3AHW | pdb_00003ahw

Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 2'-monophosphate

• PDB DOI: https://doi.org/10.2210/pdb3AHW/pdb

• Classification: HYDROLASE
• Organism(s): Ustilago sphaerogena
• Mutation(s): No 


• Deposited: 2010-05-04 Released: 2010-07-07 
• Deposition Author(s): Noguchi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 
  0.144 (Depositor), 0.148 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Conformational variation revealed by the crystal structure of RNase U2A complexed with Ca ion and 2'-adenylic acid at 1.03 angstrom resolution.

Noguchi, S.

(2010) Protein Pept Lett 17: 1559-1561

• PubMed: 20858208 
• DOI: https://doi.org/10.2174/0929866511009011559


• PubMed Abstract: 
  

  Asparagine can be non-enzymatically deamidated and isomerized via succinimide to isoaspartate. This post-translational modification can potentially alter the physical properties or the function of the parent protein. Asn32 of ribonuclease U2A from Ustilago sphaerogena is known to rapidly deamidate and isomerize in alkaline conditions. The crystal structure of ribonuclease U2A complexed with 2'-adenylic acid and calcium ions was determined at 1.03 Å resolution. In this structure, the region from Asp29 to Asp37 winds around a calcium ion, and the main-chain of Asn32-Gly33 adopts an extended conformation. Rotation of the side-chain of Asn32 could bring Asn32C(γ) into close proximity to Gly33N, in a conformation suitable for succinimide formation. The structure suggests that in solution the region around Asn32-Gly33 is likely to be in equilibrium between multiple conformers, with the deamidation of Asn32 proceeding when the region adopts an extended conformation.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan. [e-mail]

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: 12.9 kDa 
• Atom Count: 1,090 
• Modeled Residue Count: 114 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease U2	A	114	Ustilago sphaerogena	Mutation(s): 0  EC: 3.1.27.4 (PDB Primary Data), 4.6.1.20 (UniProt)
UniProt
Find proteins for P00654 (Ustilago sphaerogena) Explore P00654  Go to UniProtKB:  P00654

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2AM	B [auth A]	ADENOSINE-2'-MONOPHOSPHATE C10 H14 N5 O7 P QDFHPFSBQFLLSW-KQYNXXCUSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free:  0.144 (Depositor), 0.148 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.994	α = 90
b = 35.94	β = 103.42
c = 36.151	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Noguchi, S.

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-10-16
  Changes: Data collection, Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary