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: 41.58 kDa 
• Atom Count: 3241 
• Modelled Residue Count: 370 
• Deposited Residue Count: 376 
• Unique protein chains: 1

1HRU

THE STRUCTURE OF THE YRDC GENE PRODUCT FROM E.COLI

• PDB DOI: 10.2210/pdb1HRU/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-12-21 Released: 2001-01-31 
• Deposition Author(s): Teplova, M., Tereshko, V., Sanishvili, R., Joachimiak, A., Bushueva, T., Anderson, W.F., Egli, M., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.214 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 

Literature

The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding.

Teplova, M., Tereshko, V., Sanishvili, R., Joachimiak, A., Bushueva, T., Anderson, W.F., Egli, M.

(2000) Protein Sci 9: 2557-2566

• PubMed: 11206077 
• DOI: 10.1110/ps.9.12.2557
• Primary Citation of Related Structures:  
  1HRU


• PubMed Abstract: 
  

The yrdC family of genes codes for proteins that occur both independently and as a domain in proteins that have been implicated in regulation. An example for the latter case is the sua5 gene from yeast. SuaS was identified as a suppressor of a translation initiation defect in cytochrome c and is required for normal growth in yeast (Na JG, Pinto I, Hampsey M, 1992, Genetics 11:791-801). However, the function of the Sua5 protein remains unknown; Sua5 could act either at the transcriptional or the posttranscriptional levels to compensate for an aberrant translation start codon in the cyc gene. To potentially learn more about the function of YrdC and proteins featuring this domain, the crystal structure of the YrdC protein from Escherichia coli was determined at a resolution of 2.0 A. YrdC adopts a new fold with no obvious similarity to those of other proteins with known three-dimensional (3D) structure. The protein features a large concave surface on one side that exhibits a positive electrostatic potential. The dimensions of this depression, its curvature, and the fact that conserved basic amino acids are located at its floor suggest that YrdC may be a nucleic acid binding protein. An investigation of YrdC's binding affinities for single- and double-stranded RNA and DNA fragments as well as tRNAs demonstrates that YrdC binds preferentially to double-stranded RNA. Our work provides evidence that 3D structures of functionally uncharacterized gene products with unique sequences can yield novel folds and functional insights.

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Organizational Affiliation: 

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YRDC GENE PRODUCT	A, B	188	Escherichia coli	Mutation(s): 2  Gene Names: yrdC EC: 2.7.7.87
UniProt
Find proteins for P45748 (Escherichia coli (strain K12)) Explore P45748  Go to UniProtKB:  P45748

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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: 2.00 Å
• R-Value Free: 0.214 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.5	α = 90
b = 71.65	β = 103.25
c = 55.28	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-12-21 
• Released Date: 2001-01-31 
Deposition Author(s): Teplova, M., Tereshko, V., Sanishvili, R., Joachimiak, A., Bushueva, T., Anderson, W.F., Egli, M., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2001-01-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance