Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 14.85 kDa 
• Atom Count: 1161 
• Residue Count: 130 
• Unique protein chains: 1

207L

MUTANT HUMAN LYSOZYME C77A

• DOI: 10.2210/pdb207L/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1996-03-26 Released: 1996-10-14 
• Deposition Author(s): Matsushima, M., Song, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å

Literature

A role of PDI in the reductive cleavage of mixed disulfides.

Nakamura, S., Matsushima, M., Song, H., Kikuchi, M.

(1996) J Biochem 120: 525-530

• PubMed: 8902616 
• DOI: 10.1093/oxfordjournals.jbchem.a021445
• Primary Citation of Related Structures:  
  207L, 208L


• PubMed Abstract: 
  

We previously reported that protein disulfide isomerase (PDI) can dissociate the glutathione molecule in vitro from the mutant human lysozyme (hLZM) C77A-a, which is modified with glutathione at Cys95; however, it seems structurally difficult for PDI to attack either the disulfide bond or the side chain of the cysteine residue of a mixed disulfide. To investigate the function of PDI, we introduced several glutathione and cysteine derivatives at Cys95, instead of the glutathione of C77A-a. Using thiol compounds modified by 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB), we could easily modify the free thiol group of C77A-b (C77A with no glutathionylation), without denaturation. For all of the modifications we tested, a negative correlation was found between the initial rate and the acceleration ratio of the reductive cleavage of mixed disulfides with PDI. A mutant PDI (hPDIM), which has no thiol-disulfide exchange activity, suppressed the reductive cleavage of the mixed disulfide of C77A-a with hPDI, suggesting that hPDI non-covalently interacted with the substrates. Taking account of the results of the structural analysis, we conclude that one of the functions of PDI in vivo lies in relaxing the structure around the disulfide bond, as well as in exchanging the thiol-disulfide bonds.

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Related Citations: 

• Structure of a Glutathionylated Human Lysozyme: A Folding Intermediate Mimic in the Formation of a Disulfide Bond
  Inaka, K., Miki, K., Kikuchi, M., Taniyama, Y., Matsushima, M.
  (1995) Acta Crystallogr D Biol Crystallogr 51: 619

• Pdi and Glutathione-Mediated Reduction of the Glutathionylated Variant of Human Lysozyme
  Hayano, T., Inaka, K., Otsu, M., Taniyama, Y., Miki, K., Matsushima, M., Kikuchi, M.
  (1993) FEBS Lett 328: 203

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Organizational Affiliation: 

Protein Engineering Research Institute, Osaka.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	A	130	Homo sapiens	Mutation(s): 1  Gene Names: LYZ, LZM EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens) Explore P61626  Go to UniProtKB:  P61626
NIH Common Fund Data Resources
PHAROS:  P61626 GTEx:  ENSG00000090382

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SC2	A	N-ACETYL-L-CYSTEINE C5 H9 N O3 S PWKSKIMOESPYIA-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.64	α = 90
b = 60.7	β = 90
c = 32.97	γ = 90

Software Package:

Software Name	Purpose
WELMS	data collection
PROTEIN	data reduction
PROTEIN	model building
PROLSQ	refinement
WELMS	data reduction
PROTEIN	data scaling
PROTEIN	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-03-26 
• Released Date: 1996-10-14 
Deposition Author(s): Matsushima, M., Song, H.

Revision History 

• Version 1.0: 1996-10-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2018-04-04
  Changes: Data collection