207L

MUTANT HUMAN LYSOZYME C77A

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


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

  • 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 ...

    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.

    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
    Organizational Affiliation: 

    Protein Engineering Research Institute, Osaka.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOZYMEA130Homo sapiensMutation(s): 1 
Gene Names: LYZ, LZM
EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P61626 (Homo sapiens)
Explore P61626 
Go to UniProtKB:  P61626
PHAROS:  P61626
GTEx:  ENSG00000090382
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SC2 (Subject of Investigation/LOI)
Query on SC2
Download Ideal Coordinates CCD File 
 B [auth A]N-ACETYL-L-CYSTEINE
C5 H9 N O3 S
PWKSKIMOESPYIA-BYPYZUCNSA-N		 Ligand Interaction
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 = 57.64α = 90
b = 60.7β = 90
c = 32.97γ = 90
Software Package:
Software NamePurpose
WELMSdata collection
PROTEINdata reduction
PROTEINmodel building
PROLSQrefinement
WELMSdata reduction
PROTEINdata scaling
PROTEINphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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