3QI6 | pdb_00003qi6

Crystal Structure of Cystathionine gamma-synthase MetB (Cgs) from Mycobacterium ulcerans Agy99


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.241 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.200 (Depositor) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3QI6

This is version 1.7 of the entry. See complete history

Literature

Structure of the cystathionine [gamma]-synthase MetB from Mycobacterium ulcerans

Clifton, M.C.Abendroth, J.Edwards, T.E.Leibly, D.J.Gillespie, A.K.Ferrell, M.Dieterich, S.H.Exley, I.Staker, B.L.Myler, P.J.Van Voorhis, W.C.Stewart, L.J.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1154-1158

  • DOI: https://doi.org/10.1107/S1744309111029575
  • Primary Citation Related Structures: 
    3QHX, 3QI6

  • PubMed Abstract: 

    Cystathionine γ-synthase (CGS) is a transulfurication enzyme that catalyzes the first specific step in L-methionine biosynthesis by the reaction of O(4)-succinyl-L-homoserine and L-cysteine to produce L-cystathionine and succinate. Controlling the first step in L-methionine biosythesis, CGS is an excellent potential drug target. Mycobacterium ulcerans is a slow-growing mycobacterium that is the third most common form of mycobacterial infection, mainly infecting people in Africa, Australia and Southeast Asia. Infected patients display a variety of skin ailments ranging from indolent non-ulcerated lesions as well as ulcerated lesions. Here, the crystal structure of CGS from M. ulcerans covalently linked to the cofactor pyridoxal phosphate (PLP) is reported at 1.9 Å resolution. A second structure contains PLP as well as a highly ordered HEPES molecule in the active site acting as a pseudo-ligand. These results present the first structure of a CGS from a mycobacterium and allow comparison with other CGS enzymes. This is also the first structure reported from the pathogen M. ulcerans.


  • Organizational Affiliation
    • Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA. mclifton@embios.com

Macromolecule Content 

  • Total Structure Weight: 165.91 kDa 
  • Atom Count: 12,485 
  • Modeled Residue Count: 1,488 
  • Deposited Residue Count: 1,568 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cystathionine gamma-synthase MetB (Cgs)
A, B, C, D
392Mycobacterium ulcerans Agy99Mutation(s): 0 
Gene Names: metBMUL_0201
EC: 2.5.1.48
UniProt
Find proteins for A0PKT3 (Mycobacterium ulcerans (strain Agy99))
Explore A0PKT3 
Go to UniProtKB:  A0PKT3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0PKT3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth B],
J [auth B],
L [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
M [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.241 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.200 (Depositor) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.956α = 90
b = 106.924β = 113.67
c = 100.307γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-07
    Changes: Database references, Refinement description
  • Version 1.3: 2012-03-28
    Changes: Database references
  • Version 1.4: 2015-04-22
    Changes: Database references
  • Version 1.5: 2017-11-08
    Changes: Refinement description
  • Version 1.6: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.7: 2023-12-06
    Changes: Data collection