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.

Macromolecule Content

• Total Structure Weight: 33.43 kDa 
• Atom Count: 2446 
• Modelled Residue Count: 294 
• Deposited Residue Count: 300 
• Unique protein chains: 1

1YM5

Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.

• PDB DOI: 10.2210/pdb1YM5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-01-20 Released: 2005-08-02 
• Deposition Author(s): Liger, D., Quevillon-Cheruel, S., Sorel, I., Bremang, M., Blondeau, K., Aboulfath, I., Janin, J., Van Tilbeurgh, H., Leulliot, N., Paris-Sud Yeast Structural Genomics (YSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.251 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily

Liger, D., Quevillon-Cheruel, S., Sorel, I., Bremang, M., Blondeau, K., Aboulfath, I., Janin, J., van Tilbeurgh, H., Leulliot, N.

(2005) Proteins 60: 778-786

• PubMed: 16021630 
• DOI: 10.1002/prot.20548
• Primary Citation of Related Structures:  
  1YM5


• PubMed Abstract: 
  

In the Pseudomonas bacterial genomes, the PhzF proteins are involved in the production of phenazine derivative antibiotic and antifungal compounds. The PhzF superfamily however also encompasses proteins in all genomes from bacteria to eukaryotes, for which no function has been assigned. We have determined the three dimensional crystal structure at 2.05 A resolution of YHI9, the yeast member of the PhzF family. YHI9 has a fold similar to bacterial diaminopimelate epimerase, revealing a bimodular structure with an internal symmetry. Residue conservation identifies a putative active site at the interface between the two domains. Evolution of this protein by gene duplication, gene fusion and domain swapping from an ancestral gene containing the "hot dog" fold, identifies the protein as a "kinked double hot dog" fold.

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Organizational Affiliation: 

Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Orsay, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region	A	300	Saccharomyces cerevisiae	Mutation(s): 0  EC: 5.1
UniProt
Find proteins for P38765 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38765  Go to UniProtKB:  P38765

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.251 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.188	α = 90
b = 81.188	β = 90
c = 98.146	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-20 
• Released Date: 2005-08-02 
Deposition Author(s): Liger, D., Quevillon-Cheruel, S., Sorel, I., Bremang, M., Blondeau, K., Aboulfath, I., Janin, J., Van Tilbeurgh, H., Leulliot, N., Paris-Sud Yeast Structural Genomics (YSG)

Revision History  

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance