Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 44.58 kDa 
• Atom Count: 3473 
• Residue Count: 396 
• Unique protein chains: 1

1LUV

CATALYTIC AND STRUCTURAL EFFECTS OF AMINO-ACID SUBSTITUTION AT HIS 30 IN HUMAN MANGANESE SUPEROXIDE DISMUTASE: INSERTION OF VAL CGAMMA INTO THE SUBSTRATE ACCESS CHANNEL

• DOI: 10.2210/pdb1LUV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-23 Released: 2002-06-19 
• Deposition Author(s): Hearn, A.S., Stroupe, M.E., Ramilo, C.A., Luba, J.P., Cabelli, D.E., Tainer, J.A., Silverman, D.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.288 
• R-Value Work: 0.254 
• R-Value Observed: 0.254 

Literature

Catalytic and structural effects of amino acid substitution at histidine 30 in human manganese superoxide dismutase: insertion of valine C gamma into the substrate access channel

Hearn, A.S., Stroupe, M.E., Cabelli, D.E., Ramilo, C.A., Luba, J.P., Tainer, J.A., Nick, H.S., Silverman, D.N.

(2003) Biochemistry 42: 2781-2789

• PubMed: 12627943 
• DOI: 10.1021/bi0266481
• Primary Citation of Related Structures:  
  1LUW, 1LUV


• PubMed Abstract: 
  

Catalysis of the disproportionation of superoxide by human manganese superoxide dismutase (MnSOD) is characterized by an initial burst of catalysis followed by a much slower region that is zero order in superoxide and due to a product inhibition by peroxide anion. We have prepared site-specific mutants with replacements at His30, the side chain of which lies along the substrate access channel and is about 5.8 A from the metal. Using pulse radiolysis to generate superoxide, we have determined that kcat/K(m) was decreased and product inhibition increased for H30V MnSOD, both by 1-2 orders of magnitude, compared with wild type, H30N, and H30Q MnSOD. These effects are not attributed to the redox potentials, which are similar for all of these variants. An investigation of the crystal structure of H30V Mn(III)SOD compared with wild type, H30Q, and H30N Mn(III)SOD showed the positions of two gamma carbons of Val30 in the active site; Cgamma1 overlaps Cgamma of His30 in wild type, and Cgamma2 extends into the substrate access channel and occupies the approximate position of a water molecule in the wild type. The data suggest that Cgamma2 of the Val side chain has significantly interrupted catalysis by this overlap into the access channel with possible overlap with the substrate-product binding site. This is supported by comparison of the crystal structure of H30V MnSOD with that of azide bound to Mn(III)SOD from Thermus thermophilus and by visible absorption spectra showing that azide binding to the metal in H30V Mn(III)SOD is abolished. Moreover, the presence of Val30 caused a 100-fold decrease in the rate constant for dissociation of the product-inhibited complex compared with wild type.

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Organizational Affiliation: 

Department of Pharmacology, University of Florida, Gainesville, Florida 32610-0267, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn]	A, B	198	Homo sapiens	Mutation(s): 0  Gene Names: SOD2 EC: 1.15.1.1
Find proteins for P04179 (Homo sapiens) Explore P04179  Go to UniProtKB:  P04179
NIH Common Fund Data Resources
PHAROS:  P04179 GTEx:  ENSG00000112096

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	A, B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.288 
• R-Value Work: 0.254 
• R-Value Observed: 0.254 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.901	α = 90
b = 79.901	β = 90
c = 241.125	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-23 
• Released Date: 2002-06-19 
Deposition Author(s): Hearn, A.S., Stroupe, M.E., Ramilo, C.A., Luba, J.P., Cabelli, D.E., Tainer, J.A., Silverman, D.N.

Revision History 

• Version 1.0: 2002-06-19
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description