Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 44.58 kDa 
• Atom Count: 3822 
• Residue Count: 402 
• Unique protein chains: 1

1YUZ

Partially Reduced State of Nigerythrin

• DOI: 10.2210/pdb1YUZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Desulfovibrio vulgaris str. Hildenborough
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-02-14 Released: 2005-06-21 
• Deposition Author(s): Iyer, R.B., Silaghi-Dumitrescu, R., Kurtz, D.M., Lanzilotta, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.208 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Literature

High-resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins.

Iyer, R.B., Silaghi-Dumitrescu, R., Kurtz, D.M., Lanzilotta, W.N.

(2005) J Biol Inorg Chem 10: 407-416

• PubMed: 15895271 
• DOI: 10.1007/s00775-005-0650-8
• Primary Citation of Related Structures:  
  1YV1, 1YUZ, 1YUX


• PubMed Abstract: 
  

High-resolution crystal structures of Desulfovibrio vulgaris nigerythrin (DvNgr), a member of the rubrerythrin (Rbr) family, demonstrate an approximately 2-A movement of one iron (Fe1) of the diiron site from a carboxylate to a histidine ligand upon conversion of the mixed-valent ([Fe2(II),Fe1(III)]) to diferrous states, even at cryogenic temperatures. This Glu<-->His ligand "toggling" of one iron, which also occurs in DvRbr, thus, appears to be a characteristic feature of Rbr-type diiron sites. Unique features of DvNgr revealed by these structures include redox-induced flipping of a peptide carbonyl that reversibly forms a hydrogen bond to the histidine ligand to Fe1 of the diiron site, an intra-subunit proximal orientation of the rubredoxin-(Rub)-like and diiron domains, and an electron transfer pathway consisting of six covalent and two hydrogen bonds connecting the Rub-like iron with Fe2 of the diiron site. This pathway can account for DvNgr's relatively rapid peroxidase turnover. The characteristic combination of iron sites together with the redox-dependent iron toggling between protein ligands can account for the selectivity of Rbrs for hydrogen peroxide over dioxygen.

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Organizational Affiliation: 

Department of Chemistry, University of Georgia, Athens, GA 30602, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nigerythrin	A, B	202	Desulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  Gene Names: ngr, DVU_0019
Find proteins for P30820 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)) Explore P30820  Go to UniProtKB:  P30820

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	A, B	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
FE2	A, B	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.208 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.666	α = 90
b = 72.315	β = 90
c = 119.02	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-14 
• Released Date: 2005-06-21 
Deposition Author(s): Iyer, R.B., Silaghi-Dumitrescu, R., Kurtz, D.M., Lanzilotta, W.N.

Revision History 

• Version 1.0: 2005-06-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance