5UKI | pdb_00005uki

Mn2+ and Zn2+ requirements for the lariat debranching enzyme, Dbr1

• PDB DOI: https://doi.org/10.2210/pdb5UKI/pdb

• Classification: HYDROLASE
• Organism(s): Entamoeba histolytica
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-01-22 Released: 2018-02-21 
• Deposition Author(s): Macbeth, M.R., Ransey, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn2+/Mn2+heterobinucleation.

Ransey, E., Paredes, E., Dey, S.K., Das, S.R., Heroux, A., Macbeth, M.R.

(2017) FEBS Lett 591: 2003-2010

• PubMed: 28504306 
• DOI: https://doi.org/10.1002/1873-3468.12677
• Primary Citation of Related Structures:  
  5UKI


• PubMed Abstract: 
  

  The RNA lariat debranching enzyme, Dbr1, is a metallophosphoesterase that cleaves 2'-5' phosphodiester bonds within intronic lariats. Previous reports have indicated that Dbr1 enzymatic activity is supported by diverse metal ions including Ni ²⁺ , Mn ²⁺ , Mg ²⁺ , Fe ²⁺ , and Zn ²⁺ . While in initial structures of the Entamoeba histolytica Dbr1 only one of the two catalytic metal-binding sites were observed to be occupied (with a Mn ²⁺ ion), recent structures determined a Zn ²⁺ /Fe ²⁺ heterobinucleation. We solved a high-resolution X-ray crystal structure (1.8 Å) of the E. histolytica Dbr1 and determined a Zn ²⁺ /Mn ²⁺ occupancy. ICP-AES corroborate this finding, and in vitro debranching assays with fluorescently labeled branched substrates confirm activity.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
Department of Chemistry and Center for Nucleic Acids & Technology, Carnegie Mellon University, Pittsburgh, PA, USA.
National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY, USA.
Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 40.7 kDa 
• Atom Count: 3,035 
• Modeled Residue Count: 351 
• Deposited Residue Count: 351 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA lariat debranching enzyme, putative	A	351	Entamoeba histolytica	Mutation(s): 0  Gene Names: EHI_062730 EC: 3.1.4
UniProt
Find proteins for C4M1P9 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4M1P9  Go to UniProtKB:  C4M1P9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.341	α = 90
b = 70.92	β = 90
c = 109.266	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXCD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Macbeth, M.R., Ransey, L.

Revision History  

• Version 1.0: 2018-02-21
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references