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 and generated by PISA (software)

Biological Assembly 2  

 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 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.28 kDa 
• Atom Count: 3937 
• Modelled Residue Count: 436 
• Deposited Residue Count: 459 
• Unique protein chains: 1

1P1V

Crystal Structure of FALS-associated human Copper-Zinc Superoxide Dismutase (CuZnSOD) Mutant D125H to 1.4A

• PDB DOI: 10.2210/pdb1P1V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2003-04-14 Released: 2003-08-26 
• Deposition Author(s): Elam, J.S., Malek, K., Rodriguez, J.A., Doucette, P.A., Taylor, A.B., Hayward, L.J., Cabelli, D.E., Valentine, J.S., Hart, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.212 
• R-Value Work: 0.146 
• R-Value Observed: 0.146 

Literature

An Alternative Mechanism of Bicarbonate-mediated Peroxidation by Copper-Zinc Superoxide Dismutase: RATES ENHANCED VIA PROPOSED ENZYME-ASSOCIATED PEROXYCARBONATE INTERMEDIATE

Elam, J.S., Malek, K., Rodriguez, J.A., Doucette, P.A., Taylor, A.B., Hayward, L.J., Cabelli, D.E., Valentine, J.S., Hart, P.J.

(2003) J Biol Chem 278: 21032-21039

• PubMed: 12649272 
• DOI: 10.1074/jbc.M300484200
• Primary Citation of Related Structures:  
  1P1V


• PubMed Abstract: 
  

Hydrogen peroxide can interact with the active site of copper-zinc superoxide dismutase (SOD1) to generate a powerful oxidant. This oxidant can either damage amino acid residues at the active site, inactivating the enzyme (the self-oxidative pathway), or oxidize substrates exogenous to the active site, preventing inactivation (the external oxidative pathway). It is well established that the presence of bicarbonate anion dramatically enhances the rate of oxidation of exogenous substrates. Here, we show that bicarbonate also substantially enhances the rate of self-inactivation of human wild type SOD1. Together, these observations suggest that the strong oxidant formed by hydrogen peroxide and SOD1 in the presence of bicarbonate arises from a pathway mechanistically distinct from that producing the oxidant in its absence. Self-inactivation rates are further enhanced in a mutant SOD1 protein (L38V) linked to the fatal neurodegenerative disorder, familial amyotrophic lateral sclerosis. The 1.4 A resolution crystal structure of pathogenic SOD1 mutant D125H reveals the mode of oxyanion binding in the active site channel and implies that phosphate anion attenuates the bicarbonate effect by competing for binding to this site. The orientation of the enzyme-associated oxyanion suggests that both the self-oxidative and external oxidative pathways can proceed through an enzyme-associated peroxycarbonate intermediate.

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Organizational Affiliation: 

Department of Biochemistry and the X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B, C	153	Homo sapiens	Mutation(s): 2  Gene Names: SOD1 EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens) Explore P00441  Go to UniProtKB:  P00441
PHAROS:  P00441

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], G [auth B], J [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A, B, C	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.212 
• R-Value Work: 0.146 
• R-Value Observed: 0.146 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.449	α = 90
b = 101.14	β = 90
c = 143.08	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-14 
• Released Date: 2003-08-26 
Deposition Author(s): Elam, J.S., Malek, K., Rodriguez, J.A., Doucette, P.A., Taylor, A.B., Hayward, L.J., Cabelli, D.E., Valentine, J.S., Hart, P.J.

Revision History  

• Version 1.0: 2003-08-26
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations