Inactive conformation of engineered human cystathionine gamma lyase (E59N, R119L, E339V) to depleting methionine

  • Classification: LYASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21
  • Mutation(s): Yes 

  • Deposited: 2016-10-31 Released: 2017-10-11 
  • Deposition Author(s): Yan, W., Zhang, Y.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

Experimental Data Snapshot

  • Resolution: 2.95 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Structural Snapshots of an Engineered Cystathionine-gamma-lyase Reveal the Critical Role of Electrostatic Interactions in the Active Site.

Yan, W.Stone, E.Zhang, Y.J.

(2017) Biochemistry 56: 876-885

  • DOI: https://doi.org/10.1021/acs.biochem.6b01172
  • Primary Citation of Related Structures:  
    5TSU, 5TT2

  • PubMed Abstract: 

    Enzyme therapeutics that can degrade l-methionine (l-Met) are of great interest as numerous malignancies are exquisitely sensitive to l-Met depletion. To exhaust the pool of methionine in human serum, we previously engineered an l-Met-degrading enzyme based on the human cystathionine-γ-lyase scaffold (hCGL-NLV) to circumvent immunogenicity and stability issues observed in the preclinical application of bacterially derived methionine-γ-lyases. To gain further insights into the structure-activity relationships governing the chemistry of the hCGL-NLV lead molecule, we undertook a biophysical characterization campaign that captured crystal structures (2.2 Å) of hCGL-NLV with distinct reaction intermediates, including internal aldimine, substrate-bound, gem-diamine, and external aldimine forms. Curiously, an alternate form of hCGL-NLV that crystallized under higher-salt conditions revealed a locally unfolded active site, correlating with inhibition of activity as a function of ionic strength. Subsequent mutational and kinetic experiments pinpointed that a salt bridge between the phosphate of the essential cofactor pyridoxal 5'-phosphate (PLP) and residue R62 plays an important role in catalyzing β- and γ-eliminations. Our study suggests that solvent ions such as NaCl disrupt electrostatic interactions between R62 and PLP, decreasing catalytic efficiency.

  • Organizational Affiliation

    Department of Molecular Biosciences and ‡Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin, Texas 78712, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine gamma-lyaseA [auth C],
B [auth D]
422Homo sapiensMutation(s): 3 
Gene Names: CTH
UniProt & NIH Common Fund Data Resources
Find proteins for P32929 (Homo sapiens)
Explore P32929 
Go to UniProtKB:  P32929
PHAROS:  P32929
GTEx:  ENSG00000116761 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32929
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.95 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.224α = 90
b = 120.224β = 90
c = 125.622γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA154754
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM104896
Welch FoundationUnited StatesF-1778

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence