Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.53 kDa 
• Atom Count: 3625 
• Modelled Residue Count: 432 
• Deposited Residue Count: 462 
• Unique protein chains: 1

2GEM

2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A

• PDB DOI: 10.2210/pdb2GEM/pdb

• Classification: CHAPERONE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-03-20 Released: 2006-08-01 
• Deposition Author(s): Nichols, C.E., Stammers, D.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

Structural Characterization of Salmonella typhimurium YeaZ, an M22 O-Sialoglycoprotein Endopeptidase Homolog

Nichols, C.E., Johnson, C., Lockyer, M., Charles, I.G., Lamb, H.K., Hawkins, A.R., Stammers, D.K.

(2006) Proteins 64: 111-123

• PubMed: 16617437 
• DOI: 10.1002/prot.20982
• Primary Citation of Related Structures:  
  2GEL, 2GEM


• PubMed Abstract: 
  

The Salmonella typhimurium "yeaZ" gene (StyeaZ) encodes an essential protein of unknown function (StYeaZ), which has previously been annotated as a putative homolog of the Pasteurella haemolytica M22 O-sialoglycoprotein endopeptidase Gcp. YeaZ has also recently been reported as the first example of an RPF from a gram-negative bacterial species. To further characterize the properties of StYeaZ and the widely occurring MK-M22 family, we describe the purification, biochemical analysis, crystallization, and structure determination of StYeaZ. The crystal structure of StYeaZ reveals a classic two-lobed actin-like fold with structural features consistent with nucleotide binding. However, microcalorimetry experiments indicated that StYeaZ neither binds polyphosphates nor a wide range of nucleotides. Additionally, biochemical assays show that YeaZ is not an active O-sialoglycoprotein endopeptidase, consistent with the lack of the critical zinc binding motif. We present a detailed comparison of YeaZ with available structural homologs, the first reported structural analysis of an MK-M22 family member. The analysis indicates that StYeaZ has an unusual orientation of the A and B lobes which may require substantial relative movement or interaction with a partner protein in order to bind ligands. Comparison of the fold of YeaZ with that of a known RPF domain from a gram-positive species shows significant structural differences and therefore potentially distinctive RPF mechanisms for these two bacterial classes.

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Organizational Affiliation: 

Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Gram negative resuscitation promoting factor	A, B	231	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: yegS, yeaZ
UniProt
Find proteins for Q7CQE0 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q7CQE0  Go to UniProtKB:  Q7CQE0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.7	α = 90
b = 40.7	β = 90
c = 464.83	γ = 120

Software Package:

Software Name	Purpose
ProDC	data collection
DENZO	data reduction
SOLVE	phasing
CNS	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-03-20 
• Released Date: 2006-08-01 
Deposition Author(s): Nichols, C.E., Stammers, D.K.

Revision History  

• Version 1.0: 2006-08-01
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection, Refinement description