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations