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.

Macromolecule Content

• Total Structure Weight: 66.24 kDa 
• Atom Count: 4582 
• Modelled Residue Count: 518 
• Deposited Residue Count: 538 
• Unique protein chains: 1

2AB5

bI3 LAGLIDADG Maturase

• PDB DOI: 10.2210/pdb2AB5/pdb

• Classification: PROTEIN BINDING
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-07-14 Released: 2005-08-30 
• Deposition Author(s): Longo, A., Leonard, C.W., Bassi, G.S., Berndt, D., Krahn, J.M., Hall, T.M., Weeks, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.265 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Literature

Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase

Longo, A., Leonard, C.W., Bassi, G.S., Berndt, D., Krahn, J.M., Hall, T.M., Weeks, K.M.

(2005) Nat Struct Mol Biol 12: 779-787

• PubMed: 16116439 
• DOI: 10.1038/nsmb976
• Primary Citation of Related Structures:  
  2AB5


• PubMed Abstract: 
  

LAGLIDADG endonucleases bind across adjacent major grooves via a saddle-shaped surface and catalyze DNA cleavage. Some LAGLIDADG proteins, called maturases, facilitate splicing by group I introns, raising the issue of how a DNA-binding protein and an RNA have evolved to function together. In this report, crystallographic analysis shows that the global architecture of the bI3 maturase is unchanged from its DNA-binding homologs; in contrast, the endonuclease active site, dispensable for splicing facilitation, is efficiently compromised by a lysine residue replacing essential catalytic groups. Biochemical experiments show that the maturase binds a peripheral RNA domain 50 A from the splicing active site, exemplifying long-distance structural communication in a ribonucleoprotein complex. The bI3 maturase nucleic acid recognition saddle interacts at the RNA minor groove; thus, evolution from DNA to RNA function has been mediated by a switch from major to minor groove interaction.

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Organizational Affiliation: 

Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA maturase	A, B	269	Saccharomyces cerevisiae	Mutation(s): 13  Gene Names: cytochrome b intron bi3
UniProt
Find proteins for Q9ZZW7 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q9ZZW7  Go to UniProtKB:  Q9ZZW7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.265 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.6	α = 90
b = 80.2	β = 115.5
c = 66.4	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-07-14 
• Released Date: 2005-08-30 
Deposition Author(s): Longo, A., Leonard, C.W., Bassi, G.S., Berndt, D., Krahn, J.M., Hall, T.M., Weeks, K.M.

Revision History  

• Version 1.0: 2005-08-30
  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: 2017-10-11
  Changes: Refinement description