5TT2

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

  • Method: X-RAY DIFFRACTION
  • 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


Literature

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

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cystathionine gamma-lyaseA [auth C], B [auth D]422Homo sapiensMutation(s): 3 
Gene Names: CTH
EC: 4.4.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P32929 (Homo sapiens)
Explore P32929 
Go to UniProtKB:  P32929
PHAROS:  P32929
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A [auth C], B [auth D]L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-10-31 
  • Released Date: 2017-10-11 
  • Deposition Author(s): Yan, W., Zhang, Y.

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