1I41

CYSTATHIONINE GAMMA-SYNTHASE IN COMPLEX WITH THE INHIBITOR APPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of cystathionine gamma-synthase inhibitor complexes rationalize the increased affinity of a novel inhibitor.

Steegborn, C.Laber, B.Messerschmidt, A.Huber, R.Clausen, T.

(2001) J Mol Biol 311: 789-801

  • DOI: 10.1006/jmbi.2001.4880
  • Primary Citation of Related Structures:  
    1I43, 1I41, 1I48

  • PubMed Abstract: 
  • Cystathionine gamma-synthase catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of antimicrobials and herbicides. We solved the crystal structures of complexes of cystathionine gamma-synthase (CGS) from Nicotiana tabacum with inhibitors of different compound classes ...

    Cystathionine gamma-synthase catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of antimicrobials and herbicides. We solved the crystal structures of complexes of cystathionine gamma-synthase (CGS) from Nicotiana tabacum with inhibitors of different compound classes. The complex with the substrate analog dl-E-2-amino-5-phosphono-3-pentenoic acid verifies the carboxylate-binding function of Arg423 and identifies the phosphate-binding pocket of the active site. The structure shows the function of Lys165 in specificity determination and suggests a role for the flexible side-chain of Tyr163 in catalysis. The importance of hydrophobic interactions for binding to the active-site center is highlighted by the complex with 3-(phosphonomethyl)pyridine-2-carboxylic acid. The low affinity of this compound is due to the non-optimal arrangement of the functional groups binding to the phosphate and carboxylate-recognition site, respectively. The newly identified inhibitor 5-carboxymethylthio-3-(3'-chlorophenyl)-1,2,4-oxadiazol, in contrast, shows the highest affinity to CGS reported so far. This affinity is due to binding to an additional active-site pocket not used by the physiological substrates. The inhibitor binds to the carboxylate-recognition site, and its tightly bent conformation enables it to occupy the novel binding pocket between Arg423 and Ser388. The described structures suggest improvements for known inhibitors and give guidelines for the development of new lead compounds.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, Planegg-Martinsried, D-82152, Germany. steegbo@biochem.mpg.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYSTATHIONINE GAMMA-SYNTHASE
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
445Nicotiana tabacumMutation(s): 0 
Gene Names: metB
EC: 4.2.99.9
Find proteins for Q9ZPL5 (Nicotiana tabacum)
Explore Q9ZPL5 
Go to UniProtKB:  Q9ZPL5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEN
Query on HEN

Download Ideal Coordinates CCD File 
M [auth A] , N [auth B] , O [auth C] , P [auth D] , Q [auth E] , R [auth F] , S [auth G] , T [auth H] , 
M [auth A],  N [auth B],  O [auth C],  P [auth D],  Q [auth E],  R [auth F],  S [auth G],  T [auth H],  U [auth I],  V [auth J],  W [auth K],  X [auth L]
2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-IMINO]-5-PHOSPHONO-PENT-3-ENOIC ACID
C13 H18 N2 O10 P2
VKWJKURKEYQKKW-ZCOJICPHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HENKi :  27000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 312.2α = 90
b = 166β = 90.2
c = 161.8γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance